[Fink-users] thanks and best wishes

[Viv Kendon]

Before I leave, I just want to say a BIG thank you to all for the help 
and support over the years.  It has been very much appreciated and has 
enabled me to get much more done than I would have fighting the problems 
on my own.  I am now running Linux Mint on my (somewhat aging) Mac 
hardware, hence I'm no longer using fink.  Although knowing fink has 
certainly made the transition easier.

all the best,
-- Viv

P.S., would I recommend Linux on macs?  Not without knowing more about 
your use case: you'd need to try it for yourself.  It (mostly) works for 
me, and for older hardware it _may_ be better than upgrading MacOS (I 
need security updates).

--
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Re: [Fink-users] python27-2.7.12-1 build failed on 10.9.5

[Viv Kendon]

On 12 Jul 2016, at 20:53, Viv Kendon  wrote:

> 
> On 12 Jul 2016, at 20:50, Daniel Johnson  wrote:
> 
>> 
>>> On Jul 12, 2016, at 7:29 AM, Viv Kendon  wrote:
>>> 
>>> I’m having trouble building python27 on 10.9.5 (case sensitive file system):
>>> 
>>> building '_tkinter' extension
>>> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall 
>>> -Wstrict-p
>>> rototypes -DWITH_APPINIT=1 -I. -IInclude -I./Include -I/sw/include 
>>> -I/sw/src/fin
>>> k.build/python27-2.7.12-1/Python-2.7.12/Include 
>>> -I/sw/src/fink.build/python27-2.
>>> 7.12-1/Python-2.7.12 -c 
>>> /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modul
>>> es/_tkinter.c -o 
>>> build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.
>>> 7.12-1/Python-2.7.12/Modules/_tkinter.o -I/sw/include -I/opt/X11/include
>>> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall 
>>> -Wstrict-p
>>> rototypes -DWITH_APPINIT=1 -I. -IInclude -I./Include -I/sw/include 
>>> -I/sw/src/fin
>>> k.build/python27-2.7.12-1/Python-2.7.12/Include 
>>> -I/sw/src/fink.build/python27-2.
>>> 7.12-1/Python-2.7.12 -c 
>>> /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modul
>>> es/tkappinit.c -o 
>>> build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2
>>> .7.12-1/Python-2.7.12/Modules/tkappinit.o -I/sw/include -I/opt/X11/include
>>> gcc -L/sw/lib -bundle 
>>> /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/libpyth
>>> on2.7.dylib -L/sw/lib -L/sw/lib -I. -IInclude -I./Include -I/sw/include 
>>> build/te
>>> mp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modu
>>> les/_tkinter.o 
>>> build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.7.
>>> 12-1/Python-2.7.12/Modules/tkappinit.o -L/sw/lib -L. -o 
>>> build/lib.macosx-10.9-x8
>>> 6_64-2.7/_tkinter.so -L/sw/libs -ltcl -ltk
>>> ld: warning: directory not found for option '-L/sw/libs'
>>> *** WARNING: renaming "_tkinter" since importing it failed: 
>>> dlopen(build/lib.mac
>>> osx-10.9-x86_64-2.7/_tkinter.so, 2): Symbol not found: 
>>> __os_trace_with_buffer
>>> Referenced from: /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib
>>> Expected in: /usr/lib/libSystem.B.dylib
>>> in /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib
>>> 
>>> 
>>> 
>>> Python build finished, but the necessary bits to build these modules were 
>>> not fo
>>> und:
>>> bsddb185   dl imageop
>>> linuxaudiodev  ossaudiodevspwd
>>> sunaudiodev
>>> To find the necessary bits, look in setup.py in detect_modules() for the 
>>> module'
>>> s name.
>>> (Fink package build should have 7 missing)
>>> 
>>> 
>>> Failed to build these modules:
>>> _tkinter
>>> 
>>> 
>>> Package manager version: 0.39.3
>>> Distribution version: selfupdate-rsync Mon Jul 11 10:06:43 2016, 10.9, 
>>> x86_64
>>> Trees: local/main stable/main
>>> Xcode.app: 6.2
>>> Xcode command-line tools: 6.2.0.0.1.1424975374
>>> Max. Fink build jobs:  18
>>> 
>>> and
>>> 
>>> XQuartz 2.7.10_beta2 (xorg-server 1.18.3)
>>> 
>>> which seems like it might be part of the problem, because there have been 
>>> various library updates, I believe.  I rebuilt some of the gtk packages to 
>>> no avail, maybe I didn’t pick the right ones?
>>> 
>>> many thanks,
>>> — Viv
>>> 
>> 
>> Python doesn’t use GTK or glib at all.
>> 
>> I think it must be the XQuartz beta. It seems to have an inappropriate 
>> library, /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib, which is 
>> actually part of clang’s address sanitizer debugging tool. It must have been 
>> included by mistake and/or they left debugging code in that is built for a 
>> newer OS. It’s looking for a symbol called “__os_trace_with_buffer” in 
>> libSystem but that symbol doesn’t exist as of 10.11. I suspect it’s from 
>> 10.12. So this looks like a buggy XQuartz release. Python builds fine for me 
>> on 10.11 with non-beta XQuartz.
>> 
>> Daniel
>> 
> Many thanks, I will take this over to the XQuartz-dev list and see what they 
> say.
> 
> — Viv

For the record, I got the following:

> 
> On Jul 13, 2016, at 9:55 AM, Jeremy Huddlest

Re: [Fink-users] python27-2.7.12-1 build failed on 10.9.5

[Viv Kendon]

On 12 Jul 2016, at 20:50, Daniel Johnson  wrote:

> 
>> On Jul 12, 2016, at 7:29 AM, Viv Kendon  wrote:
>> 
>> I’m having trouble building python27 on 10.9.5 (case sensitive file system):
>> 
>> building '_tkinter' extension
>> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall 
>> -Wstrict-p
>> rototypes -DWITH_APPINIT=1 -I. -IInclude -I./Include -I/sw/include 
>> -I/sw/src/fin
>> k.build/python27-2.7.12-1/Python-2.7.12/Include 
>> -I/sw/src/fink.build/python27-2.
>> 7.12-1/Python-2.7.12 -c 
>> /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modul
>> es/_tkinter.c -o 
>> build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.
>> 7.12-1/Python-2.7.12/Modules/_tkinter.o -I/sw/include -I/opt/X11/include
>> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall 
>> -Wstrict-p
>> rototypes -DWITH_APPINIT=1 -I. -IInclude -I./Include -I/sw/include 
>> -I/sw/src/fin
>> k.build/python27-2.7.12-1/Python-2.7.12/Include 
>> -I/sw/src/fink.build/python27-2.
>> 7.12-1/Python-2.7.12 -c 
>> /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modul
>> es/tkappinit.c -o 
>> build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2
>> .7.12-1/Python-2.7.12/Modules/tkappinit.o -I/sw/include -I/opt/X11/include
>> gcc -L/sw/lib -bundle 
>> /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/libpyth
>> on2.7.dylib -L/sw/lib -L/sw/lib -I. -IInclude -I./Include -I/sw/include 
>> build/te
>> mp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modu
>> les/_tkinter.o 
>> build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.7.
>> 12-1/Python-2.7.12/Modules/tkappinit.o -L/sw/lib -L. -o 
>> build/lib.macosx-10.9-x8
>> 6_64-2.7/_tkinter.so -L/sw/libs -ltcl -ltk
>> ld: warning: directory not found for option '-L/sw/libs'
>> *** WARNING: renaming "_tkinter" since importing it failed: 
>> dlopen(build/lib.mac
>> osx-10.9-x86_64-2.7/_tkinter.so, 2): Symbol not found: __os_trace_with_buffer
>> Referenced from: /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib
>> Expected in: /usr/lib/libSystem.B.dylib
>> in /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib
>> 
>> 
>> 
>> Python build finished, but the necessary bits to build these modules were 
>> not fo
>> und:
>> bsddb185   dl imageop
>> linuxaudiodev  ossaudiodevspwd
>> sunaudiodev
>> To find the necessary bits, look in setup.py in detect_modules() for the 
>> module'
>> s name.
>> (Fink package build should have 7 missing)
>> 
>> 
>> Failed to build these modules:
>> _tkinter
>> 
>> 
>> Package manager version: 0.39.3
>> Distribution version: selfupdate-rsync Mon Jul 11 10:06:43 2016, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 6.2
>> Xcode command-line tools: 6.2.0.0.1.1424975374
>> Max. Fink build jobs:  18
>> 
>> and
>> 
>> XQuartz 2.7.10_beta2 (xorg-server 1.18.3)
>> 
>> which seems like it might be part of the problem, because there have been 
>> various library updates, I believe.  I rebuilt some of the gtk packages to 
>> no avail, maybe I didn’t pick the right ones?
>> 
>> many thanks,
>> — Viv
>> 
> 
> Python doesn’t use GTK or glib at all.
> 
> I think it must be the XQuartz beta. It seems to have an inappropriate 
> library, /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib, which is 
> actually part of clang’s address sanitizer debugging tool. It must have been 
> included by mistake and/or they left debugging code in that is built for a 
> newer OS. It’s looking for a symbol called “__os_trace_with_buffer” in 
> libSystem but that symbol doesn’t exist as of 10.11. I suspect it’s from 
> 10.12. So this looks like a buggy XQuartz release. Python builds fine for me 
> on 10.11 with non-beta XQuartz.
> 
> Daniel
> 
Many thanks, I will take this over to the XQuartz-dev list and see what they 
say.

— Viv
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
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[Fink-users] python27-2.7.12-1 build failed on 10.9.5

[Viv Kendon]

I’m having trouble building python27 on 10.9.5 (case sensitive file system):

building '_tkinter' extension
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-p
rototypes -DWITH_APPINIT=1 -I. -IInclude -I./Include -I/sw/include -I/sw/src/fin
k.build/python27-2.7.12-1/Python-2.7.12/Include -I/sw/src/fink.build/python27-2.
7.12-1/Python-2.7.12 -c /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modul
es/_tkinter.c -o build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.
7.12-1/Python-2.7.12/Modules/_tkinter.o -I/sw/include -I/opt/X11/include
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-p
rototypes -DWITH_APPINIT=1 -I. -IInclude -I./Include -I/sw/include -I/sw/src/fin
k.build/python27-2.7.12-1/Python-2.7.12/Include -I/sw/src/fink.build/python27-2.
7.12-1/Python-2.7.12 -c /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modul
es/tkappinit.c -o build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2
.7.12-1/Python-2.7.12/Modules/tkappinit.o -I/sw/include -I/opt/X11/include
gcc -L/sw/lib -bundle /sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/libpyth
on2.7.dylib -L/sw/lib -L/sw/lib -I. -IInclude -I./Include -I/sw/include build/te
mp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.7.12-1/Python-2.7.12/Modu
les/_tkinter.o build/temp.macosx-10.9-x86_64-2.7/sw/src/fink.build/python27-2.7.
12-1/Python-2.7.12/Modules/tkappinit.o -L/sw/lib -L. -o build/lib.macosx-10.9-x8
6_64-2.7/_tkinter.so -L/sw/libs -ltcl -ltk
ld: warning: directory not found for option '-L/sw/libs'
*** WARNING: renaming "_tkinter" since importing it failed: dlopen(build/lib.mac
osx-10.9-x86_64-2.7/_tkinter.so, 2): Symbol not found: __os_trace_with_buffer
  Referenced from: /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in /opt/X11/lib/asan/libclang_rt.asan_osx_dynamic.dylib



Python build finished, but the necessary bits to build these modules were not fo
und:
bsddb185   dl imageop 
linuxaudiodev  ossaudiodevspwd
sunaudiodev   
To find the necessary bits, look in setup.py in detect_modules() for the module'
s name.
(Fink package build should have 7 missing)


Failed to build these modules:
_tkinter  


Package manager version: 0.39.3
Distribution version: selfupdate-rsync Mon Jul 11 10:06:43 2016, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.2
Xcode command-line tools: 6.2.0.0.1.1424975374
Max. Fink build jobs:  18

and

XQuartz 2.7.10_beta2 (xorg-server 1.18.3)

which seems like it might be part of the problem, because there have been 
various library updates, I believe.  I rebuilt some of the gtk packages to no 
avail, maybe I didn’t pick the right ones?

many thanks,
— Viv


--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: [Fink-users] pyqt5-mac-py27-5.6-1 build failed on 10.9 looking for dbus headers

[Viv Kendon]

On 29 Apr 2016, at 00:48, Daniel Johnson  wrote:

> 
>> On Apr 28, 2016, at 7:17 PM, Daniel Johnson  
>> wrote:
>> 
>>> 
>>> On Apr 28, 2016, at 1:10 PM, Sean Lake  wrote:
>>> 
>>> I'm running into the same problem on Mac OS X 10.10.
>>> 
>>> fink --version
>>> Package manager version: 0.39.3
>>> Distribution version: selfupdate-rsync Thu Apr 28 09:44:46 2016, 10.10, 
>>> x86_64
>>> Trees: local/main stable/main
>>> 
>>> On Wed, Apr 27, 2016 at 3:44 PM, Viv Kendon  wrote:
>>>> Doing an “update-all”,
>>>> 
>>>> make[1]: Entering directory 
>>>> '/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus'
>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
>>>>  -c -pipe -stdlib=libc++ -fno-exceptions -O2 -std=gnu++11 -isysroot 
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
>>>>  -mmacosx-version-min=10.9 -Wall -W -fPIC -DSIP_PROTECTED_IS_PUBLIC 
>>>> -Dprotected=public -DQT_NO_DEBUG -DQT_PLUGIN -DQT_CORE_LIB -I. -I. 
>>>> -isystem /sw/include/python2.7 -isystem /sw/include/dbus-1.0 -I. 
>>>> -I/sw/lib/qt5-mac/lib/QtCore.framework/Headers -I. 
>>>> -I/sw/lib/qt5-mac/share/qt5/mkspecs/macx-clang -F/sw/lib/qt5-mac/lib -o 
>>>> dbus.o dbus.cpp
>>>> /sw/lib/qt5-mac/bin/moc -DSIP_PROTECTED_IS_PUBLIC -Dprotected=public 
>>>> -DQT_NO_DEBUG -DQT_PLUGIN -DQT_CORE_LIB -D__APPLE__ -D__GNUC__=4 
>>>> -D__APPLE_CC__ -I/sw/lib/qt5-mac/share/qt5/mkspecs/macx-clang 
>>>> -I/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus 
>>>> -I/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus 
>>>> -I/sw/include/python2.7 -I/sw/include/dbus-1.0 
>>>> -I/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus 
>>>> -I/sw/lib/qt5-mac/lib/QtCore.framework/Headers -I/sw/include/dbus-1.0 
>>>> -I/sw/lib/dbus-1.0/include -I/sw/include/glib-2.0 
>>>> -I/sw/lib/glib-2.0/include -I/sw/include/freetype2 -I/sw/include 
>>>> -I/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1
>>>>  
>>>> -I/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/include
>>>>  
>>>> -I/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
>>>>  
>>>> -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include
>>>>  -F/sw/lib/qt5-mac/lib helper.h -o moc_helper.cpp
>>>> In file included from dbus.cpp:27:
>>>> In file included from /sw/include/dbus-1.0/dbus/dbus-python.h:33:
>>>> /sw/include/dbus-1.0/dbus/dbus.h:29:10: fatal error: 
>>>> 'dbus/dbus-arch-deps.h'
>>>>file not found
>>>> #include 
>>>>   ^
>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
>>>>  -c -pipe -stdlib=libc++ -fno-exceptions -O2 -std=gnu++11 -isysroot 
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
>>>>  -mmacosx-version-min=10.9 -Wall -W -fPIC -DSIP_PROTECTED_IS_PUBLIC 
>>>> -Dprotected=public -DQT_NO_DEBUG -DQT_PLUGIN -DQT_CORE_LIB -I. -I. 
>>>> -isystem /sw/include/python2.7 -isystem /sw/include/dbus-1.0 -I. 
>>>> -I/sw/lib/qt5-mac/lib/QtCore.framework/Headers -I. 
>>>> -I/sw/lib/qt5-mac/share/qt5/mkspecs/macx-clang -F/sw/lib/qt5-mac/lib -o 
>>>> moc_helper.o moc_helper.cpp
>>>> 1 error generated.
>>>> Makefile:505: recipe for target 'dbus.o' failed
>>>> make[1]: *** [dbus.o] Error 1
>>>> make[1]: *** Waiting for unfinished jobs
>>>> In file included from moc_helper.cpp:9:
>>>> In file included from ./helper.h:34:
>>>> /sw/include/dbus-1.0/dbus/dbus.h:29:10: fatal error: 
>>>> 'dbus/dbus-arch-deps.h'
>>>>file not found
>>>> #include 
>>>>   ^
>>>> 1 error generated.
>>>> Makefile:508: recipe for target 'moc_helper.o' failed
>>>> make[1]: *** [moc_helper.o] Error 1
>>>> make[1]: Leaving directory 
>>>> '/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus'
>>>> Makefile:1670: recipe for target 'sub-dbus-make_first-

[Fink-users] pyqt5-mac-py27-5.6-1 build failed on 10.9 looking for dbus headers

[Viv Kendon]

Doing an “update-all”,

make[1]: Entering directory 
'/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus'
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
 -c -pipe -stdlib=libc++ -fno-exceptions -O2 -std=gnu++11 -isysroot 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
 -mmacosx-version-min=10.9 -Wall -W -fPIC -DSIP_PROTECTED_IS_PUBLIC 
-Dprotected=public -DQT_NO_DEBUG -DQT_PLUGIN -DQT_CORE_LIB -I. -I. -isystem 
/sw/include/python2.7 -isystem /sw/include/dbus-1.0 -I. 
-I/sw/lib/qt5-mac/lib/QtCore.framework/Headers -I. 
-I/sw/lib/qt5-mac/share/qt5/mkspecs/macx-clang -F/sw/lib/qt5-mac/lib -o dbus.o 
dbus.cpp
/sw/lib/qt5-mac/bin/moc -DSIP_PROTECTED_IS_PUBLIC -Dprotected=public 
-DQT_NO_DEBUG -DQT_PLUGIN -DQT_CORE_LIB -D__APPLE__ -D__GNUC__=4 -D__APPLE_CC__ 
-I/sw/lib/qt5-mac/share/qt5/mkspecs/macx-clang 
-I/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus 
-I/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus 
-I/sw/include/python2.7 -I/sw/include/dbus-1.0 
-I/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus 
-I/sw/lib/qt5-mac/lib/QtCore.framework/Headers -I/sw/include/dbus-1.0 
-I/sw/lib/dbus-1.0/include -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include 
-I/sw/include/freetype2 -I/sw/include 
-I/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1
 
-I/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/include
 
-I/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
 
-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include
 -F/sw/lib/qt5-mac/lib helper.h -o moc_helper.cpp
In file included from dbus.cpp:27:
In file included from /sw/include/dbus-1.0/dbus/dbus-python.h:33:
/sw/include/dbus-1.0/dbus/dbus.h:29:10: fatal error: 'dbus/dbus-arch-deps.h'
  file not found
#include 
 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
 -c -pipe -stdlib=libc++ -fno-exceptions -O2 -std=gnu++11 -isysroot 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk
 -mmacosx-version-min=10.9 -Wall -W -fPIC -DSIP_PROTECTED_IS_PUBLIC 
-Dprotected=public -DQT_NO_DEBUG -DQT_PLUGIN -DQT_CORE_LIB -I. -I. -isystem 
/sw/include/python2.7 -isystem /sw/include/dbus-1.0 -I. 
-I/sw/lib/qt5-mac/lib/QtCore.framework/Headers -I. 
-I/sw/lib/qt5-mac/share/qt5/mkspecs/macx-clang -F/sw/lib/qt5-mac/lib -o 
moc_helper.o moc_helper.cpp
1 error generated.
Makefile:505: recipe for target 'dbus.o' failed
make[1]: *** [dbus.o] Error 1
make[1]: *** Waiting for unfinished jobs
In file included from moc_helper.cpp:9:
In file included from ./helper.h:34:
/sw/include/dbus-1.0/dbus/dbus.h:29:10: fatal error: 'dbus/dbus-arch-deps.h'
  file not found
#include 
 ^
1 error generated.
Makefile:508: recipe for target 'moc_helper.o' failed
make[1]: *** [moc_helper.o] Error 1
make[1]: Leaving directory 
'/sw/src/fink.build/pyqt5-mac-py27-5.6-1/PyQt5_gpl-5.6/dbus'
Makefile:1670: recipe for target 'sub-dbus-make_first-ordered' failed
make: *** [sub-dbus-make_first-ordered] Error 2

Package manager version: 0.39.3
Distribution version: selfupdate-rsync Tue Apr 26 21:48:17 2016, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.2
Xcode command-line tools: 6.2.0.0.1.1424975374
Max. Fink build jobs:  18

 fink list -ti dbus
Information about 9406 packages read in 1 seconds.
 i  dbus1.8.20-1Message bus system for applications
 i  dbus-glib1.2-dev0.86-3  Message bus system for applications
 i  dbus-glib1.2-shlibs 0.86-3  Message bus system for applications
 i  dbus1.3-dev 1.8.20-1Message bus system for applications
 i  dbus1.3-shlibs  1.8.20-1Message bus system for applications
 i  pydbus-py27 0.84.0-5Simple interprocess messaging system
 i  pydbus-py27-dev 0.84.0-5Development libraries for pydbus-py27
 i  qt4-base-mac-qtdbus-shlibs  4.8.7-2 Qt D-Bus library (mac)
 i  qt4-base-x11-qtdbus-shlibs  4.7.3-140   Qt D-Bus library (x11)
 i  qt5-mac-qtdbus-shlibs   5.6.0-1 Qt D-Bus library (mac)

 ls /sw/include/dbus-1.0/dbus/
total 424
 0 ./   32 dbus-message.h
 0 ../   8 dbus-misc.h
 8 dbus-address.h8 dbus-pending-call.h
 8 dbus-bus.h   48 dbus-protocol.h
56 dbus-connection.h 8 dbus-python.h
 8 dbus-errors.h16 dbus-server.h
48 dbus-glib-bindings.h 16 dbus-shared.h
 8 dbus-glib-error-enum.h8 dbus-signature.h
 8 dbus-glib-lowlevel.h  8 dbus-syntax.h
32 dbus-glib.h  24 dbus-threads.h
24 dbus-gtype-specialized.h 16 dbus-types.h
16 dbus-macros.h 8 dbus.h
 8 dbus-memory

Re: [Fink-users] Update to openssl100-dev-1.0.2g-1 breaks libapache2-mod-php5 and spyder-mac-py27 (via qt4-base-mac)

[Viv Kendon]

On 9 Mar 2016, at 12:56, Daniel Johnson  wrote:

> 
>> On Mar 7, 2016, at 10:57 AM, Alexander Hansen  
>> wrote:
>> 
>>> 
>>> On Mar 7, 2016, at 07:17, Christian Ebert  wrote:
>>> 
>>> * Richard Walker on Monday, March 07, 2016 at 12:41:07 +1100
 After doing a selfupdate/update-all this morning I now get this
 message on starting Apache:
 
 apache2: Syntax error on line 242 of /sw/etc/apache2/apache2.conf:
 Syntax error on line 1 of /sw/etc/apache2/mods-enabled/php5.load:
 Cannot load /sw/lib/apache2/modules/libphp5.so into server:
 dlopen(/sw/lib/apache2/modules/libphp5.so, 10): Symbol not found:
 _SSLv2_client_method\n  Referenced from:
 /sw/lib/apache2/modules/libphp5.so\n  Expected in:
 /sw/lib/libssl.1.0.0.dylib\n in /sw/lib/apache2/modules/libphp5.so
>>> 
>>> I got a similar error from python27
>>> 
 It seems that libphp5.so attempts to call SSLv2_client_method() and
 now fails to find it.
 
 It seems that the reason is that in OpenSSL 1.0.2g, SSLv2 calls are
 now disabled by default,
 and that even enabling them at build-time is not enough:
 http://www.openssl.org/news/secadv/20160301.txt
>>> 
>>> In the case of python, fink rebuild python27 fixed the problem.
>>> 
>>> Christian
>>> --
>>> theatre - books - texts - movies
>>> Black Trash Productions at home: http://www.blacktrash.org
>>> Black Trash Productions on Facebook:
>>> http://www.facebook.com/blacktrashproductions
>>> 
>> 
>> I’ve cc’ed the python27 maintainer (who is also the openssl100 maintainer) 
>> since this probably indicates that python* needs a versioned dependency on 
>> openssl100 and a revision bump.
>> 
>> If rebuilding libapache2-mod-php5 makes that work, a similar update would be 
>> needed there.
>> 
>> --
>> Alexander Hansen, Ph.D.
>> Fink User Liaison
> 
> I love when libraries drop symbols in a minor update.
> 
> I’ve updated all my packages to depend on 1.0.2g but there are a number of 
> others that need updating too.
> 
> Daniel
> 

This also broke spyder-mac-py27:

Traceback (most recent call last):
  File "/sw/bin/spyder-mac-py27.py", line 3, in 
start_app.main()
  File "/sw/lib/python2.7/site-packages/spyderlib/start_app.py", line 72, in 
main
from spyderlib import spyder
  File "/sw/lib/python2.7/site-packages/spyderlib/spyder.py", line 106, in 

from spyderlib.plugins.inspector import ObjectInspector
  File "/sw/lib/python2.7/site-packages/spyderlib/plugins/inspector.py", line 
32, in 
from spyderlib.widgets.browser import WebView
  File "/sw/lib/python2.7/site-packages/spyderlib/widgets/browser.py", line 11, 
in 
from spyderlib.qt.QtWebKit import QWebView, QWebPage
  File "/sw/lib/python2.7/site-packages/spyderlib/qt/QtWebKit.py", line 10, in 

from PyQt4.QtWebKit import *  # analysis:ignore
ImportError: 
dlopen(/sw/lib/qt4-mac/lib/python2.7/site-packages/PyQt4/QtWebKit.so, 2): 
Symbol not found: _SSLv2_client_method
  Referenced from: /sw/lib/qt4-mac/lib/QtNetwork.framework/Versions/4/QtNetwork
  Expected in: /sw/lib/libssl.1.0.0.dylib
 in /sw/lib/qt4-mac/lib/QtNetwork.framework/Versions/4/QtNetwork

I rebuilt qt4-base-mac (and everything that comes with it), and that seems to 
have done the trick.  But because I was compiling on a different machine to the 
one I want to run spyder on, it was a bit epic persuading that machine to 
binary install the rebuilt copy (I had to remove everything recursively and 
delete the debs).

— Viv
--
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Re: [Fink-users] cryptography-py27-1.1.1-2 build failure

[Viv Kendon]

On 10 Mar 2016, at 00:00, Daniel Johnson  wrote:

> 
>> On Mar 9, 2016, at 5:36 PM, Viv Kendon  wrote:
>> 
>> (maintainer Cc’d) with everything else updated:
>> 
>> writing manifest file 'src/cryptography.egg-info/SOURCES.txt'
>> running build_ext
>> generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_commoncrypto.c'
>> creating build/temp.macosx-10.9-x86_64-2.7
>> generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_padding.c'
>> generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_constant_time.c'
>> generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_openssl.c'
>> building '_openssl' extension
>> creating build/temp.macosx-10.9-x86_64-2.7/build
>> creating build/temp.macosx-10.9-x86_64-2.7/build/temp.macosx-10.9-x86_64-2.7
>> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall 
>> -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c 
>> build/temp.macosx-10.9-x86_64-2.7/_openssl.c -o 
>> build/temp.macosx-10.9-x86_64-2.7/build/temp.macosx-10.9-x86_64-2.7/_openssl.o
>> build/temp.macosx-10.9-x86_64-2.7/_openssl.c:718:6: error: conflicting types 
>> for
>> 'BIO_new_mem_buf'
>> BIO *BIO_new_mem_buf(void *, int);
>>^
>> /sw/include/openssl/bio.h:692:6: note: previous declaration is here
>> BIO *BIO_new_mem_buf(const void *buf, int len);
>>^
>> 1 error generated.
>> error: command 'gcc' failed with exit status 1
>> ### execution of /sw/bin/python2.7 failed, exit code 1
>> ### execution of /tmp/fink.SCP4y failed, exit code 1
>> 
>> 
>> 
>> Package manager version: 0.39.3
>> Distribution version: selfupdate-rsync Wed Mar  9 22:06:46 2016, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 6.2
>> Xcode command-line tools: 6.2.0.0.1.1424975374
>> Max. Fink build jobs:  18
>> 
>> and case-sensitive file system.
>> 
>> many thanks,
>> — Viv
> 
> I just updated to version 1.2.3 which fixed it.
> 
> Thanks
> 
> Daniel

Great, that works for me, too.

many thanks,
— Viv
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[Fink-users] cryptography-py27-1.1.1-2 build failure

[Viv Kendon]

(maintainer Cc’d) with everything else updated:

writing manifest file 'src/cryptography.egg-info/SOURCES.txt'
running build_ext
generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_commoncrypto.c'
creating build/temp.macosx-10.9-x86_64-2.7
generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_padding.c'
generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_constant_time.c'
generating cffi module 'build/temp.macosx-10.9-x86_64-2.7/_openssl.c'
building '_openssl' extension
creating build/temp.macosx-10.9-x86_64-2.7/build
creating build/temp.macosx-10.9-x86_64-2.7/build/temp.macosx-10.9-x86_64-2.7
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall 
-Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c 
build/temp.macosx-10.9-x86_64-2.7/_openssl.c -o 
build/temp.macosx-10.9-x86_64-2.7/build/temp.macosx-10.9-x86_64-2.7/_openssl.o
build/temp.macosx-10.9-x86_64-2.7/_openssl.c:718:6: error: conflicting types for
  'BIO_new_mem_buf'
BIO *BIO_new_mem_buf(void *, int);
 ^
/sw/include/openssl/bio.h:692:6: note: previous declaration is here
BIO *BIO_new_mem_buf(const void *buf, int len);
 ^
1 error generated.
error: command 'gcc' failed with exit status 1
### execution of /sw/bin/python2.7 failed, exit code 1
### execution of /tmp/fink.SCP4y failed, exit code 1



Package manager version: 0.39.3
Distribution version: selfupdate-rsync Wed Mar  9 22:06:46 2016, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.2
Xcode command-line tools: 6.2.0.0.1.1424975374
Max. Fink build jobs:  18

and case-sensitive file system.

many thanks,
— Viv
--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
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Re: [Fink-users] case-sensitive problem installing ncarray-oct382-1.0.3-1

[Viv Kendon]

On 26 Jan 2016, at 05:27, Alexander Hansen  wrote:

> 
>> On Jan 25, 2016, at 23:21, Viv Kendon  wrote:
>> 
>> fink -b install ncarray-oct382
>> ...
>> Failed: directory /sw/src/fink.build/ncarray-oct382-1.0.3-1/ncArray doesn't 
>> exist, check the package description
>> 
>> At least, I think it is a case-sensitive problem.  I built all of octave382 
>> on one case-sensitive machine, and am now pulling binaries onto two other 
>> machines.  All should be the same as
>> 
>> Package manager version: 0.39.2
>> Distribution version: selfupdate-rsync Tue Jan 26 06:20:53 2016, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 6.2
>> Xcode command-line tools: 6.2.0.0.1.1424975374
>> 
>> but they aren’t completely identical because I had trouble with ocs-oct382 
>> on one machine only.  So clearly that’s my problem, but ncarray failed on 
>> both machines I tried to binary install on, as above.
>> 
>> many thanks,
>> — Viv
>> 
>> 
> 
> It looks like upstream had “ncArray” at one point, and that got changed but I 
> didn’t notice because I’m on case-insensitive.  I just updated it in CVS.
> 
> Thanks!
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> 

Great, it all worked this time.
many thanks,
— Viv
--
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[Fink-users] case-sensitive problem installing ncarray-oct382-1.0.3-1

[Viv Kendon]

fink -b install ncarray-oct382
...
Selecting previously deselected package fink-buildlock-ncarray-oct382-1.0.3-1.
(Reading database ... 315605 files and directories currently installed.)
Unpacking fink-buildlock-ncarray-oct382-1.0.3-1 (from 
.../fink-buildlock-ncarray-oct382-1.0.3-1_2016.01.25-21.58.02_darwin-x86_64.deb)
 ...
Setting up fink-buildlock-ncarray-oct382-1.0.3-1 (2016.01.25-21.58.02) ...

env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner --no-same-permissions -xvf 
/sw/src/ncarray-1.0.3.tar.gz
...
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-ncarray-oct382-1.0.3-1
(Reading database ... 315606 files and directories currently installed.)
Removing fink-buildlock-ncarray-oct382-1.0.3-1 ...
Failed: directory /sw/src/fink.build/ncarray-oct382-1.0.3-1/ncArray doesn't 
exist, check the package description

At least, I think it is a case-sensitive problem.  I built all of octave382 on 
one case-sensitive machine, and am now pulling binaries onto two other 
machines.  All should be the same as

Package manager version: 0.39.2
Distribution version: selfupdate-rsync Tue Jan 26 06:20:53 2016, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.2
Xcode command-line tools: 6.2.0.0.1.1424975374

but they aren’t completely identical because I had trouble with ocs-oct382 on 
one machine only.  So clearly that’s my problem, but ncarray failed on both 
machines I tried to binary install on, as above.

many thanks,
— Viv



--
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[Fink-users] pyqt4-mac-py27-4.11.4-1 case-sensitive install error

[Viv Kendon]

I just hit a case-sensitive install error:

/bin/cp -r README /sw/src/fink.build/root-pyqt4-mac-py27-4.11.4-1/sw/share/doc/p
yqt4-mac-py27/
/bin/cp -r Thanks /sw/src/fink.build/root-pyqt4-mac-py27-4.11.4-1/sw/share/doc/p
yqt4-mac-py27/
cp: Thanks: No such file or directory

filename should be THANKS for those of us with case-sensitive file systems :)

Package manager version: 0.39.2
Distribution version: selfupdate-rsync Mon Jan  4 17:54:24 2016, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.2
Xcode command-line tools: 6.2.0.0.1.1424975374
Max. Fink build jobs:  18

many thanks,
— Viv



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Re: [Fink-users] Missing debs after update to 10.9 tree

[Viv Kendon]

On 5 Oct 2015, at 21:22, Viv Kendon  wrote:

> On 5 Oct 2015, at 20:57, Alexander Hansen  wrote:
>> 
>>> On Oct 5, 2015, at 12:39, Viv Kendon  wrote:
>>> 
>>> On 5 Oct 2015, at 15:36, Alexander Hansen  
>>> wrote:
>>> 
>>>>> On Oct 4, 2015, at 16:46, Hanspeter Niederstrasser 
>>>>>  wrote:
>>>>> 
>>>>> On 10/4/2015 5:02 PM, Alexander Hansen wrote:
>>>>>> 
>>>>>>> On Oct 4, 2015, at 14:22, Viv Kendon  wrote:
>>>>>>> 
>>>>>>> continuing with “update-all” I got:
>>>>>>> 
>>>>>>> The following packages must be temporarily removed, but there are no 
>>>>>>> .debs to
>>>>>>> restore them from:
>>>>>>> libev4 libev4
>>>>>>> 
>>>>>>> /sw/fink-64# ls 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*
>>>>>>> ls: 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*: No such file or 
>>>>>>> directory
>>>>>>> 
>>>>>>> And indeed, the debs are still in my 10.7 tree.
>>>>>>> 
>>>>>>> /sw/fink-63# ls 10.7/stable/main/binary-darwin-x86_64/libs/*ev4*
>>>>>>> 72 
>>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.15-1_darwin-x86_64.deb
>>>>>>> 72 
>>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.19-1_darwin-x86_64.deb
>>>>>>> 208 
>>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.15-1_darwin-x86_64.deb
>>>>>>> 216 
>>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.19-1_darwin-x86_64.deb
>>>>>>> 
>>>>>>> Should I manually move or copy them over to match the dangling 
>>>>>>> symlinks? Is there a way to get any other missing debs fixed up, other 
>>>>>>> than finding out like this, when they are actually needed?
>>>>>>> 
>>>>>>> 10.9.5, case-sensitive, fink -V
>>>>>>> Package manager version: 0.39.1
>>>>>>> 
>>>>>>> gcc -v
>>>>>>> Configured with: 
>>>>>>> --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>>>>>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>>>>> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
>>>>>>> Target: x86_64-apple-darwin13.4.0
>>>>>>> 
>>>>>>> Got to this version of fink earlier today by doing fink selfupdate 
>>>>>>> twice (first one gave me the warning about old symlink).  Unfortunately 
>>>>>>> I don’t have the screen output from doing that to see what might have 
>>>>>>> gone wrong.
>>>>>>> 
>>>>>>> many thanks,
>>>>>>> — Viv
>>>>>> 
>>>>>> Hmm, the fink-0.39.x update was supposed to have taken care of that.  
>>>>>> fink doesn’t try again if it detects a non-dangling symlink.
>>>>>> 
>>>>>> fink searches for .deb files in the 10.7 directory and just copies them 
>>>>>> over to the 10.9-libcxx directory (including the full paths, of course). 
>>>>>>  I don’t happen to have a shell script handy to do that, though.
>>>>> 
>>>>> I also had the failure of my debs being copied over (on 10.9).
>>>>> 
>>>>> Of note, I had 10.9-libcxx in my Trees: line in fink.conf before the 
>>>>> update in order to easier update files on both trees.  Don't know if 
>>>>> that's relevant and the transmutation of multiple of symlinks (I had 
>>>>> 10.9.old generated) confused the moving script.
>>>>> 
>>>>> Hanspeter
>>>>> 
>>>> 
>>>> A potential workaround would be to edit /sw/lib/fink/postinstall.pl as 
>>>> root and change line 273 to 
>>>> 
>>>> if (1) {
>>>> 
>>>> Then run postinstall.pl .  After that run “fink reinstall fink” to remove 
>>>> the manual modification so that fink doesn’t keep trying to copy .debs 
>>>> every time you update it.
>>>> 
>>>> -- 
>>>> Alexander Hansen, Ph.D.
>>>> Fink User Liaison
>>> 
&g

Re: [Fink-users] Missing debs after update to 10.9 tree

[Viv Kendon]

On 5 Oct 2015, at 20:57, Alexander Hansen  wrote:
> 
>> On Oct 5, 2015, at 12:39, Viv Kendon  wrote:
>> 
>> On 5 Oct 2015, at 15:36, Alexander Hansen  
>> wrote:
>> 
>>>> On Oct 4, 2015, at 16:46, Hanspeter Niederstrasser 
>>>>  wrote:
>>>> 
>>>> On 10/4/2015 5:02 PM, Alexander Hansen wrote:
>>>>> 
>>>>>> On Oct 4, 2015, at 14:22, Viv Kendon  wrote:
>>>>>> 
>>>>>> continuing with “update-all” I got:
>>>>>> 
>>>>>> The following packages must be temporarily removed, but there are no 
>>>>>> .debs to
>>>>>> restore them from:
>>>>>> libev4 libev4
>>>>>> 
>>>>>> /sw/fink-64# ls 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*
>>>>>> ls: 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*: No such file or 
>>>>>> directory
>>>>>> 
>>>>>> And indeed, the debs are still in my 10.7 tree.
>>>>>> 
>>>>>> /sw/fink-63# ls 10.7/stable/main/binary-darwin-x86_64/libs/*ev4*
>>>>>> 72 
>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.15-1_darwin-x86_64.deb
>>>>>> 72 
>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.19-1_darwin-x86_64.deb
>>>>>> 208 
>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.15-1_darwin-x86_64.deb
>>>>>> 216 
>>>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.19-1_darwin-x86_64.deb
>>>>>> 
>>>>>> Should I manually move or copy them over to match the dangling symlinks? 
>>>>>> Is there a way to get any other missing debs fixed up, other than 
>>>>>> finding out like this, when they are actually needed?
>>>>>> 
>>>>>> 10.9.5, case-sensitive, fink -V
>>>>>> Package manager version: 0.39.1
>>>>>> 
>>>>>> gcc -v
>>>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>>>>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>>>> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
>>>>>> Target: x86_64-apple-darwin13.4.0
>>>>>> 
>>>>>> Got to this version of fink earlier today by doing fink selfupdate twice 
>>>>>> (first one gave me the warning about old symlink).  Unfortunately I 
>>>>>> don’t have the screen output from doing that to see what might have gone 
>>>>>> wrong.
>>>>>> 
>>>>>> many thanks,
>>>>>> — Viv
>>>>> 
>>>>> Hmm, the fink-0.39.x update was supposed to have taken care of that.  
>>>>> fink doesn’t try again if it detects a non-dangling symlink.
>>>>> 
>>>>> fink searches for .deb files in the 10.7 directory and just copies them 
>>>>> over to the 10.9-libcxx directory (including the full paths, of course).  
>>>>> I don’t happen to have a shell script handy to do that, though.
>>>> 
>>>> I also had the failure of my debs being copied over (on 10.9).
>>>> 
>>>> Of note, I had 10.9-libcxx in my Trees: line in fink.conf before the 
>>>> update in order to easier update files on both trees.  Don't know if 
>>>> that's relevant and the transmutation of multiple of symlinks (I had 
>>>> 10.9.old generated) confused the moving script.
>>>> 
>>>> Hanspeter
>>>> 
>>> 
>>> A potential workaround would be to edit /sw/lib/fink/postinstall.pl as root 
>>> and change line 273 to 
>>> 
>>> if (1) {
>>> 
>>> Then run postinstall.pl .  After that run “fink reinstall fink” to remove 
>>> the manual modification so that fink doesn’t keep trying to copy .debs 
>>> every time you update it.
>>> 
>>> -- 
>>> Alexander Hansen, Ph.D.
>>> Fink User Liaison
>> 
>> Cool, I gave that a try and after about 8GB of copying I seem to have a full 
>> complement of .debs in 10.9-libcxx, to judge by the sizes of the dirs.
>> 
>> ls 10.9/stable/main/binary-darwin-x86_64/libs/*ev
>> 72 
>> /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.15-1_darwin-x86_64.deb
>> 72 
>> /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_

Re: [Fink-users] Missing debs after update to 10.9 tree

[Viv Kendon]

On 5 Oct 2015, at 15:36, Alexander Hansen  wrote:

>> On Oct 4, 2015, at 16:46, Hanspeter Niederstrasser  
>> wrote:
>> 
>> On 10/4/2015 5:02 PM, Alexander Hansen wrote:
>>> 
>>>> On Oct 4, 2015, at 14:22, Viv Kendon  wrote:
>>>> 
>>>> continuing with “update-all” I got:
>>>> 
>>>> The following packages must be temporarily removed, but there are no .debs 
>>>> to
>>>> restore them from:
>>>>  libev4 libev4
>>>> 
>>>> /sw/fink-64# ls 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*
>>>> ls: 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*: No such file or 
>>>> directory
>>>> 
>>>> And indeed, the debs are still in my 10.7 tree.
>>>> 
>>>> /sw/fink-63# ls 10.7/stable/main/binary-darwin-x86_64/libs/*ev4*
>>>> 72 
>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.15-1_darwin-x86_64.deb
>>>> 72 
>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.19-1_darwin-x86_64.deb
>>>> 208 
>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.15-1_darwin-x86_64.deb
>>>> 216 
>>>> 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.19-1_darwin-x86_64.deb
>>>> 
>>>> Should I manually move or copy them over to match the dangling symlinks? 
>>>> Is there a way to get any other missing debs fixed up, other than finding 
>>>> out like this, when they are actually needed?
>>>> 
>>>> 10.9.5, case-sensitive, fink -V
>>>> Package manager version: 0.39.1
>>>> 
>>>> gcc -v
>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
>>>> Target: x86_64-apple-darwin13.4.0
>>>> 
>>>> Got to this version of fink earlier today by doing fink selfupdate twice 
>>>> (first one gave me the warning about old symlink).  Unfortunately I don’t 
>>>> have the screen output from doing that to see what might have gone wrong.
>>>> 
>>>> many thanks,
>>>> — Viv
>>> 
>>> Hmm, the fink-0.39.x update was supposed to have taken care of that.  fink 
>>> doesn’t try again if it detects a non-dangling symlink.
>>> 
>>>  fink searches for .deb files in the 10.7 directory and just copies them 
>>> over to the 10.9-libcxx directory (including the full paths, of course).  I 
>>> don’t happen to have a shell script handy to do that, though.
>> 
>> I also had the failure of my debs being copied over (on 10.9).
>> 
>> Of note, I had 10.9-libcxx in my Trees: line in fink.conf before the 
>> update in order to easier update files on both trees.  Don't know if 
>> that's relevant and the transmutation of multiple of symlinks (I had 
>> 10.9.old generated) confused the moving script.
>> 
>> Hanspeter
>> 
> 
> A potential workaround would be to edit /sw/lib/fink/postinstall.pl as root 
> and change line 273 to 
> 
> if (1) {
> 
> Then run postinstall.pl .  After that run “fink reinstall fink” to remove the 
> manual modification so that fink doesn’t keep trying to copy .debs every time 
> you update it.
> 
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison

Cool, I gave that a try and after about 8GB of copying I seem to have a full 
complement of .debs in 10.9-libcxx, to judge by the sizes of the dirs.

 ls 10.9/stable/main/binary-darwin-x86_64/libs/*ev
 72 
/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.15-1_darwin-x86_64.deb
 72 
/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.19-1_darwin-x86_64.deb
208 
/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/libev4_4.15-1_darwin-x86_64.deb
216 
/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/libev4_4.19-1_darwin-x86_64.deb

looks much more promising.  And update-all is now proceeding.  

I notice it has copied over my “local” .debs, but not the corresponding 
finkinfo files.  That’s easy to fix of course.

Many thanks for the fix, much appreciated.
— Viv
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[Fink-users] Missing debs after update to 10.9 tree

[Viv Kendon]

continuing with “update-all” I got:

The following packages must be temporarily removed, but there are no .debs to
restore them from:
  libev4 libev4

/sw/fink-64# ls 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*
ls: 10.9/stable/main/binary-darwin-x86_64/libs/*ev4*: No such file or directory

And indeed, the debs are still in my 10.7 tree.  

/sw/fink-63# ls 10.7/stable/main/binary-darwin-x86_64/libs/*ev4*
 72 
10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.15-1_darwin-x86_64.deb
 72 
10.7/stable/main/binary-darwin-x86_64/libs/libev4-shlibs_4.19-1_darwin-x86_64.deb
208 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.15-1_darwin-x86_64.deb
216 10.7/stable/main/binary-darwin-x86_64/libs/libev4_4.19-1_darwin-x86_64.deb

Should I manually move or copy them over to match the dangling symlinks? Is 
there a way to get any other missing debs fixed up, other than finding out like 
this, when they are actually needed?

10.9.5, case-sensitive, fink -V
Package manager version: 0.39.1

gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0

Got to this version of fink earlier today by doing fink selfupdate twice (first 
one gave me the warning about old symlink).  Unfortunately I don’t have the 
screen output from doing that to see what might have gone wrong.

many thanks,
— Viv
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Re: [Fink-users] openmpi 1.10.0-1 - ln: /sw/bin/vtCC: File exists

[Viv Kendon]

On 4 Oct 2015, at 20:59, Alexander Hansen  wrote:

>>> 
>>> A rebuild normally includes a reinstall if you’re building the same version 
>>> as the currently installed one, so that’s not surprising.  However, if 
>>> those files were indeed changed by the openmpi-shlibs install, that would 
>>> be another matter, since the pre-removal and post-install scripts are run 
>>> for the main package only.
>>> 
>>> At least we’ve determined that vtCC wasn’t present in the root directory.  
>>> What happens if you remove openmpi (leaving the shlibs) and install it?
>> 
>> openmpi is not installed (according to fink), which is why only 
>> openmpi-shlibs was reinstalled.  So trying to install openmpi gives the same 
>> error:
>> 
>> fink list openmpi
>> Information about 9257 packages read in 1 seconds.
>>openmpi  1.10.0-1 MPI implementation for parallel computing
>> i   openmpi-shlibs   1.10.0-1 Shared libraries for openmpi package
>> fink install openmpi
>> Password:
>> Information about 9257 packages read in 0 seconds.
>> The following package will be installed or updated:
>> openmpi
>> Reading buildlock packages...
>>   All buildlocks accounted for.
>> /sw/bin/dpkg-lockwait -i 
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.0-1_darwin-x86_64.deb
>> (Reading database ... 380816 files and directories currently installed.)
>> Preparing to replace openmpi 1.10.0-1 (using 
>> .../openmpi_1.10.0-1_darwin-x86_64.deb) ...
>> Unpacking replacement openmpi ...
>> Setting up openmpi (1.10.0-1) ...
>> Clearing dependency_libs of .la files being installed
>> ln: /sw/bin/vtCC: File exists
>> /sw/bin/dpkg: error processing openmpi (--install):
>> subprocess post-installation script returned error exit status 1
>> Errors were encountered while processing:
>> openmpi
>> ### execution of /sw/bin/dpkg-lockwait failed, exit code 1
>> Failed: can't install package openmpi-1.10.0-1
>> 
>> ls -l /sw/bin/vt*
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 20:36 /sw/bin/vtCC@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 20:36 /sw/bin/vtc++@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 20:36 /sw/bin/vtcxx@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 20:36 /sw/bin/vtf77@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 20:36 /sw/bin/vtf90@ -> vtwrapper
>> 624 -rwxr-xr-x  1 root  admin  318760 Oct  4 19:48 /sw/bin/vtfilter*
>> 664 -rwxr-xr-x  1 root  admin  336860 Oct  4 19:48 /sw/bin/vtfilter-mpi*
>>  8 lrwxr-xr-x  1 root  admin   8 Oct  4 20:36 /sw/bin/vtfiltergen@ -> 
>> vtfilter
>>  8 lrwxr-xr-x  1 root  admin  12 Oct  4 20:36 /sw/bin/vtfiltergen-mpi@ 
>> -> vtfilter-mpi
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 20:36 /sw/bin/vtfort@ -> 
>> vtwrapper
>> 24 -rwxr-xr-x  1 root  admin9205 Oct  4 19:48 /sw/bin/vtrun*
>>  8 -rwxr-xr-x  1 root  admin1612 Oct  4 19:48 /sw/bin/vtsetup*
>> 1096 -rw-r--r--  1 root  admin  557402 Oct  4 19:48 /sw/bin/vtsetup.jar
>> 1104 -rwxr-xr-x  1 root  admin  563296 Oct  4 19:48 /sw/bin/vtunify*
>> 1272 -rwxr-xr-x  1 root  admin  649392 Oct  4 19:48 /sw/bin/vtunify-mpi*
>> 328 -rwxr-xr-x  1 root  admin  166016 Oct  4 19:48 /sw/bin/vtwrapper*
>> 
>> 19:48 is the rebuild time, i.e., when the openmpi deb was created, 20:36 is 
>> the attempt to install openmpi time.  So for the record, the 18:02 timestamp 
>> above was from another failed attempt to install openmpi, when I kicked off 
>> update-all again.
>> 
>> fink remove openmpi
>> Information about 9257 packages read in 1 seconds.
>> WARNING: openmpi is not installed, skipping.
>> No packages to remove
>> 
>> So it looks like it doesn’t clean up after the failed attempt to install.  
>> Is there another way to get rid of the not quite installed files and try 
>> again?
>> 
>> many thanks,
>> — Viv
>> 
>> 
> 
> Use “sudo dpkg -r openmpi” to remove the partially installed package (dpkg 
> has a slightly different view of what is installed than fink does).  Then 
> verify whether /sw/bin/vtCC is still around.  If it is, manually remove it.  
> If not then try to “fink install openmpi” again.

Great, that worked:

 sudo dpkg -r openmpi
Password:
dpkg: dependency problems prevent removal of openmpi:
 fftw-mpi depends on openmpi.
/sw/bin/dpkg: error processing openmpi (--remove):
 dependency problems - not removing
Errors were encountered while processing:
 openmpi
 fink remove fftw-mpi
Information about 9257 packages read in 1 seconds.
Reading buildlock packages...
All buildlocks accounted for.
/sw/bin/dpkg-lockwait --remove fftw-mpi
(Reading database ... 380816 files and directories currently installed.)
Removing fftw-mpi ...
install-info(fftw.info): deleting entry `* fftw: (fftw) ...'
 sudo dpkg -r openmpi
(Reading database ... 380755 files and directories currently installed.)
Removing openmpi ...
 ls -l /sw/bin/vt*
ls: /sw/bin/vt*: No such file or directory
 fink install openmpi
Information about 9257 packages read in 1 seconds.

Re: [Fink-users] openmpi 1.10.0-1 - ln: /sw/bin/vtCC: File exists

[Viv Kendon]

On 4 Oct 2015, at 20:20, Alexander Hansen  wrote:
> 
>> On Oct 4, 2015, at 11:56, Viv Kendon  wrote:
>> 
>> On 4 Oct 2015, at 19:32, Alexander Hansen  
>> wrote:
>>> 
>>>> On Oct 4, 2015, at 09:37, Viv Kendon  wrote:
>>>> 
>>>> Having trouble unpacking openmpi:
>>>> 
>>>> /sw/bin/dpkg-lockwait -i 
>>>> /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.0-1_darwin-x86_64.deb
>>>> (Reading database ... 380816 files and directories currently installed.)
>>>> Preparing to replace openmpi 1.10.0-1 (using 
>>>> .../openmpi_1.10.0-1_darwin-x86_64.deb) ...
>>>> Unpacking replacement openmpi ...
>>>> Setting up openmpi (1.10.0-1) ...
>>>> Clearing dependency_libs of .la files being installed
>>>> ln: /sw/bin/vtCC: File exists
>>>> /sw/bin/dpkg: error processing openmpi (--install):
>>>> subprocess post-installation script returned error exit status 1
>>>> Errors were encountered while processing:
>>>> openmpi
>>>> 
>>>> It didn’t give me a “please include this” set of info, let me know if I 
>>>> left out anything you need about my configuration:  10.9.5, 
>>>> case-sensitive,  fink -V
>>>> Package manager version: 0.39.1
>>>> 
>>>> fink list -t openmpi
>>>> Information about 9257 packages read in 0 seconds.
>>>>  openmpi 1.10.0-1MPI implementation for parallel computing
>>>> i  openmpi-shlibs  1.10.0-1Shared libraries for openmpi package
>>>> 
>>>> gcc -v
>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>>> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
>>>> Target: x86_64-apple-darwin13.4.0
>>>> 
>>>> ls -l /sw/bin/vt*
>>>> 8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtCC@ -> vtwrapper
>>>> 8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtc++@ -> 
>>>> vtwrapper
>>>> 8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtcxx@ -> 
>>>> vtwrapper
>>>> 8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtf77@ -> 
>>>> vtwrapper
>>>> 8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtf90@ -> 
>>>> vtwrapper
>>>> 624 -rwxr-xr-x  1 root  admin  318760 Oct  4 14:53 /sw/bin/vtfilter*
>>>> 664 -rwxr-xr-x  1 root  admin  336860 Oct  4 14:53 /sw/bin/vtfilter-mpi*
>>>> 8 lrwxr-xr-x  1 root  admin   8 Oct  4 15:56 /sw/bin/vtfiltergen@ -> 
>>>> vtfilter
>>>> 8 lrwxr-xr-x  1 root  admin  12 Oct  4 15:56 /sw/bin/vtfiltergen-mpi@ 
>>>> -> vtfilter-mpi
>>>> 8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtfort@ -> 
>>>> vtwrapper
>>>> 24 -rwxr-xr-x  1 root  admin9205 Oct  4 14:53 /sw/bin/vtrun*
>>>> 8 -rwxr-xr-x  1 root  admin1612 Oct  4 14:53 /sw/bin/vtsetup*
>>>> 1096 -rw-r--r--  1 root  admin  557402 Oct  4 14:53 /sw/bin/vtsetup.jar
>>>> 1104 -rwxr-xr-x  1 root  admin  563296 Oct  4 14:53 /sw/bin/vtunify*
>>>> 1272 -rwxr-xr-x  1 root  admin  649392 Oct  4 14:53 /sw/bin/vtunify-mpi*
>>>> 328 -rwxr-xr-x  1 root  admin  166016 Oct  4 14:53 /sw/bin/vtwrapper*
>>>> 
>>>> (the 14:53 timestamps are from when I tried it first, and openmpi-shlibs 
>>>> was installed successfully; 15:56 is when it failed the second time, after 
>>>> restarting “update-all")
>>>> 
>>>> many thanks,
>>>> — Viv
>>>> ———
>>> 
>>> There’s a note in the packaging about “case sensitive hackery”, but it 
>>> appears not to have taken effect.  It looks like vtCC still gets installed, 
>>> and then the PostInstScript tries to run
>>> 
>>>ln -s /sw/bin/vtwrapper /sw/bin/vtCC
>>> 
>>> which fails due to vtCC already existing.  
>>> 
>>> Since I don’t have a case-sensisitve system handy, could I please get you 
>>> to do a “fink -kK rebuild openmpi” ?  That way I can do some forensics on 
>>> the build and root directories to see whether the scripts are doing the 
>>> right thing?
>>> 
>>> The first thing to look for is the output of "ls 
>>> /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vt*
>>> 
>> done:
>> 
>>

Re: [Fink-users] openmpi 1.10.0-1 - ln: /sw/bin/vtCC: File exists

[Viv Kendon]

On 4 Oct 2015, at 19:32, Alexander Hansen  wrote:
> 
>> On Oct 4, 2015, at 09:37, Viv Kendon  wrote:
>> 
>> Having trouble unpacking openmpi:
>> 
>> /sw/bin/dpkg-lockwait -i 
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.0-1_darwin-x86_64.deb
>> (Reading database ... 380816 files and directories currently installed.)
>> Preparing to replace openmpi 1.10.0-1 (using 
>> .../openmpi_1.10.0-1_darwin-x86_64.deb) ...
>> Unpacking replacement openmpi ...
>> Setting up openmpi (1.10.0-1) ...
>> Clearing dependency_libs of .la files being installed
>> ln: /sw/bin/vtCC: File exists
>> /sw/bin/dpkg: error processing openmpi (--install):
>> subprocess post-installation script returned error exit status 1
>> Errors were encountered while processing:
>> openmpi
>> 
>> It didn’t give me a “please include this” set of info, let me know if I left 
>> out anything you need about my configuration:  10.9.5, case-sensitive,  fink 
>> -V
>> Package manager version: 0.39.1
>> 
>> fink list -t openmpi
>> Information about 9257 packages read in 0 seconds.
>>   openmpi 1.10.0-1MPI implementation for parallel computing
>> i  openmpi-shlibs  1.10.0-1Shared libraries for openmpi package
>> 
>> gcc -v
>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
>> Target: x86_64-apple-darwin13.4.0
>> 
>> ls -l /sw/bin/vt*
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtCC@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtc++@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtcxx@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtf77@ -> vtwrapper
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtf90@ -> vtwrapper
>> 624 -rwxr-xr-x  1 root  admin  318760 Oct  4 14:53 /sw/bin/vtfilter*
>> 664 -rwxr-xr-x  1 root  admin  336860 Oct  4 14:53 /sw/bin/vtfilter-mpi*
>>  8 lrwxr-xr-x  1 root  admin   8 Oct  4 15:56 /sw/bin/vtfiltergen@ -> 
>> vtfilter
>>  8 lrwxr-xr-x  1 root  admin  12 Oct  4 15:56 /sw/bin/vtfiltergen-mpi@ 
>> -> vtfilter-mpi
>>  8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtfort@ -> 
>> vtwrapper
>> 24 -rwxr-xr-x  1 root  admin9205 Oct  4 14:53 /sw/bin/vtrun*
>>  8 -rwxr-xr-x  1 root  admin1612 Oct  4 14:53 /sw/bin/vtsetup*
>> 1096 -rw-r--r--  1 root  admin  557402 Oct  4 14:53 /sw/bin/vtsetup.jar
>> 1104 -rwxr-xr-x  1 root  admin  563296 Oct  4 14:53 /sw/bin/vtunify*
>> 1272 -rwxr-xr-x  1 root  admin  649392 Oct  4 14:53 /sw/bin/vtunify-mpi*
>> 328 -rwxr-xr-x  1 root  admin  166016 Oct  4 14:53 /sw/bin/vtwrapper*
>> 
>> (the 14:53 timestamps are from when I tried it first, and openmpi-shlibs was 
>> installed successfully; 15:56 is when it failed the second time, after 
>> restarting “update-all")
>> 
>> many thanks,
>> — Viv
>> ———
> 
> There’s a note in the packaging about “case sensitive hackery”, but it 
> appears not to have taken effect.  It looks like vtCC still gets installed, 
> and then the PostInstScript tries to run
> 
> ln -s /sw/bin/vtwrapper /sw/bin/vtCC
> 
> which fails due to vtCC already existing.  
> 
> Since I don’t have a case-sensisitve system handy, could I please get you to 
> do a “fink -kK rebuild openmpi” ?  That way I can do some forensics on the 
> build and root directories to see whether the scripts are doing the right 
> thing?
> 
> The first thing to look for is the output of "ls 
> /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vt*
> 
done:

ls /sw/src/fink.build/root-openmpi-1.10.0-1/sw
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtc++@
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtcc@
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtcxx@
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtf77@
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtf90@
 624 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfilter*
 664 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfilter-mpi*
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfiltergen@
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfiltergen-mpi@
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfort@
  24 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtrun*
   8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtsetup*
1096 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtsetup.jar
1104

[Fink-users] openmpi 1.10.0-1 - ln: /sw/bin/vtCC: File exists

[Viv Kendon]

Having trouble unpacking openmpi:

/sw/bin/dpkg-lockwait -i 
/sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.0-1_darwin-x86_64.deb
(Reading database ... 380816 files and directories currently installed.)
Preparing to replace openmpi 1.10.0-1 (using 
.../openmpi_1.10.0-1_darwin-x86_64.deb) ...
Unpacking replacement openmpi ...
Setting up openmpi (1.10.0-1) ...
Clearing dependency_libs of .la files being installed
ln: /sw/bin/vtCC: File exists
/sw/bin/dpkg: error processing openmpi (--install):
 subprocess post-installation script returned error exit status 1
Errors were encountered while processing:
 openmpi

It didn’t give me a “please include this” set of info, let me know if I left 
out anything you need about my configuration:  10.9.5, case-sensitive,  fink -V
Package manager version: 0.39.1

 fink list -t openmpi
Information about 9257 packages read in 0 seconds.
openmpi 1.10.0-1MPI implementation for parallel computing
 i  openmpi-shlibs  1.10.0-1Shared libraries for openmpi package

gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0

ls -l /sw/bin/vt*
   8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtCC@ -> vtwrapper
   8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtc++@ -> vtwrapper
   8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtcxx@ -> vtwrapper
   8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtf77@ -> vtwrapper
   8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtf90@ -> vtwrapper
 624 -rwxr-xr-x  1 root  admin  318760 Oct  4 14:53 /sw/bin/vtfilter*
 664 -rwxr-xr-x  1 root  admin  336860 Oct  4 14:53 /sw/bin/vtfilter-mpi*
   8 lrwxr-xr-x  1 root  admin   8 Oct  4 15:56 /sw/bin/vtfiltergen@ -> 
vtfilter
   8 lrwxr-xr-x  1 root  admin  12 Oct  4 15:56 /sw/bin/vtfiltergen-mpi@ -> 
vtfilter-mpi
   8 lrwxr-xr-x  1 root  admin   9 Oct  4 15:56 /sw/bin/vtfort@ -> vtwrapper
  24 -rwxr-xr-x  1 root  admin9205 Oct  4 14:53 /sw/bin/vtrun*
   8 -rwxr-xr-x  1 root  admin1612 Oct  4 14:53 /sw/bin/vtsetup*
1096 -rw-r--r--  1 root  admin  557402 Oct  4 14:53 /sw/bin/vtsetup.jar
1104 -rwxr-xr-x  1 root  admin  563296 Oct  4 14:53 /sw/bin/vtunify*
1272 -rwxr-xr-x  1 root  admin  649392 Oct  4 14:53 /sw/bin/vtunify-mpi*
 328 -rwxr-xr-x  1 root  admin  166016 Oct  4 14:53 /sw/bin/vtwrapper*

(the 14:53 timestamps are from when I tried it first, and openmpi-shlibs was 
installed successfully; 15:56 is when it failed the second time, after 
restarting “update-all")

many thanks,
— Viv
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Re: [Fink-users] octave382-atlas-x11-qtx11 fails to find freetype header

[Viv Kendon]

On 2 Aug 2015, at 22:51, Alexander Hansen  wrote:

> 
>> On Aug 2, 2015, at 13:24, Viv Kendon  wrote:
>> 
>> Trying to build octave382-atlas-x11-qtx11 on 10.9.5 (case sensitive file 
>> system) 
>> Package manager version: 0.38.6
>> Distribution version: selfupdate-rsync Sun Aug  2 20:44:02 2015, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 6.2
>> Xcode command-line tools: 6.2.0.0.1.1424975374
>> Max. Fink build jobs:  18
>> 
>> it fails with:
>> 
>> libtool: compile:  oct-cxx -DHAVE_CONFIG_H -I. -I.. 
>> -I../liboctave/cruft/misc -I../liboctave/array -I../liboctave/numeric 
>> -I../liboctave/numeric -I../liboctave/operators -I../liboctave/operators 
>> -I../liboctave/system -I../liboctave/util -I./octave-value -I./operators 
>> -Iparse-tree -I./parse-tree -Icorefcn -I./corefcn -I../libgnu -I../libgnu 
>> -I/sw/include -I/sw/include/freetype2 -I/usr/X11/include -I/sw/include -Wall 
>> -W -Wshadow -Wold-style-cast -Wformat -Wpointer-arith -Wwrite-strings 
>> -Wcast-align -Wcast-qual -O3 -MD -D_THREAD_SAFE -pthread -MT 
>> dldfcn/dldfcn_colamd_la-colamd.lo -MD -MP -MF 
>> dldfcn/.deps/dldfcn_colamd_la-colamd.Tpo -c dldfcn/colamd.cc  -fno-common 
>> -DPIC -o dldfcn/.libs/dldfcn_colamd_la-colamd.o
>> In file included from dldfcn/amd.cc:44:
>> In file included from ../liboctave/util/oct-sparse.h:77:
>> /sw/include/suitesparse/cs.h:422:14: warning: 'cs_ci_house' has C-linkage 
>> specified, but returns user-defined type 'cs_complex_t' (aka 
>> 'complex') which is incompatible with C [-Wreturn-type-c-linkage]
>> cs_complex_t cs_ci_house (cs_complex_t *x, double *beta, int n) ;
>>^
>> /sw/include/suitesparse/cs.h:562:14: warning: 'cs_cl_house' has C-linkage 
>> specified, but returns user-defined type 'cs_complex_t' (aka 
>> 'complex') which is incompatible with C [-Wreturn-type-c-linkage]
>> cs_complex_t cs_cl_house (cs_complex_t *x, double *beta, cs_long_t n) ;
>>^
>> In file included from dldfcn/__init_fltk__.cc:84:
>> In file included from corefcn/gl-render.h:43:
>> In file included from corefcn/graphics.h:49:
>> In file included from corefcn/txt-eng-ft.h:31:
>> /usr/X11R6/include/ft2build.h:56:10: fatal error: 
>> 'freetype/config/ftheader.h' file not found
>> #include 
>>^
>> 
>> I checked obvious things like the links from /usr/X11 to /opt/X11, the 
>> existence of said file:
>> 
>> # locate ftheader.h
>> /opt/X11/include/freetype2/freetype/config/ftheader.h
>> /sw/include/freetype2/config/ftheader.h
>> 
>> and note that if it is meant to find the fink header there is no “freetype” 
>> subdir, but it might not find the X11 one since /usr/X11/include/freetype2 
>> is not given as an include.  
>> 
>> # fink list -ti freetype
>> Information about 11661 packages read in 1 seconds.
>> i  freetype219 2.6-1   TrueType font rendering library, headers
>> i  freetype219-shlibs  2.6-1   TrueType font rendering library, 
>> shared libs
>> i  system-pkgconfig-freetype2  16.2.10-1   [virtual pkgconfig 
>> package representing freetype2]
>> 
>> I have the full log available and build dir if it would help to check 
>> anything else?  
>> 
>> many thanks,
>> — Viv
> 
> I don’t reproduce this here (10.10.4/Xcode 6.4)
> 
> Do you have /sw/include/freetype2/ft2build.h ?  The flag ordering in the 
> build ("-I/sw/include/freetype2 -I/usr/X11/include") *intentionally* has been 
> set to pick up Fink’s freetype rather than X11’s, and thus I’d think that  
> /sw/include/freetype2/ft2build.h would be found first by the "#include 
> " directive in corefcn/txt-eng-ft.h .  
> 
Yup:

# ls -l /sw/include/freetype2/ft2build.h 
8 -rw-r--r--  1 root  admin  2383 Aug  2 14:22 /sw/include/freetype2/ft2build.h

newly refreshed by today’s update-all.  And it contains what it should as far 
as I can tell.  I agree it makes no sense for the X11 version to have been 
included instead of the fink one.

many thanks,
— Viv
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[Fink-users] octave382-atlas-x11-qtx11 fails to find freetype header

[Viv Kendon]

Trying to build octave382-atlas-x11-qtx11 on 10.9.5 (case sensitive file 
system) 
Package manager version: 0.38.6
Distribution version: selfupdate-rsync Sun Aug  2 20:44:02 2015, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.2
Xcode command-line tools: 6.2.0.0.1.1424975374
Max. Fink build jobs:  18

it fails with:

libtool: compile:  oct-cxx -DHAVE_CONFIG_H -I. -I.. -I../liboctave/cruft/misc 
-I../liboctave/array -I../liboctave/numeric -I../liboctave/numeric 
-I../liboctave/operators -I../liboctave/operators -I../liboctave/system 
-I../liboctave/util -I./octave-value -I./operators -Iparse-tree -I./parse-tree 
-Icorefcn -I./corefcn -I../libgnu -I../libgnu -I/sw/include 
-I/sw/include/freetype2 -I/usr/X11/include -I/sw/include -Wall -W -Wshadow 
-Wold-style-cast -Wformat -Wpointer-arith -Wwrite-strings -Wcast-align 
-Wcast-qual -O3 -MD -D_THREAD_SAFE -pthread -MT 
dldfcn/dldfcn_colamd_la-colamd.lo -MD -MP -MF 
dldfcn/.deps/dldfcn_colamd_la-colamd.Tpo -c dldfcn/colamd.cc  -fno-common -DPIC 
-o dldfcn/.libs/dldfcn_colamd_la-colamd.o
In file included from dldfcn/amd.cc:44:
In file included from ../liboctave/util/oct-sparse.h:77:
/sw/include/suitesparse/cs.h:422:14: warning: 'cs_ci_house' has C-linkage 
specified, but returns user-defined type 'cs_complex_t' (aka 'complex') 
which is incompatible with C [-Wreturn-type-c-linkage]
cs_complex_t cs_ci_house (cs_complex_t *x, double *beta, int n) ;
 ^
/sw/include/suitesparse/cs.h:562:14: warning: 'cs_cl_house' has C-linkage 
specified, but returns user-defined type 'cs_complex_t' (aka 'complex') 
which is incompatible with C [-Wreturn-type-c-linkage]
cs_complex_t cs_cl_house (cs_complex_t *x, double *beta, cs_long_t n) ;
 ^
In file included from dldfcn/__init_fltk__.cc:84:
In file included from corefcn/gl-render.h:43:
In file included from corefcn/graphics.h:49:
In file included from corefcn/txt-eng-ft.h:31:
/usr/X11R6/include/ft2build.h:56:10: fatal error: 'freetype/config/ftheader.h' 
file not found
#include 
 ^

I checked obvious things like the links from /usr/X11 to /opt/X11, the 
existence of said file:

# locate ftheader.h
/opt/X11/include/freetype2/freetype/config/ftheader.h
/sw/include/freetype2/config/ftheader.h

and note that if it is meant to find the fink header there is no “freetype” 
subdir, but it might not find the X11 one since /usr/X11/include/freetype2 is 
not given as an include.  

# fink list -ti freetype
Information about 11661 packages read in 1 seconds.
 i  freetype219 2.6-1   TrueType font rendering library, headers
 i  freetype219-shlibs  2.6-1   TrueType font rendering library, shared 
libs
 i  system-pkgconfig-freetype2  16.2.10-1   [virtual pkgconfig 
package representing freetype2]

I have the full log available and build dir if it would help to check anything 
else?  

many thanks,
— Viv
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Re: [Fink-users] case sensitive problem with cython-py27 0.22-1

[Viv Kendon]

Confirming this now works for me, many thanks, — Viv

On 22 Feb 2015, at 11:08, Daniel Johnson  wrote:

> 
>> On Feb 21, 2015, at 11:10 PM, Viv Kendon  wrote:
>> 
>> Cython-0.22/Tools/site_scons/site_tools/pyext.py
>> Cython-0.22/USAGE.txt
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-cython-py27-0.22-1
>> (Reading database ... 368896 files and directories currently installed.)
>> Removing fink-buildlock-cython-py27-0.22-1 ...
>> Failed: directory /sw/src/fink.build/cython-py27-0.22-1/cython-0.22 doesn't 
>> exist, check the package description
>> 
>> on a case-sensitive 10.9.5 system:
>> 
>>> ls /sw/src/fink.build/cython-py27-0.22-1/
>> total 0
>> 0 ./0 ../   0 Cython-0.22/
>> 
>> 
>> TIA
>> — Viv
> 
> Bleh. They changed the tarball from "Cython" to "cython" but left the name of 
> the extracted directory as "Cython" which broke on case sensitive HFS. Should 
> be fixed now.
> 
> Daniel
> 


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[Fink-users] case sensitive problem with cython-py27 0.22-1

[Viv Kendon]

Cython-0.22/Tools/site_scons/site_tools/pyext.py
Cython-0.22/USAGE.txt
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-cython-py27-0.22-1
(Reading database ... 368896 files and directories currently installed.)
Removing fink-buildlock-cython-py27-0.22-1 ...
Failed: directory /sw/src/fink.build/cython-py27-0.22-1/cython-0.22 doesn't 
exist, check the package description

on a case-sensitive 10.9.5 system:

> ls /sw/src/fink.build/cython-py27-0.22-1/
total 0
0 ./0 ../   0 Cython-0.22/


TIA
— Viv
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Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 26 Oct 2014, at 22:08, Alexander Hansen  wrote:

> 
> On Oct 26, 2014, at 2:43 PM, Viv Kendon  wrote:
> 
>> 
>> On 26 Oct 2014, at 14:07, Alexander Hansen  
>> wrote:
>> 
>>> On 10/26/14, 4:34 AM, Viv Kendon wrote:
>>>> 
>>>> On 26 Oct 2014, at 01:13, Alexander Hansen  
>>>> wrote:
>>>> 
>>>>> On 10/25/14, 3:16 PM, Viv Kendon wrote:
>>>>>> 
>>>>>> On 25 Oct 2014, at 22:43, Viv Kendon  wrote:
>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>>> On 25 Oct 2014, at 22:01, Alexander Hansen 
>>>>>>>  wrote:
>>>>>>>> 
>>>>>>>> The if-then that you fixed was _supposed_ to copy that over for 10.9 
>>>>>>>> and later.  As a workaround, maybe start a rebuild of 
>>>>>>>> octave364-atlas-x11, stop it after the patch phase, and manually do a
>>>>>>>> 
>>>>>>>> sudo cp 
>>>>>>>> /sw/src/fink.build/octave-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h 
>>>>>>>> /sw/include/octave-3.6.4/octave/
>>>>>>> 
>>>>>>> Many thanks, I did that, then restarted fink install 
>>>>>>> bundle-octave-atlas.  It went through the oct364 packages in 
>>>>>>> alphabetical order, so here is how it dies for java:
>>>>>>> 
>>>>>>> ans = 
>>>>>>> /sw/src/fink.build/java-oct364-1.2.9-3/bld/share/octave/3.6.4/packages
>>>>>>> mkdir (/var/tmp/oct-l9vVbi)
>>>>>>> untar (./java.tar, /var/tmp/oct-l9vVbi)
>>>>>>> 
>>>>>>> Error while trying to install Java package:
>>>>>>> JAVA_HOME environment variable does not properly point to a JDK
>>>>>>> Hint:
>>>>>>> JAVA_HOME should usually be set such that either:
>>>>>>> (on *nix:)
>>>>>>>   /jre/lib//client/ contains libjvm.so (file or 
>>>>>>> symlink)
>>>>>>> (on OSX:)
>>>>>>>   /../Libraries/ contains a file libclient.dylib
>>>>>>> (on Windows:)
>>>>>>>   /jre/lib// contains a file jvm.cfg
>>>>>>> ( depends on your system hardware, can be i386, x86_64, alpha, 
>>>>>>> arm, ...)
>>>>>>> 
>>>>>>> Use forward slashes as path separator, also on Windows
>>>>>>> Aborting pkg install
>>>>>>> error: called from 'pre_install' in file 
>>>>>>> /private/var/tmp/oct-l9vVbi/java/pre_install.m near line 115, column 5
>>>>>>> error: called from:
>>>>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
>>>>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>>>>>>> error:   /sw/src/fink.build/java-oct364-1.2.9-3/java/octave-forge-comp 
>>>>>>> at line 4, column 1
>>>>>>> 
>>>>>>> I then manually verified that octcdf-nc4-oct364 now installs fine.
>>>>>>> 
>>>>>>> Will I need to manually copy libcxx-fix.h for octave382 as well?  And 
>>>>>>> is the file identical to the octave364 copy, or do I need to start a 
>>>>>>> rebuild for octave382 to get the corresponding file?
>>>>>>> 
>>>>>> 
>>>>>> I tried a few oct832 packages (without doing anything about libcxx-fix.h 
>>>>>> for octave382) and they all seem to die in the same way with a java 
>>>>>> error that is very different from the above:
>>>>>> 
>>>>>> mkdir -p bld/share/octave/3.8.2/packages bld/lib/octave/3.8.2/packages
>>>>>> `which xvfb-run` 
>>>>>> /sw/src/fink.build/optiminterp-atlas-oct382-0.3.4-3/optiminterp/octave-forge-comp
>>>>>> which xvfb-run
>>>>>> No Java runtime present, requesting install.
>>>>>> 2014-10-25 23:07:33.340 octave-cli-3.8.2[45245:d07] 
>>>>>> JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote
>>>>>> ### execution of /tmp/fink.zx8W6 failed, exit code 97
>>>>>> Removing runtime build-lock...
>>>>>> Removing build-lock package...
>>>>>> /sw/bin/dpkg-lo

Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 26 Oct 2014, at 14:07, Alexander Hansen  wrote:

> On 10/26/14, 4:34 AM, Viv Kendon wrote:
>> 
>> On 26 Oct 2014, at 01:13, Alexander Hansen  
>> wrote:
>> 
>>> On 10/25/14, 3:16 PM, Viv Kendon wrote:
>>>> 
>>>> On 25 Oct 2014, at 22:43, Viv Kendon  wrote:
>>>> 
>>>>>> 
>>>>> 
>>>>> On 25 Oct 2014, at 22:01, Alexander Hansen  
>>>>> wrote:
>>>>>> 
>>>>>> The if-then that you fixed was _supposed_ to copy that over for 10.9 and 
>>>>>> later.  As a workaround, maybe start a rebuild of octave364-atlas-x11, 
>>>>>> stop it after the patch phase, and manually do a
>>>>>> 
>>>>>> sudo cp 
>>>>>> /sw/src/fink.build/octave-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h 
>>>>>> /sw/include/octave-3.6.4/octave/
>>>>> 
>>>>> Many thanks, I did that, then restarted fink install bundle-octave-atlas. 
>>>>>  It went through the oct364 packages in alphabetical order, so here is 
>>>>> how it dies for java:
>>>>> 
>>>>> ans = 
>>>>> /sw/src/fink.build/java-oct364-1.2.9-3/bld/share/octave/3.6.4/packages
>>>>> mkdir (/var/tmp/oct-l9vVbi)
>>>>> untar (./java.tar, /var/tmp/oct-l9vVbi)
>>>>> 
>>>>> Error while trying to install Java package:
>>>>> JAVA_HOME environment variable does not properly point to a JDK
>>>>>  Hint:
>>>>>  JAVA_HOME should usually be set such that either:
>>>>>  (on *nix:)
>>>>>/jre/lib//client/ contains libjvm.so (file or symlink)
>>>>>  (on OSX:)
>>>>>/../Libraries/ contains a file libclient.dylib
>>>>>  (on Windows:)
>>>>>/jre/lib// contains a file jvm.cfg
>>>>>  ( depends on your system hardware, can be i386, x86_64, alpha, 
>>>>> arm, ...)
>>>>> 
>>>>>  Use forward slashes as path separator, also on Windows
>>>>> Aborting pkg install
>>>>> error: called from 'pre_install' in file 
>>>>> /private/var/tmp/oct-l9vVbi/java/pre_install.m near line 115, column 5
>>>>> error: called from:
>>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
>>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>>>>> error:   /sw/src/fink.build/java-oct364-1.2.9-3/java/octave-forge-comp at 
>>>>> line 4, column 1
>>>>> 
>>>>> I then manually verified that octcdf-nc4-oct364 now installs fine.
>>>>> 
>>>>> Will I need to manually copy libcxx-fix.h for octave382 as well?  And is 
>>>>> the file identical to the octave364 copy, or do I need to start a rebuild 
>>>>> for octave382 to get the corresponding file?
>>>>> 
>>>> 
>>>> I tried a few oct832 packages (without doing anything about libcxx-fix.h 
>>>> for octave382) and they all seem to die in the same way with a java error 
>>>> that is very different from the above:
>>>> 
>>>> mkdir -p bld/share/octave/3.8.2/packages bld/lib/octave/3.8.2/packages
>>>> `which xvfb-run` 
>>>> /sw/src/fink.build/optiminterp-atlas-oct382-0.3.4-3/optiminterp/octave-forge-comp
>>>> which xvfb-run
>>>> No Java runtime present, requesting install.
>>>> 2014-10-25 23:07:33.340 octave-cli-3.8.2[45245:d07] 
>>>> JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote
>>>> ### execution of /tmp/fink.zx8W6 failed, exit code 97
>>>> Removing runtime build-lock...
>>>> Removing build-lock package...
>>>> /sw/bin/dpkg-lockwait -r fink-buildlock-optiminterp-atlas-oct382-0.3.4-3
>>>> 
>>>> 
>>>> java -version
>>>> java version "1.7.0_51"
>>>> Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
>>>> Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
>>>> 
>>>> Package manager version: 0.38.1
>>>> Distribution version: selfupdate-rsync Sat Oct 25 22:57:26 2014, 10.9, 
>>>> x86_64
>>>> Trees: local/main stable/main
>>>> Xcode.app: 6.0.1
>>>> Xcode command-line tools: 6.0.0.0.1.1410400753
>>>> 
>>>> 
>>>> Anyway, it is end of the day here.  Happy to keep testing tomorrow, if it 
>

Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 26 Oct 2014, at 01:13, Alexander Hansen  wrote:

> On 10/25/14, 3:16 PM, Viv Kendon wrote:
>> 
>> On 25 Oct 2014, at 22:43, Viv Kendon  wrote:
>> 
>>>> 
>>> 
>>> On 25 Oct 2014, at 22:01, Alexander Hansen  
>>> wrote:
>>>> 
>>>> The if-then that you fixed was _supposed_ to copy that over for 10.9 and 
>>>> later.  As a workaround, maybe start a rebuild of octave364-atlas-x11, 
>>>> stop it after the patch phase, and manually do a
>>>> 
>>>> sudo cp 
>>>> /sw/src/fink.build/octave-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h 
>>>> /sw/include/octave-3.6.4/octave/
>>> 
>>> Many thanks, I did that, then restarted fink install bundle-octave-atlas.  
>>> It went through the oct364 packages in alphabetical order, so here is how 
>>> it dies for java:
>>> 
>>> ans = /sw/src/fink.build/java-oct364-1.2.9-3/bld/share/octave/3.6.4/packages
>>> mkdir (/var/tmp/oct-l9vVbi)
>>> untar (./java.tar, /var/tmp/oct-l9vVbi)
>>> 
>>> Error while trying to install Java package:
>>> JAVA_HOME environment variable does not properly point to a JDK
>>>  Hint:
>>>  JAVA_HOME should usually be set such that either:
>>>  (on *nix:)
>>>/jre/lib//client/ contains libjvm.so (file or symlink)
>>>  (on OSX:)
>>>/../Libraries/ contains a file libclient.dylib
>>>  (on Windows:)
>>>/jre/lib// contains a file jvm.cfg
>>>  ( depends on your system hardware, can be i386, x86_64, alpha, arm, 
>>> ...)
>>> 
>>>  Use forward slashes as path separator, also on Windows
>>> Aborting pkg install
>>> error: called from 'pre_install' in file 
>>> /private/var/tmp/oct-l9vVbi/java/pre_install.m near line 115, column 5
>>> error: called from:
>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>>> error:   /sw/src/fink.build/java-oct364-1.2.9-3/java/octave-forge-comp at 
>>> line 4, column 1
>>> 
>>> I then manually verified that octcdf-nc4-oct364 now installs fine.
>>> 
>>> Will I need to manually copy libcxx-fix.h for octave382 as well?  And is 
>>> the file identical to the octave364 copy, or do I need to start a rebuild 
>>> for octave382 to get the corresponding file?
>>> 
>> 
>> I tried a few oct832 packages (without doing anything about libcxx-fix.h for 
>> octave382) and they all seem to die in the same way with a java error that 
>> is very different from the above:
>> 
>> mkdir -p bld/share/octave/3.8.2/packages bld/lib/octave/3.8.2/packages
>> `which xvfb-run` 
>> /sw/src/fink.build/optiminterp-atlas-oct382-0.3.4-3/optiminterp/octave-forge-comp
>> which xvfb-run
>> No Java runtime present, requesting install.
>> 2014-10-25 23:07:33.340 octave-cli-3.8.2[45245:d07] JLRequestRuntimeInstall: 
>> Error calling: CFMessagePortCreateRemote
>> ### execution of /tmp/fink.zx8W6 failed, exit code 97
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-optiminterp-atlas-oct382-0.3.4-3
>> 
>> 
>> java -version
>> java version "1.7.0_51"
>> Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
>> Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
>> 
>> Package manager version: 0.38.1
>> Distribution version: selfupdate-rsync Sat Oct 25 22:57:26 2014, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 6.0.1
>> Xcode command-line tools: 6.0.0.0.1.1410400753
>> 
>> 
>> Anyway, it is end of the day here.  Happy to keep testing tomorrow, if it 
>> would be useful.
> 
> Thanks for testing!

You are welcome, happy to help.

> The libcxx-fix.h files are the same for both Octave versions.  It may well be 
> present for your octave382 build, though--more bad shell scripting in the 364 
> version from me which wasn't present in the 382 version.

I do indeed have the 382 version correctly installed by fink.  I just rebuilt 
octave364-atlas-x11 since it showed as outdated but libcxx-fix.h still did not 
get installed by fink as it should be (I moved my manually copied version aside 
before rebuilding).  And 

dpkg -S libcxx-fix.h
octave382-atlas-x11-dev: /sw/include/octave-3.8.2/octave/libcxx-fix.h

only reports the 382 version.

Let me know if I can test/try anything else.

many thanks,
— Viv



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Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 25 Oct 2014, at 22:43, Viv Kendon  wrote:

> 
> On 25 Oct 2014, at 22:01, Alexander Hansen  
> wrote:
> 
>> On 10/25/14, 1:53 PM, Viv Kendon wrote:
>>> 
>>> On 25 Oct 2014, at 21:44, Alexander Hansen  
>>> wrote:
>>> 
>>>> On 10/25/14, 1:08 PM, Viv Kendon wrote:
>>>>> 
>>>>> On 25 Oct 2014, at 20:23, Viv Kendon  wrote:
>>>>> 
>>>>>> 
>>>>>> On 25 Oct 2014, at 19:06, Alexander Hansen  
>>>>>> wrote:
>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>> 
>>>>> I added “then” myself, and now the build gets further, but the error is 
>>>>> still libcxx-fix.h related (and I’ve updated the subject line too, since 
>>>>> we are in principle on to a different package):
>>>>> 
>>>>> find . -name NOINSTALL -print# shows which toolboxes won't be 
>>>>> installed
>>>>> 
>>>>> In file included from ov-netcdf.cc:20:
>>>>> In file included from ./ov-netcdf.h:25:
>>>>> In file included from /sw/include/octave-3.6.4/octave/../octave/oct.h:33:
>>>>> In file included from /sw/include/octave-3.6.4/octave/Matrix.h:30:
>>>>> In file included from /sw/include/octave-3.6.4/octave/mx-base.h:65:
>>>>> In file included from /sw/include/octave-3.6.4/octave/boolSparse.h:29:
>>>>> In file included from /sw/include/octave-3.6.4/octave/Sparse-op-defs.h:31:
>>>>> /sw/include/octave-3.6.4/octave/mx-inlines.cc:311:10: fatal error:
>>>>>  'libcxx-fix.h' file not found
>>>>> #include "libcxx-fix.h"
>>>>> ^
>>>>> 1 error generated.
>>>>> make: *** [ov-netcdf.o] Error 1
>>>>> 'make' returned the following error: make: Entering directory 
>>>>> `/private/var/tmp/oct-5qlvpF/octcdf/src'
>>>>> /sw/bin/mkoctfile-3.6.4 -DHAVE_OCTAVE_ -v -c ov-netcdf.cc -I/sw/include 
>>>>> -I/sw/include -DHAVE_OCTAVE_INT
>>>>> oct-cxx -c -I/sw/include -fPIC -I/sw/include/octave-3.6.4/octave/.. 
>>>>> -I/sw/include/octave-3.6.4/octave -I/sw/include -I/sw/include 
>>>>> -I/sw/include/freetype2 -I/sw/include -I/sw/include -O3 -MD 
>>>>> -I/usr/X11/include -std=c++0x -I/sw/include -I/sw/include -DHAVE_OCTAVE_ 
>>>>> -DHAVE_OCTAVE_INT ov-netcdf.cc -o ov-netcdf.o
>>>>> make: Leaving directory `/private/var/tmp/oct-5qlvpF/octcdf/src'
>>>>> error: called from 'pkg>configure_make' in file 
>>>>> /sw/share/octave/3.6.4/m/pkg/pkg.m near line 1385, column 9
>>>>> error: called from:
>>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
>>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>>>>> error:   
>>>>> /sw/src/fink.build/octcdf-nc4-oct364-1.1.7-1/octcdf/octave-forge-comp at 
>>>>> line 4, column 1
>>>>> 
>>>>> many thanks,
>>>>> — Viv
>>>> 
>>>> No, almost _EVERYTHING_ needs that once it's been introduced.
>>>> 
>>>> Could you verify whether libcxx-fix is indeed present in your 
>>>> octave364-*-dev ?
>>> 
>>> I don’t think so, dpkg -S libcxx-fix returns nothing, and a “find” at the 
>>> /sw level does not return it either.  I have the following octave packages 
>>> installed:
>>> 
>>> fink list -ti oct
>>> Information about 10297 packages read in 1 seconds.
>>> i  fink-octave-scripts 0.3.2.1-1   Convenience scripts for 
>>> Octave add-ons
>>> p  liboctave364[virtual package]
>>> p  liboctave364-dev[virtual package]
>>> p  liboctave364-gcc49  [virtual package]
>>> p  liboctave364-gcc49-dev  [virtual package]
>>> p  liboctave364-newatlas   [virtual package]
>>> p  liboctave364-newatlas-dev   [virtual package]
>>> p  liboctave364-x11[virtual package]
>>> p  liboctave364-x11-dev[virtual package]
>>> p  liboctave382[virtual package]
>>> p  liboctave382-gcc49  [virtual package]
>>> p  liboctave382-newatlas   [virtual package]
>>> p  liboctave382-x11[virtual package]
>>> i  octav

Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 25 Oct 2014, at 22:01, Alexander Hansen  wrote:

> On 10/25/14, 1:53 PM, Viv Kendon wrote:
>> 
>> On 25 Oct 2014, at 21:44, Alexander Hansen  
>> wrote:
>> 
>>> On 10/25/14, 1:08 PM, Viv Kendon wrote:
>>>> 
>>>> On 25 Oct 2014, at 20:23, Viv Kendon  wrote:
>>>> 
>>>>> 
>>>>> On 25 Oct 2014, at 19:06, Alexander Hansen  
>>>>> wrote:
>>>>> 
>>>>>> 
>>>>>> 
>>>> 
>>>> I added “then” myself, and now the build gets further, but the error is 
>>>> still libcxx-fix.h related (and I’ve updated the subject line too, since 
>>>> we are in principle on to a different package):
>>>> 
>>>> find . -name NOINSTALL -print# shows which toolboxes won't be installed
>>>> 
>>>> In file included from ov-netcdf.cc:20:
>>>> In file included from ./ov-netcdf.h:25:
>>>> In file included from /sw/include/octave-3.6.4/octave/../octave/oct.h:33:
>>>> In file included from /sw/include/octave-3.6.4/octave/Matrix.h:30:
>>>> In file included from /sw/include/octave-3.6.4/octave/mx-base.h:65:
>>>> In file included from /sw/include/octave-3.6.4/octave/boolSparse.h:29:
>>>> In file included from /sw/include/octave-3.6.4/octave/Sparse-op-defs.h:31:
>>>> /sw/include/octave-3.6.4/octave/mx-inlines.cc:311:10: fatal error:
>>>>   'libcxx-fix.h' file not found
>>>> #include "libcxx-fix.h"
>>>>  ^
>>>> 1 error generated.
>>>> make: *** [ov-netcdf.o] Error 1
>>>> 'make' returned the following error: make: Entering directory 
>>>> `/private/var/tmp/oct-5qlvpF/octcdf/src'
>>>> /sw/bin/mkoctfile-3.6.4 -DHAVE_OCTAVE_ -v -c ov-netcdf.cc -I/sw/include 
>>>> -I/sw/include -DHAVE_OCTAVE_INT
>>>> oct-cxx -c -I/sw/include -fPIC -I/sw/include/octave-3.6.4/octave/.. 
>>>> -I/sw/include/octave-3.6.4/octave -I/sw/include -I/sw/include 
>>>> -I/sw/include/freetype2 -I/sw/include -I/sw/include -O3 -MD 
>>>> -I/usr/X11/include -std=c++0x -I/sw/include -I/sw/include -DHAVE_OCTAVE_ 
>>>> -DHAVE_OCTAVE_INT ov-netcdf.cc -o ov-netcdf.o
>>>> make: Leaving directory `/private/var/tmp/oct-5qlvpF/octcdf/src'
>>>> error: called from 'pkg>configure_make' in file 
>>>> /sw/share/octave/3.6.4/m/pkg/pkg.m near line 1385, column 9
>>>> error: called from:
>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
>>>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>>>> error:   
>>>> /sw/src/fink.build/octcdf-nc4-oct364-1.1.7-1/octcdf/octave-forge-comp at 
>>>> line 4, column 1
>>>> 
>>>> many thanks,
>>>> — Viv
>>> 
>>> No, almost _EVERYTHING_ needs that once it's been introduced.
>>> 
>>> Could you verify whether libcxx-fix is indeed present in your 
>>> octave364-*-dev ?
>> 
>> I don’t think so, dpkg -S libcxx-fix returns nothing, and a “find” at the 
>> /sw level does not return it either.  I have the following octave packages 
>> installed:
>> 
>> fink list -ti oct
>> Information about 10297 packages read in 1 seconds.
>>  i  fink-octave-scripts 0.3.2.1-1   Convenience scripts for 
>> Octave add-ons
>>  p  liboctave364[virtual package]
>>  p  liboctave364-dev[virtual package]
>>  p  liboctave364-gcc49  [virtual package]
>>  p  liboctave364-gcc49-dev  [virtual package]
>>  p  liboctave364-newatlas   [virtual package]
>>  p  liboctave364-newatlas-dev   [virtual package]
>>  p  liboctave364-x11[virtual package]
>>  p  liboctave364-x11-dev[virtual package]
>>  p  liboctave382[virtual package]
>>  p  liboctave382-gcc49  [virtual package]
>>  p  liboctave382-newatlas   [virtual package]
>>  p  liboctave382-x11[virtual package]
>>  i  octave-atlas-x113.8.2-3 MATLAB-like language for computations
>>  p  octave-interpreter  [virtual package]
>>  p  octave-interpreter-newatlas [virtual package]
>>  p  octave-interpreter-x11  [virtual package]
>>  i  octave364-atlas-x11 3.6.4-11MATLAB-like language for 
>> computations
>>  i  octave364-atla

Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 25 Oct 2014, at 21:44, Alexander Hansen  wrote:

> On 10/25/14, 1:08 PM, Viv Kendon wrote:
>> 
>> On 25 Oct 2014, at 20:23, Viv Kendon  wrote:
>> 
>>> 
>>> On 25 Oct 2014, at 19:06, Alexander Hansen  
>>> wrote:
>>> 
>>>> 
>>>> 
>> 
>> I added “then” myself, and now the build gets further, but the error is 
>> still libcxx-fix.h related (and I’ve updated the subject line too, since we 
>> are in principle on to a different package):
>> 
>> find . -name NOINSTALL -print# shows which toolboxes won't be installed
>> 
>> In file included from ov-netcdf.cc:20:
>> In file included from ./ov-netcdf.h:25:
>> In file included from /sw/include/octave-3.6.4/octave/../octave/oct.h:33:
>> In file included from /sw/include/octave-3.6.4/octave/Matrix.h:30:
>> In file included from /sw/include/octave-3.6.4/octave/mx-base.h:65:
>> In file included from /sw/include/octave-3.6.4/octave/boolSparse.h:29:
>> In file included from /sw/include/octave-3.6.4/octave/Sparse-op-defs.h:31:
>> /sw/include/octave-3.6.4/octave/mx-inlines.cc:311:10: fatal error:
>>   'libcxx-fix.h' file not found
>> #include "libcxx-fix.h"
>>  ^
>> 1 error generated.
>> make: *** [ov-netcdf.o] Error 1
>> 'make' returned the following error: make: Entering directory 
>> `/private/var/tmp/oct-5qlvpF/octcdf/src'
>> /sw/bin/mkoctfile-3.6.4 -DHAVE_OCTAVE_ -v -c ov-netcdf.cc -I/sw/include 
>> -I/sw/include -DHAVE_OCTAVE_INT
>> oct-cxx -c -I/sw/include -fPIC -I/sw/include/octave-3.6.4/octave/.. 
>> -I/sw/include/octave-3.6.4/octave -I/sw/include -I/sw/include 
>> -I/sw/include/freetype2 -I/sw/include -I/sw/include -O3 -MD 
>> -I/usr/X11/include -std=c++0x -I/sw/include -I/sw/include -DHAVE_OCTAVE_ 
>> -DHAVE_OCTAVE_INT ov-netcdf.cc -o ov-netcdf.o
>> make: Leaving directory `/private/var/tmp/oct-5qlvpF/octcdf/src'
>> error: called from 'pkg>configure_make' in file 
>> /sw/share/octave/3.6.4/m/pkg/pkg.m near line 1385, column 9
>> error: called from:
>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
>> error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>> error:   
>> /sw/src/fink.build/octcdf-nc4-oct364-1.1.7-1/octcdf/octave-forge-comp at 
>> line 4, column 1
>> 
>> many thanks,
>> — Viv
> 
> No, almost _EVERYTHING_ needs that once it's been introduced.
> 
> Could you verify whether libcxx-fix is indeed present in your octave364-*-dev 
> ?

I don’t think so, dpkg -S libcxx-fix returns nothing, and a “find” at the /sw 
level does not return it either.  I have the following octave packages 
installed:

fink list -ti oct 
Information about 10297 packages read in 1 seconds.
 i  fink-octave-scripts 0.3.2.1-1   Convenience scripts for Octave 
add-ons
 p  liboctave364[virtual package]
 p  liboctave364-dev[virtual package]
 p  liboctave364-gcc49  [virtual package]
 p  liboctave364-gcc49-dev  [virtual package]
 p  liboctave364-newatlas   [virtual package]
 p  liboctave364-newatlas-dev   [virtual package]
 p  liboctave364-x11[virtual package]
 p  liboctave364-x11-dev[virtual package]
 p  liboctave382[virtual package]
 p  liboctave382-gcc49  [virtual package]
 p  liboctave382-newatlas   [virtual package]
 p  liboctave382-x11[virtual package]
 i  octave-atlas-x113.8.2-3 MATLAB-like language for computations
 p  octave-interpreter  [virtual package]
 p  octave-interpreter-newatlas [virtual package]
 p  octave-interpreter-x11  [virtual package]
 i  octave364-atlas-x11 3.6.4-11MATLAB-like language for 
computations
 i  octave364-atlas-x11-dev 3.6.4-11MATLAB-like language for 
computations
 i  octave364-atlas-x11-shlibs  3.6.4-11MATLAB-like language 
for computations
 i  octave364-docs  3.6.4-1 Documentation for Octave, various formats
 p  octave364-interpreter   [virtual package]
 p  octave364-interpreter-newatlas  [virtual package]
 p  octave364-interpreter-x11   [virtual package]
 i  octave382-atlas-x11 3.8.2-3 MATLAB-like language for computations
 p  octave382-interpreter   [virtual package]
 p  octave382-interpreter-newatlas  [virtual package]
 p  octave382-interpreter-x11   [virtual package]

many thanks,
— Viv
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Re: [Fink-users] octave364 - octcdf-nc4-oct364-1.1.7-1 needs libcxx-fix.h?

[Viv Kendon]

On 25 Oct 2014, at 20:23, Viv Kendon  wrote:

> 
> On 25 Oct 2014, at 19:06, Alexander Hansen  
> wrote:
> 
>> 
>> 
>> 
>> Yeah, that's bad shell scripting from me. :-)  I just fixed that in CVS.
> 
> Still needs a “then” I think after the ;

I added “then” myself, and now the build gets further, but the error is still 
libcxx-fix.h related (and I’ve updated the subject line too, since we are in 
principle on to a different package):

find . -name NOINSTALL -print# shows which toolboxes won't be installed

In file included from ov-netcdf.cc:20:
In file included from ./ov-netcdf.h:25:
In file included from /sw/include/octave-3.6.4/octave/../octave/oct.h:33:
In file included from /sw/include/octave-3.6.4/octave/Matrix.h:30:
In file included from /sw/include/octave-3.6.4/octave/mx-base.h:65:
In file included from /sw/include/octave-3.6.4/octave/boolSparse.h:29:
In file included from /sw/include/octave-3.6.4/octave/Sparse-op-defs.h:31:
/sw/include/octave-3.6.4/octave/mx-inlines.cc:311:10: fatal error: 
  'libcxx-fix.h' file not found
#include "libcxx-fix.h"
 ^
1 error generated.
make: *** [ov-netcdf.o] Error 1
'make' returned the following error: make: Entering directory 
`/private/var/tmp/oct-5qlvpF/octcdf/src'
/sw/bin/mkoctfile-3.6.4 -DHAVE_OCTAVE_ -v -c ov-netcdf.cc -I/sw/include 
-I/sw/include -DHAVE_OCTAVE_INT 
oct-cxx -c -I/sw/include -fPIC -I/sw/include/octave-3.6.4/octave/.. 
-I/sw/include/octave-3.6.4/octave -I/sw/include -I/sw/include 
-I/sw/include/freetype2 -I/sw/include -I/sw/include -O3 -MD -I/usr/X11/include 
-std=c++0x -I/sw/include -I/sw/include -DHAVE_OCTAVE_ -DHAVE_OCTAVE_INT 
ov-netcdf.cc -o ov-netcdf.o
make: Leaving directory `/private/var/tmp/oct-5qlvpF/octcdf/src'
error: called from 'pkg>configure_make' in file 
/sw/share/octave/3.6.4/m/pkg/pkg.m near line 1385, column 9
error: called from:
error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
error:   /sw/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
error:   /sw/src/fink.build/octcdf-nc4-oct364-1.1.7-1/octcdf/octave-forge-comp 
at line 4, column 1

many thanks,
— Viv
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Re: [Fink-users] need java 1.6 for octave364?

[Viv Kendon]

On 25 Oct 2014, at 19:06, Alexander Hansen  wrote:

> On 10/25/14, 10:35 AM, Viv Kendon wrote:
>> 
> 
> 
> 
>>  # manually install libcxx-fix.h
>>  if [ -e 
>> /sw/src/fink.build/octave-atlas-x11-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h]
>>cp 
>> /sw/src/fink.build/octave-atlas-x11-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h
>>  
>> /sw/src/fink.build/root-octave-atlas-x11-3.6.4-11/sw/include/octave-3.6.4/octave/
>>  fi
>> /tmp/fink.GFvqJ: line 45: syntax error near unexpected token `fi’
>> 
>> which doesn’t look like a java issue?  This is for
>> 
>> Package manager version: 0.38.1
>> Distribution version: selfupdate-rsync Sat Oct 25 09:25:32 2014, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 6.0.1
>> Xcode command-line tools: 6.0.0.0.1.1410400753
>> Max. Fink build jobs:  18
>> 
>> and I think it died in octave-atlas-x11 but my remote window closed just as 
>> I was checking that.
>> 
>> many thanks,
>> — Viv
>> 
> 
> Yeah, that's bad shell scripting from me. :-)  I just fixed that in CVS.

Still needs a “then” I think after the ;

many thanks,
— Viv
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Re: [Fink-users] Failed: phase installing: cran-javagd-r31-0.6-1-1 failed

[Viv Kendon]

Jack,

No dice, after rebuilding r-base the error is still the same. Fink is fully up 
to date and /usr/local doesn’t exist.  I checked the freshly built R really did 
get installed:

ls -l /sw/bin/R
8 lrwxr-xr-x  1 root  admin  63 Oct 25 18:42 /sw/bin/R@ -> 
/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R 
ls -l /sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
24 -rwxr-xr-x  1 root  admin  8866 Oct 25 18:42 
/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R*

This is a case-sensitive file system, I can’t think of anything else 
non-standard I’ve done.
I don’t currently have anything else cran-* installed, just r-base,shlibs,dev.  
Can you think of anything else I could check?

many thanks,
— Viv


On 25 Oct 2014, at 17:39, Viv Kendon  wrote:

> Jack,
> 
> Hmmm, maybe I need to rebuild R, possibly it got built with an earlier java 
> installed.  I will try that after the current thing I’m building finishes…
> 
> many thanks,
> — Viv
> 
> 
> On 25 Oct 2014, at 17:08, Jack Howarth  wrote:
> 
>> Viv,
>>On reflection, the problem looks more like with R itself...
>> 
>> pushd /sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD/.. && $BIN_R 
>> --verbose CMD install 
>> --library=/sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw/lib/R/3.1/site-library
>>  JavaGD
>> /sw/src/fink.build/cran-javagd-r31-0.6-1-1 
>> /sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD
>> install: illegal option -- -
>> usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
>>   [-o owner] file1 file2
>>   install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
>>   [-o owner] file1 ... fileN directory
>>   install -d [-v] [-g group] [-m mode] [-o owner] directory ...
>> 
>> Did you 'fink self update' and 'fink update-all' first? I don't have any 
>> problems with 'fink install cran-javagd-r31' here.
>>    Jack
>> ps Of course, you also want to move /usr/local aside to make sure there 
>> isn't any third-party packages interfering with fink.
>> 
>> On Sat, Oct 25, 2014 at 11:43 AM, Viv Kendon  wrote:
>> Jack,
>> 
>> well, fink thinks it is installed:
>> 
>> i  system-java 1.7.0-1 [virtual package representing Java 1.7.0]
>> i  system-java-dev 1.7.0-1 [virtual package representing Java SDK 1.7.0]
>> i  system-java17   1.7.0-1 [virtual package representing Java 1.7.0]
>> i  system-java17-dev   1.7.0-1 [virtual package representing Java 
>> 1.7.0 development headers]
>> 
>>>> java -version
>> java version "1.7.0_51"
>> Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
>> Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
>> 
>> This is a headless machine, could I have missed some licence agreement step 
>> for it??
>> 
>> many thanks,
>> — Viv
>> 
>> 
>> On 25 Oct 2014, at 13:07, Jack Howarth  wrote:
>> 
>>> Viv,
>>> Do you have Oracle JDK installed? Depending on whether you have already 
>>> installed JRE 1.7 and 1.8, it can be download from...
>>> 
>>> http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html
>>> 
>>> or
>>> 
>>> http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
>>> 
>>> I have only tested the against JDK7 so can't say how much breakage in the 
>>> packages using java will be
>>> caused by building fink against JDK8 instead.
>>>Jack
>>> 
>>> On Sat, Oct 25, 2014 at 5:24 AM, Viv Kendon  wrote:
>>> Hope this is enough of the relevant details:
>>> 
>>> * building 'JavaGD_0.6-1.tar.gz'
>>> 
>>> /bin/rm -rf /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1
>>> /bin/mkdir -p /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw
>>> /bin/mkdir -p /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/DEBIAN
>>> /usr/sbin/chown -R fink-bld:fink-bld 
>>> /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1
>>> sudo -u fink-bld [ENV] sh -c /tmp/fink.DVqRm
>>> /tmp/fink.SkoUV
>>> #!/bin/sh -ev
>>>  BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
>>> 
>>>  mkdir -p 
>>> /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw/lib/R/3.1/site-library
>>>  pushd /sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD/.. && $BIN_R 
>>> --verbose CMD install 
>>> --library=/sw/src/fink.build/root-cran-javagd-r31-

Re: [Fink-users] need java 1.6 for octave364?

[Viv Kendon]

On 25 Oct 2014, at 17:10, Alexander Hansen  wrote:

> On 10/25/14, 8:32 AM, Alexander Hansen wrote:
> 
>> 
>> 
>> Ah right.  java-oct.info would be the only other place. :-)  It got
>> added because it finally seems to build, and the io package uses it for
>> some functions.
>> 
> 
> Oh, and Jack H. did some testing and it looked like java-oct364 really may 
> not get along with newer Javas.

I tried it anyway and “fink install bundle-octave-atlas” got as far as

 # manually install libcxx-fix.h
 if [ -e 
/sw/src/fink.build/octave-atlas-x11-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h]
   cp 
/sw/src/fink.build/octave-atlas-x11-3.6.4-11/octave-3.6.4/liboctave/libcxx-fix.h
 
/sw/src/fink.build/root-octave-atlas-x11-3.6.4-11/sw/include/octave-3.6.4/octave/
 fi
/tmp/fink.GFvqJ: line 45: syntax error near unexpected token `fi’

which doesn’t look like a java issue?  This is for 

Package manager version: 0.38.1
Distribution version: selfupdate-rsync Sat Oct 25 09:25:32 2014, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.0.1
Xcode command-line tools: 6.0.0.0.1.1410400753
Max. Fink build jobs:  18

and I think it died in octave-atlas-x11 but my remote window closed just as I 
was checking that.

many thanks,
— Viv
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Re: [Fink-users] Failed: phase installing: cran-javagd-r31-0.6-1-1 failed

[Viv Kendon]

Jack,

well, fink thinks it is installed:

 i  system-java 1.7.0-1 [virtual package representing Java 1.7.0]
 i  system-java-dev 1.7.0-1 [virtual package representing Java SDK 1.7.0]
 i  system-java17   1.7.0-1 [virtual package representing Java 1.7.0]
 i  system-java17-dev   1.7.0-1 [virtual package representing Java 
1.7.0 development headers]

 >> java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)

This is a headless machine, could I have missed some licence agreement step for 
it??

many thanks,
— Viv


On 25 Oct 2014, at 13:07, Jack Howarth  wrote:

> Viv,
>  Do you have Oracle JDK installed? Depending on whether you have already 
> installed JRE 1.7 and 1.8, it can be download from...
> 
> http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html
> 
> or
> 
> http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
> 
> I have only tested the against JDK7 so can't say how much breakage in the 
> packages using java will be 
> caused by building fink against JDK8 instead.
>     Jack
> 
> On Sat, Oct 25, 2014 at 5:24 AM, Viv Kendon  wrote:
> Hope this is enough of the relevant details:
> 
> * building 'JavaGD_0.6-1.tar.gz'
> 
> /bin/rm -rf /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1
> /bin/mkdir -p /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw
> /bin/mkdir -p /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/DEBIAN
> /usr/sbin/chown -R fink-bld:fink-bld 
> /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1
> sudo -u fink-bld [ENV] sh -c /tmp/fink.DVqRm
> /tmp/fink.SkoUV
> #!/bin/sh -ev
>   BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
> 
>   mkdir -p 
> /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw/lib/R/3.1/site-library
>   pushd /sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD/.. && $BIN_R 
> --verbose CMD install 
> --library=/sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw/lib/R/3.1/site-library
>  JavaGD
> /sw/src/fink.build/cran-javagd-r31-0.6-1-1 
> /sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD
> install: illegal option -- -
> usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
>[-o owner] file1 file2
>install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
>[-o owner] file1 ... fileN directory
>install -d [-v] [-g group] [-m mode] [-o owner] directory ...
> ### execution of /tmp/fink.SkoUV failed, exit code 64
> ### execution of /tmp/fink.DVqRm failed, exit code 64
> 
> 
> Package manager version: 0.38.1
> Distribution version: selfupdate-rsync Sat Oct 25 09:25:32 2014, 10.9, x86_64
> Trees: local/main stable/main
> Xcode.app: 6.0.1
> Xcode command-line tools: 6.0.0.0.1.1410400753
> Max. Fink build jobs:  18
> 
> Many thanks,
> — Viv
> 


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Re: [Fink-users] need java 1.6 for octave364?

[Viv Kendon]

On 25 Oct 2014, at 16:15, Alexander Hansen  wrote:

> On 10/25/14, 1:57 AM, Viv Kendon wrote:
>> 
>> On 25 Oct 2014, at 07:01, Alexander Hansen  
>> wrote:
>> 
>>> On 10/24/14, 3:01 PM, Viv Kendon wrote:
>>>> 
>>>> On 24 Oct 2014, at 00:52, Alexander Hansen  
>>>> wrote:
>>>> 
>>>>> 
>>>>> On Oct 23, 2014, at 4:42 PM, Gary K. Olson  wrote:
>>>>> 
>>>>>> When I attempt to build a number of octave364 packages, I get the 
>>>>>> following:
>>>>>> 
>>>>>> Can't resolve dependency "system-java16-dev" for package 
>>>>>> "octave-3.8.2-1" (no matching packages/versions found)
>>>>>> Exiting with failure.
>>>>>> 
>>>>>> Do I need to run java1.6 or can I change the info dependency to java1.8. 
>>>>>> If the former, than I will have to see if Apple still has an Apple 
>>>>>> approved java 1.6 that I can download. Thanks for all your help.
>>>>>> 
>>>>>> Oh, by the way, are we running an unstable tree with 10.10?  When I 
>>>>>> attempt to selfupdate fink-0.38.1 with the unstable option enabled in 
>>>>>> finkconf, fink will not update, so I assume we still only have a stable 
>>>>>> tree in 10.10.
>>>>>> 
>>>>>> Gary K. Olson
>>>>>> --
>>>>>> ___
>>>>>> Fink-users mailing list
>>>>>> Fink-users@lists.sourceforge.net
>>>>>> List archive:
>>>>>> http://news.gmane.org/gmane.os.macosx.fink.user
>>>>>> Subscription management:
>>>>>> https://lists.sourceforge.net/lists/listinfo/fink-users
>>>>> 
>>>>> Umm, you shouldn’t see be seeing anything referencing octave-3.8.2-1 for 
>>>>> octave364 packages.  If that’s indeed correct, let me know the specific 
>>>>> packages which are doing the wrong thing.
>>>>> 
>>>>> I’m not 100% sure whether Octave-3.8.2 really requires Java 1.6 or not; I 
>>>>> haven’t had time yet to confirm this on a fresh Yosemite.  There’s still 
>>>>> an Apple-approved Java 1.6 which works on Yosemite, though —  "Java for 
>>>>> OS X 2014-001” from http://support.apple.com/kb/DL1572.
>>>> 
>>>> Also having problems with octave updating here on 10.9,
>>>> Can't resolve dependency "system-java16-dev" for package
>>>> "octave-atlas-x11-3.8.2-2" (no matching packages/versions found)
>>>> because I have java 1.7 on this machine.
>>>> 
>>>> I thought I’d try replacing  java 1.6 with 1.7 in octave-3.8.2.info and 
>>>> see what happened, so I copied it to my local tree and edited, but then I 
>>>> get when trying fink install bundle-octave-atlas
>>>> 
>>>> (1) octave-atlas: MATLAB-like language for computations
>>>> (2) octave-atlas-x11: MATLAB-like language for computations
>>>> 
>>>> Pick one: [1] 2
>>>> Can't resolve dependency "dicom-oct364" for package
>>>> "bundle-octave364-atlas-20131113-1" (no matching packages/versions found)
>>>> Exiting with failure.
>>>> 
>>>> and indeed, fink list dicom shows
>>>> 
>>>>  dicom-oct343 0.1.1-7  Octave DICOM interface
>>>>  dicom-oct360 0.1.1-7  Octave DICOM interface
>>>>  dicom-oct361 0.1.1-7  Octave DICOM interface
>>>>  dicom-oct362 0.1.1-7  Octave DICOM interface
>>>>  dicom-oct363 0.1.1-7  Octave DICOM interface
>>>> 
>>>> but I can’t follow all the pattern substitution to see what is wrong 
>>>> there.  I don’t think it is trying to install anything from octave 364, I 
>>>> think it is just checking the consistency of all the interleaved octave 
>>>> info files and barfing at the first thing it doesn’t like?
>>>> 
>>>> I removed all my octave 364 packages before trying this.
>>>> 
>>>> many thanks,
>>>> — Viv
>>>> 
>>>> 
>>>> 
>>> 
>>> If it builds, I'm going to use just "system-java-dev" and "

[Fink-users] Failed: phase installing: cran-javagd-r31-0.6-1-1 failed

[Viv Kendon]

Hope this is enough of the relevant details:

* building 'JavaGD_0.6-1.tar.gz'

/bin/rm -rf /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1
/bin/mkdir -p /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw
/bin/mkdir -p /sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld 
/sw/src/fink.build/root-cran-javagd-r31-0.6-1-1
sudo -u fink-bld [ENV] sh -c /tmp/fink.DVqRm
/tmp/fink.SkoUV
#!/bin/sh -ev
  BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
  
  mkdir -p 
/sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw/lib/R/3.1/site-library
  pushd /sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD/.. && $BIN_R 
--verbose CMD install 
--library=/sw/src/fink.build/root-cran-javagd-r31-0.6-1-1/sw/lib/R/3.1/site-library
 JavaGD
/sw/src/fink.build/cran-javagd-r31-0.6-1-1 
/sw/src/fink.build/cran-javagd-r31-0.6-1-1/JavaGD
install: illegal option -- -
usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
   [-o owner] file1 file2
   install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
   [-o owner] file1 ... fileN directory
   install -d [-v] [-g group] [-m mode] [-o owner] directory ...
### execution of /tmp/fink.SkoUV failed, exit code 64
### execution of /tmp/fink.DVqRm failed, exit code 64


Package manager version: 0.38.1
Distribution version: selfupdate-rsync Sat Oct 25 09:25:32 2014, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 6.0.1
Xcode command-line tools: 6.0.0.0.1.1410400753
Max. Fink build jobs:  18

Many thanks,
— Viv
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Re: [Fink-users] need java 1.6 for octave364?

[Viv Kendon]

On 25 Oct 2014, at 07:01, Alexander Hansen  wrote:

> On 10/24/14, 3:01 PM, Viv Kendon wrote:
>> 
>> On 24 Oct 2014, at 00:52, Alexander Hansen  
>> wrote:
>> 
>>> 
>>> On Oct 23, 2014, at 4:42 PM, Gary K. Olson  wrote:
>>> 
>>>> When I attempt to build a number of octave364 packages, I get the 
>>>> following:
>>>> 
>>>> Can't resolve dependency "system-java16-dev" for package "octave-3.8.2-1" 
>>>> (no matching packages/versions found)
>>>> Exiting with failure.
>>>> 
>>>> Do I need to run java1.6 or can I change the info dependency to java1.8. 
>>>> If the former, than I will have to see if Apple still has an Apple 
>>>> approved java 1.6 that I can download. Thanks for all your help.
>>>> 
>>>> Oh, by the way, are we running an unstable tree with 10.10?  When I 
>>>> attempt to selfupdate fink-0.38.1 with the unstable option enabled in 
>>>> finkconf, fink will not update, so I assume we still only have a stable 
>>>> tree in 10.10.
>>>> 
>>>> Gary K. Olson
>>>> --
>>>> ___
>>>> Fink-users mailing list
>>>> Fink-users@lists.sourceforge.net
>>>> List archive:
>>>> http://news.gmane.org/gmane.os.macosx.fink.user
>>>> Subscription management:
>>>> https://lists.sourceforge.net/lists/listinfo/fink-users
>>> 
>>> Umm, you shouldn’t see be seeing anything referencing octave-3.8.2-1 for 
>>> octave364 packages.  If that’s indeed correct, let me know the specific 
>>> packages which are doing the wrong thing.
>>> 
>>> I’m not 100% sure whether Octave-3.8.2 really requires Java 1.6 or not; I 
>>> haven’t had time yet to confirm this on a fresh Yosemite.  There’s still an 
>>> Apple-approved Java 1.6 which works on Yosemite, though —  "Java for OS X 
>>> 2014-001” from http://support.apple.com/kb/DL1572.
>> 
>> Also having problems with octave updating here on 10.9,
>> Can't resolve dependency "system-java16-dev" for package
>> "octave-atlas-x11-3.8.2-2" (no matching packages/versions found)
>> because I have java 1.7 on this machine.
>> 
>> I thought I’d try replacing  java 1.6 with 1.7 in octave-3.8.2.info and see 
>> what happened, so I copied it to my local tree and edited, but then I get 
>> when trying fink install bundle-octave-atlas
>> 
>> (1) octave-atlas: MATLAB-like language for computations
>> (2) octave-atlas-x11: MATLAB-like language for computations
>> 
>> Pick one: [1] 2
>> Can't resolve dependency "dicom-oct364" for package
>> "bundle-octave364-atlas-20131113-1" (no matching packages/versions found)
>> Exiting with failure.
>> 
>> and indeed, fink list dicom shows
>> 
>>  dicom-oct343 0.1.1-7  Octave DICOM interface
>>  dicom-oct360 0.1.1-7  Octave DICOM interface
>>  dicom-oct361 0.1.1-7  Octave DICOM interface
>>  dicom-oct362 0.1.1-7  Octave DICOM interface
>>  dicom-oct363 0.1.1-7  Octave DICOM interface
>> 
>> but I can’t follow all the pattern substitution to see what is wrong there.  
>> I don’t think it is trying to install anything from octave 364, I think it 
>> is just checking the consistency of all the interleaved octave info files 
>> and barfing at the first thing it doesn’t like?
>> 
>> I removed all my octave 364 packages before trying this.
>> 
>> many thanks,
>> — Viv
>> 
>> 
>> 
> 
> If it builds, I'm going to use just "system-java-dev" and "system-java", 
> since we've got a hideous mix of Apple Java 1.6, Oracle Java 1.7 and Oracle 
> Java 1.8.
> 
> There wasn't any need to remove the other packages.  What's going on is:
> 
> 1)  I accidentally replaced 3.6.4 with 3.8.2 rather than appending 3.8.2 to 
> the supported Octave versions for the dicom package, and
> 
> 2)  I forgot to add blocking out 343-363 for 10.9.
> 
> I just put an updated version in CVS to fix this.
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/

Cool, thanks, I just selfupdated and see the revised info file that fixes this. 
 But I now realise that bundle-octave installs 364 not 382 and there is no 
“bundle” for 382.  I am happy to test on 10.9 with java 1.7, but I cannot 
figure out what to change in local copies of the octave info files to get the 
java 1.6 dependency to go away.  So far I copied only octave-3.8.2.info (and 
three patch files), but editing that by itself clearly isn’t enough.

many thanks,
— Viv


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Re: [Fink-users] need java 1.6 for octave364?

[Viv Kendon]

On 24 Oct 2014, at 00:52, Alexander Hansen  wrote:

> 
> On Oct 23, 2014, at 4:42 PM, Gary K. Olson  wrote:
> 
>> When I attempt to build a number of octave364 packages, I get the following:
>> 
>> Can't resolve dependency "system-java16-dev" for package "octave-3.8.2-1" 
>> (no matching packages/versions found)
>> Exiting with failure.
>> 
>> Do I need to run java1.6 or can I change the info dependency to java1.8. If 
>> the former, than I will have to see if Apple still has an Apple approved 
>> java 1.6 that I can download. Thanks for all your help.
>> 
>> Oh, by the way, are we running an unstable tree with 10.10?  When I attempt 
>> to selfupdate fink-0.38.1 with the unstable option enabled in finkconf, fink 
>> will not update, so I assume we still only have a stable tree in 10.10.
>> 
>> Gary K. Olson
>> --
>> ___
>> Fink-users mailing list
>> Fink-users@lists.sourceforge.net
>> List archive:
>> http://news.gmane.org/gmane.os.macosx.fink.user
>> Subscription management:
>> https://lists.sourceforge.net/lists/listinfo/fink-users
> 
> Umm, you shouldn’t see be seeing anything referencing octave-3.8.2-1 for 
> octave364 packages.  If that’s indeed correct, let me know the specific 
> packages which are doing the wrong thing.
> 
> I’m not 100% sure whether Octave-3.8.2 really requires Java 1.6 or not; I 
> haven’t had time yet to confirm this on a fresh Yosemite.  There’s still an 
> Apple-approved Java 1.6 which works on Yosemite, though —  "Java for OS X 
> 2014-001” from http://support.apple.com/kb/DL1572.  

Also having problems with octave updating here on 10.9, 
Can't resolve dependency "system-java16-dev" for package
"octave-atlas-x11-3.8.2-2" (no matching packages/versions found)
because I have java 1.7 on this machine.

I thought I’d try replacing  java 1.6 with 1.7 in octave-3.8.2.info and see 
what happened, so I copied it to my local tree and edited, but then I get when 
trying fink install bundle-octave-atlas

(1) octave-atlas: MATLAB-like language for computations
(2) octave-atlas-x11: MATLAB-like language for computations

Pick one: [1] 2
Can't resolve dependency "dicom-oct364" for package
"bundle-octave364-atlas-20131113-1" (no matching packages/versions found)
Exiting with failure.

and indeed, fink list dicom shows

 dicom-oct343 0.1.1-7  Octave DICOM interface
 dicom-oct360 0.1.1-7  Octave DICOM interface
 dicom-oct361 0.1.1-7  Octave DICOM interface
 dicom-oct362 0.1.1-7  Octave DICOM interface
 dicom-oct363 0.1.1-7  Octave DICOM interface

but I can’t follow all the pattern substitution to see what is wrong there.  I 
don’t think it is trying to install anything from octave 364, I think it is 
just checking the consistency of all the interleaved octave info files and 
barfing at the first thing it doesn’t like?

I removed all my octave 364 packages before trying this.

many thanks,
— Viv




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[Fink-users] compiling: re-alpine-2.02-4 failed

[Viv Kendon]

So I have alpine-alpha working nicely, but it seems I need this patch

http://sourceforge.net/p/re-alpine/bugs/16/

for my local smtp server because I get this error:

warning: Server bug: non-empty initial GSSAPI challenge

with fink’s current alpine-alpha.  Trying to compile re-alpine to see whether 
it contains the patch fails with

libtool: compile:  gcc -DHAVE_CONFIG_H -I../../../include -I../../../include 
-I/sw/include -I/sw/include -g -D_THREAD_SAFE -Dbsd -g -O2 -MT wpcomm.lo -MD 
-MP -MF .deps/wpcomm.Tpo -c wpcomm.c -o wpcomm.o >/dev/null 2>&1
mv -f .deps/wpcomm.Tpo .deps/wpcomm.Plo
/bin/sh ../../../libtool --tag=CC   --mode=link gcc -g -D_THREAD_SAFE  -Dbsd -g 
-O2 -rpath 
'/sw/src/fink.build/re-alpine-2.02-4/re-alpine-2.02/web/src/alpined.d/../../lib'
 -version-info 1:0:0 -lintl -L/sw/lib -L/sw/lib -o libwpcomm.la -rpath 
/sw/src/fink.build/re-alpine-2.02-4/re-alpine-2.02/web/src/alpined.d/../../lib 
wpcomm.lo  -ltcl -lgssapi_krb5 -lssl -lldap  -lncurses -llber -lssl -framework 
Carbon -framework ApplicationServices -framework Security
libtool: link: gcc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o 
.libs/libwpcomm.1.dylib  .libs/wpcomm.o   /sw/lib/libintl.dylib -L/sw/lib -ltcl 
-lgssapi_krb5 /sw/lib/libldap.dylib -lncurses /sw/lib/liblber.dylib -lssl 
-framework Carbon -framework ApplicationServices -framework Security
-framework Carbon -framework ApplicationServices -framework Security 
-install_name  
/sw/src/fink.build/re-alpine-2.02-4/re-alpine-2.02/web/src/alpined.d/../../lib/libwpcomm.1.dylib
 -compatibility_version 2 -current_version 2.0 -Wl,-single_module
libtool: link: dsymutil .libs/libwpcomm.1.dylib || :
libtool: link: (cd ".libs" && rm -f "libwpcomm.dylib" && ln -s 
"libwpcomm.1.dylib" "libwpcomm.dylib")
libtool: link: /usr/bin/ar cru .libs/libwpcomm.a  wpcomm.o
libtool: link: ranlib .libs/libwpcomm.a
libtool: link: ( cd ".libs" && rm -f "libwpcomm.la" && ln -s "../libwpcomm.la" 
"libwpcomm.la" )
gcc -DHAVE_CONFIG_H   -I../../../include -I../../../include -I/sw/include 
-I/sw/include -g -D_THREAD_SAFE  -Dbsd -g -O2 -MT alpined.o -MD -MP -MF 
.deps/alpined.Tpo -c -o alpined.o alpined.c
alpined.c:763:50: error: no member named 'result' in 'struct Tcl_Interp'
  ...case TCL_OK  : peReturn(cs, "OK", interp->result); break;
  ~~  ^
alpined.c:764:55: error: no member named 'result' in 'struct Tcl_Interp'
  ...case TCL_ERROR  : peReturn(cs, "ERROR", interp->result); break;
 ~~  ^
alpined.c:765:55: error: no member named 'result' in 'struct Tcl_Interp'
  ...case TCL_BREAK  : peReturn(cs, "BREAK", interp->result); break;
 ~~  ^
alpined.c:766:56: error: no member named 'result' in 'struct Tcl_Interp'
  ...case TCL_RETURN : peReturn(cs, "RETURN", interp->result); break;
  ~~  ^
alpined.c:7699:49: warning: passing 'imapuid_t *' (aka 'unsigned long *') to
  parameter of type 'long *' converts between pointers to integer types with
  different sign [-Wpointer-sign]
else if(Tcl_GetLongFromObj(interp, objv[1], &uid) != TCL_OK){
^~~~
/sw/include/tclDecls.h:160:28: note: passing argument to parameter 'longPtr'
  here
Tcl_Obj *objPtr, long *longPtr);
   ^
alpined.c:7863:49: warning: passing 'imapuid_t *' (aka 'unsigned long *') to
  parameter of type 'long *' converts between pointers to integer types with
  different sign [-Wpointer-sign]
else if(Tcl_GetLongFromObj(interp, objv[1], &uid) != TCL_OK){
^~~~
/sw/include/tclDecls.h:160:28: note: passing argument to parameter 'longPtr'
  here
Tcl_Obj *objPtr, long *longPtr);
   ^
alpined.c:9636:7: warning: format specifies type 'int' but the argument has type
  'unsigned long' [-Wformat]
strlen(prefix), prefix,
^~
/usr/include/secure/_stdio.h:57:62: note: expanded from macro 'snprintf'
  __builtin___snprintf_chk (str, len, 0, __darwin_obsz(str), __VA_ARGS__)
 ^
alpined.c:10818:10: warning: using the result of an assignment as a condition
  without parentheses [-Wparentheses]
if(s = peAuthException())
   ~~^~~
alpined.c:10818:10: note: place parentheses around the assignment to silence
  this warning
if(s = peAuthException())
 ^
   ()
alpined.c:10818:10: note: use '==' to turn this assignment into an equality
  comparison
if(s = peAuthException())
 ^
 ==
alpined.c:10847:45: warning: cast to 'void *' from smaller integer type 'int'
  [-Wint-to-void-pointer-cast

[Fink-users] py27-0.2.7-1 has a case sensitive build problem

[Viv Kendon]

[maintainer CC'd]

env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner 
--no-same-permissions -xvf /sw/src/pyaudio-0.2.7.tar.gz
PyAudio-0.2.7/
PyAudio-0.2.7/CHANGELOG
PyAudio-0.2.7/docs/
PyAudio-0.2.7/docs/.buildinfo
PyAudio-0.2.7/docs/.doctrees/

PyAudio-0.2.7/test/wire_full.py
PyAudio-0.2.7/test/wire_half.py
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-pyaudio-py27-0.2.7-1
(Reading database ... 296605 files and directories currently 
installed.)
Removing fink-buildlock-pyaudio-py27-0.2.7-1 ...
Failed: directory 
/sw/src/fink.build/pyaudio-py27-0.2.7-1/pyaudio-0.2.7 
doesn't exist, check the package description

Needs a case-sensitive file system fix.  Same on both 10.7 
and 10.9, have not tried 10.4

many thanks,
-- Viv
________
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tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] libsndfile1-1.0.25-3 failed on 10.7

[Viv Kendon]

On Fri, 24 Jan 2014, Daniel Johnson wrote:

>
> On Jan 24, 2014, at 5:00 PM, Viv Kendon  wrote:
>
>> Just got the following doing "update-all" (not sure I've gone far enough 
>> back, can supply more if needed)
>>
>> 

>>  _vorbis_read_sample in ogg_vorbis.o
>>  "_vorbis_version_string", referenced from:
>>  _ogg_vorbis_open in ogg_vorbis.o
>> ld: symbol(s) not found for architecture x86_64
>> clang: error: linker command failed with exit code 1 (use -v to see 
>> invocation)
>> make[2]: *** [libsndfile.la] Error 1
>>
>> Package manager version: 0.36.3.1
>> Distribution version: selfupdate-rsync Fri Jan 24 19:37:40 2014, 10.7, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 4.6.1
>> Xcode command-line tools: 4.6.0.0.1.1362189000
>> Max. Fink build jobs:  4
>>
>> Not urgent, not sure what I have installed that needs it...
>
> This was caused by a recent change in the libvorbis package. I've now patched 
> libsndfile1 to build with it.
>
> Daniel

Great, now builds fine for me.
many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] libzbar-py27 0.10-2 segfault

[Viv Kendon]

I just had reason to install and try to use libzbar, and it 
causes a segfault when I try to import it:

/sw/bin/python2.7
Python 2.7.6 (default, Nov 17 2013, 01:54:12)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.27)] on 
darwin
Type "help", "copyright", "credits" or "license" for more 
information.
>>> import zbar
Segmentation fault: 11

I think this might be related to the crash I was getting 
with spyder on 10.9, but have not yet tested that (as I'm on 
a 10.7 machine and the moment).

Any suggestions for debugging or fixing this greatly 
appreciated!  Am I simply doing the wrong thing and there 
isn't a python module to import?  I was trying to use it 
with this 
http://code.google.com/p/qtqr/source/browse/qrtools.py
which does try to do import zbar

many thanks,
-- Viv
____
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tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] spyder-x11-py27 segfault on 10.9

[Viv Kendon]

I'm back.  Will start a new thread since what I've found 
isn't spyder or 10.9 specific, but wanted to link this 
thread to it: look for a new thread on libzbar-py27 0.10-2

-- Viv

On Fri, 27 Dec 2013, Viv Kendon wrote:

> OK, I came back to debugging this and removed all -py27
> packages except libxml2-py27 on which other packages depend.
> Then I reinstalled spyder-x11-py27 with only the packages it
> needs.  It now works.  So there is some other -py27 package
> that is causing the segfault.  When I get a chance, I will
> install one by one and test as I go until I find it, and
> report back.  But it may be a while before I can do this...
>
> -- Viv
>
> On Fri, 20 Dec 2013, Viv Kendon wrote:
>
>> when I start spyder from an xterm prompt, I get the
>> following in the xterm:
>>
>> /sw/lib/python2.7/site-packages/IPython/frontend.py:30:
>> UserWarning: The top-level `frontend` package has been
>> deprecated. All its subpackages have been moved to the top
>> `IPython` level.
>>   warn("The top-level `frontend` package has been
>> deprecated. "
>> /sw/bin/spyder-x11-py27: line 3:  3966 Segmentation fault:
>> 11  /sw/bin/spyder-x11-py27.py
>>
>> I see the splash screen start up and load some stuff before
>> it dies.
>>
>> This is a fresh fink on 10.9 case sensitive file system.
>> I tried rebuilding ipython and spyder, but to no avail.  Is
>> there anything else I can do to help debug this?
>>
>> many thanks,
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>>
>>
>>
>> --
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>
>
> 
> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
> tel: +44 113 343 4864  Physics and Astronomy
> Quantum Information GroupUniversity of Leeds
>
> I am working to contract as part of UCU's action short of a strike from
> 1st November in support of fair pay in HE.  It may take longer than usual
> for me to respond to your message.
>  For more info see http://www.ucu.org.uk/hepay13
>  To join the union and the action http://www.ucu.org.uk/join
>
>
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[Fink-users] libsndfile1-1.0.25-3 failed on 10.7

[Viv Kendon]

_vorbis.o
   _vorbis_close in ogg_vorbis.o
   "_vorbis_comment_init", referenced from:
   _ogg_vorbis_open in ogg_vorbis.o
   _vorbis_read_header in ogg_vorbis.o
   _vorbis_write_header in ogg_vorbis.o
   "_vorbis_comment_query", referenced from:
   _vorbis_read_header in ogg_vorbis.o
   "_vorbis_dsp_clear", referenced from:
   _vorbis_read_header in ogg_vorbis.o
   _vorbis_close in ogg_vorbis.o
   "_vorbis_info_clear", referenced from:
   _ogg_vorbis_open in ogg_vorbis.o
   _vorbis_read_header in ogg_vorbis.o
   _vorbis_close in ogg_vorbis.o
   "_vorbis_info_init", referenced from:
   _ogg_vorbis_open in ogg_vorbis.o
   _vorbis_read_header in ogg_vorbis.o
   _vorbis_write_header in ogg_vorbis.o
   "_vorbis_synthesis", referenced from:
   _vorbis_read_sample in ogg_vorbis.o
   "_vorbis_synthesis_blockin", referenced from:
   _vorbis_read_sample in ogg_vorbis.o
   "_vorbis_synthesis_headerin", referenced from:
   _ogg_vorbis_open in ogg_vorbis.o
   _vorbis_read_header in ogg_vorbis.o
   "_vorbis_synthesis_init", referenced from:
   _vorbis_read_header in ogg_vorbis.o
   "_vorbis_synthesis_pcmout", referenced from:
   _vorbis_read_sample in ogg_vorbis.o
   "_vorbis_synthesis_read", referenced from:
   _vorbis_read_sample in ogg_vorbis.o
   "_vorbis_version_string", referenced from:
   _ogg_vorbis_open in ogg_vorbis.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v 
to see invocation)
make[2]: *** [libsndfile.la] Error 1

Package manager version: 0.36.3.1
Distribution version: selfupdate-rsync Fri Jan 24 19:37:40 
2014, 10.7, x86_64
Trees: local/main stable/main
Xcode.app: 4.6.1
Xcode command-line tools: 4.6.0.0.1.1362189000
Max. Fink build jobs:  4

Not urgent, not sure what I have installed that needs it...

TIA
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] Using the bindist

[Viv Kendon]

On Wed, 27 Nov 2013, Martin Costabel wrote:

> On 26/11/13 23:08, Viv Kendon wrote:
> []
>> Having been running my own private bindists to save
>> compiling the same thing for several similar macs, I
>> discovered this some years ago[*], some of the bindist code
>> has been disabled or removed from fink when there was no
>> official bindist.  I was advised then to use sudo apt-get
>> update followed by sudo apt-get dist-upgrade after setting
>> the correct lines in /sw/etc/apt/sources.list
>>
>> This works, but has the undesirable effect of not updating
>> the package descriptions, only the lists of available debs.
>> So I do run fink selfupdate after doing the apt-get
>> commands.
>>
>> It would be nice to have the bindist functionality restored,
>> but it does work OK with apt-get.
> []
>>> From: Viv Kendon 
>> To: Fink Users Mailing List
>> 
>> Date: Tue, 15 Dec 2009 15:26:56 + (GMT)
>> Subject: [Fink-users] using own binary dist with 10.6
>
> I see. You should get some medal for staying with Fink despite years of
> suffering :-)
>
> Apparently this has been broken since the first x86_64 distribution.
> Over on the fink-devel list, thesin has now found the explanation:
>
>> the issue was that apt was converting _ into %5f in the debarch
>> darwin-x86_64 = darwin-x86%5f64 in the deb file name.  So fink could
>> never find it and thus thought it wasn't present.
>
> He fixed it in Fink/PkgVersion.pm. The next fink release should bring
> the fix to everybody.

And I have now set up a bindist for 10.9 and tested it using 
fink -b with UseBinaryDist set to true and added lines in 
/sw/etc/apt/sources.list, and it works -- many thanks for 
finally fixing this!

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] spyder-x11-py27 segfault on 10.9

[Viv Kendon]

OK, I came back to debugging this and removed all -py27 
packages except libxml2-py27 on which other packages depend. 
Then I reinstalled spyder-x11-py27 with only the packages it 
needs.  It now works.  So there is some other -py27 package 
that is causing the segfault.  When I get a chance, I will 
install one by one and test as I go until I find it, and 
report back.  But it may be a while before I can do this...

-- Viv

On Fri, 20 Dec 2013, Viv Kendon wrote:

> when I start spyder from an xterm prompt, I get the
> following in the xterm:
>
> /sw/lib/python2.7/site-packages/IPython/frontend.py:30:
> UserWarning: The top-level `frontend` package has been
> deprecated. All its subpackages have been moved to the top
> `IPython` level.
>   warn("The top-level `frontend` package has been
> deprecated. "
> /sw/bin/spyder-x11-py27: line 3:  3966 Segmentation fault:
> 11  /sw/bin/spyder-x11-py27.py
>
> I see the splash screen start up and load some stuff before
> it dies.
>
> This is a fresh fink on 10.9 case sensitive file system.
> I tried rebuilding ipython and spyder, but to no avail.  Is
> there anything else I can do to help debug this?
>
> many thanks,
> -- Viv
> 
> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
> tel: +44 113 343 4864  Physics and Astronomy
> Quantum Information GroupUniversity of Leeds
>
>
>
> --
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
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[Fink-users] spyder-x11-py27 segfault on 10.9

[Viv Kendon]

when I start spyder from an xterm prompt, I get the 
following in the xterm:

/sw/lib/python2.7/site-packages/IPython/frontend.py:30: 
UserWarning: The top-level `frontend` package has been 
deprecated. All its subpackages have been moved to the top 
`IPython` level.
   warn("The top-level `frontend` package has been 
deprecated. "
/sw/bin/spyder-x11-py27: line 3:  3966 Segmentation fault: 
11  /sw/bin/spyder-x11-py27.py

I see the splash screen start up and load some stuff before 
it dies.

This is a fresh fink on 10.9 case sensitive file system.
I tried rebuilding ipython and spyder, but to no avail.  Is 
there anything else I can do to help debug this?

many thanks,
-- Viv
________
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tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds



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Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9

[Viv Kendon]

On Wed, 18 Dec 2013, Hanspeter Niederstrasser wrote:

>
>> "Between 2.6.0-2 and 2.6.0-3 it was necessary to change
>> one of the dependancies of this package from labl to
>> lablgl-x11."
>> 
>> I don't know how to format an alternative Depends entry, but
>> I think it should be OK for lablgtk2 to depend on either
>> lablgl or labgl-x11.
>
> Alternative Depends use the following format:
>
> Depends: lablgl-x11 | lablgl
>
> The order is important in that Fink will ask you which one you wish to 
> install (assuming neither is currently installed already) in the order listed 
> in the .info, and since most people will just choose 1 (the default), it is 
> wise to put the more useful alternative (according to the maintainer) first 
> in the list (but it is not a requirement).  The .deb encodes both 
> alternatives into its control file, and once a pkg with this list is 
> installed, it should be possible to switch back and forth between the two 
> alternates without the Dependee pkg (lablgtk2 in this case) complaining.
>
> Hanspeter
>

Great, many thank, that will help me to test more 
effectively in future.  I have added this to my local copies 
of the info files.

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9

[Viv Kendon]

On Tue, 17 Dec 2013, Hanspeter Niederstrasser wrote:

> On 12/17/2013 3:21 AM, Viv Kendon wrote:
>> On Mon, 16 Dec 2013, Hanspeter Niederstrasser wrote:
>> 
>>> On 12/16/2013 4:55 PM, Viv Kendon wrote:
>>>> Apologies if this has already been reported.  Doesn't seem
>>>> to be a maintainer to Cc, not Cc'ing fink-devel as I'm not
>>>> subscribed.
>>>> 
>>>> cd Togl && make togl.o CC="ocamlc.opt -verbose" CFLAGS='-c
>>>> -ccopt "-c -O -I../../src -ITogl -I/sw/include -I.
>>>> -I/usr/X11R6/include "'
>>>> make[2]: Entering directory
>>>> `/sw/src/fink.build/lablgl-x11-1.04-1/lablGL-1.04/Togl/src/Togl'
>>>> ocamlc.opt -verbose -c -ccopt "-c -O -I../../src -ITogl
>>>> -I/sw/include -I.  -I/usr/X11R6/include " togl.c
>>>> + gcc -fno-defer-pop -Wall -D_FILE_OFFSET_BITS=64
>>>> -D_REENTRANT  -c -c -O -I../../src -ITogl -I/sw/include -I.
>>>> -I/usr/X11R6/include   -I'/sw/lib/ocaml' 'togl.c'
>>>> clang: warning: argument unused during compilation:
>>>> '-fno-defer-pop'
>>>> togl.c:162:2: error: "Sorry, you will have to edit togl.c to
>>>> include the right
>>>>  tkInt.h file"
>>>> #error "Sorry, you will have to edit togl.c to include the
>>>> right tkInt.h file"
>>>> ^
>>> 
>>> Can you try the attached lablgl.info for both lablgl and lablgl-x11 ? It
>>> bumps to the latest 1.05 (our current 1.04 version is from 2008). 
>>> Hopefully
>>> it knows how to deal with the tk used on 10.9.
>>> 
>>> Hanspeter
>>> 
>> 
>> case sensitive file system typo:
>> 
>> lablgl-1.05/LablGlut/examples/caml-images/ppm.ppm
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-lablgl-1.05-1
>> (Reading database ... 274908 files and directories currently
>> installed.)
>> Removing fink-buildlock-lablgl-1.05-1 ...
>> Failed: directory
>> /sw/src/fink.build/lablgl-1.05-1/lablGL-1.05 doesn't exist,
>> check the package description
>> 
>> fixed that, but then I need the patch file:
>> 
>> lablgl-1.05/LablGlut/examples/caml-images/ppm.ppm
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-lablgl-1.05-1
>> (Reading database ... 274908 files and directories currently
>> installed.)
>> Removing fink-buildlock-lablgl-1.05-1 ...
>> Failed: Cannot read PatchFile
>> "/sw/fink/dists/local/main/finkinfo/lablgl.patch"
>> 
>> copied that out of the stable tree and lablgl compiles on
>> 10.9
>> 
>> then tried lablgl-x11 and it also compiles (with the same
>> info file mods and patch) but I then get:
>> 
>> While trying to install:
>> lablgl-x11-1.05-1
>> 
>> The following inconsistencies found:
>> Unsatisfied dependency in lablgtk2: lablgl
>> 
>> so either I need to specify both will do in lablglgtk2.info,
>> or lablgl-x11 needs to provide lablgl as well as lablgl-togl
>> and I'm not sure how to fix that in the info files...
>
> Thanks for testing lablgl-x11 on 10.9.  I've now checked in an update to CVS 
> with the case-sensitivity fix.  The lablgtk2 deadlock with lablgl-x11 and 
> lablgl is unavoidable given that lablgtk2 Depends: on one variant and they 
> conflict with each other.  I'm also not sure what can be done with Provides 
> to solve the lock.  If lablglgtk2 will behave the same with either lablgl-x11 
> and lablgl, then an alternative Depends: in lablglgtk2.info should work.
>
> If you do continue with updating unison in the 10.6 tree, please test and 
> copy the new lablgl-1.05 info file from the 10.7 tree as well (the patch is 
> unchanged).  I no longer seem to have access to my 10.6 machine to test 
> there.
>
> Hanspeter
>

I just tested your new lablgl-x11 on 10.6 (with my locally 
installed ocaml 4.01.0-1) and it compiles fine, and the 
previously compiled unison still works (actually, I can't 
test the gui remotely so that isn't a good test).  lablgl 
also compiles fine.  So it seems this should be good to go 
for 10.6 too.

Right now, I have lablgl installed on 10.9 and lablgl-x11 on 
10.6, and unison works OK on both.  In particular, the x11 
gui for unison is fine on 10.9 with lablgl.  But of course 
that may not hold for everything that need labglgtk2.  The 
package description in lablgtk2 suggests it 

[Fink-users] unison 2.45.4 in fink - updating ocaml on 10.6

[Viv Kendon]

[subject line changed]

On Tue, 17 Dec 2013, Viv Kendon wrote:

> On Mon, 16 Dec 2013, Alexander Hansen wrote:
>
>> Thanks!  I'll make getting Unison back into Fink a priority.
>
> That would be great.  I'm happy to help and test.
>
> A warning: I'm having some sort of archive compatibility
> issue testing with my 10.6 server and this newly built
> unison.  I'll head over to the unison list to try to resolve
> it, but since unison is working on local archives, the
> changes to the build I've just made could be to blame
> somehow.  Most likely it is different versions of ocaml, it
> is 4.01.0-1 on 10.9 but only 3.12.1-1 on 10.6...tomorrow
> I'll try to test between 10.9 and 10.7 and see if I can sort
> it out.
>
> -- Viv

This was indeed ocaml version problems and fairly easy to 
fix.  I copied the 10.7 ocaml.{info,patch} files to my local 
10.4 tree on my 10.6 system.  The info file already listed 
10.6, and indeed it built fine.  I then rebuilt lablgl-x11 
and lablgtk2 and unison in that order.  And now unison works 
between my 10.9 and 10.6 systems.

So I guess the newer ocaml just needs to propagate to the 
10.4 tree, and everything that build-depends on it needs to 
be told to depend on the new version and revision bumped to 
force a rebuild?  I don't know how many other packages need 
ocaml though, perhaps they don't all play nicely with the 
new version in the 10.4 tree.  I can test things on 10.6 if 
that will help.

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds



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Re: [Fink-users] Failed: phase compiling: parallel-oct364-2.0.5-6 failed

[Viv Kendon]

On Sun, 15 Dec 2013, Dominique Dhumieres wrote:

>> Now added to the distribution.
>
> This has still not propagated to me!-(
>
> Dominique
>

just saw parallel-oct.info come through, but then got:

Scanning package description files..WARNING: End of file 
reached during here-document in 
"/sw/fink/dists/stable/main/finkinfo/sci/parallel-oct.info".

on 10.6 -- a typo of some sort?

-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9

[Viv Kendon]

On Mon, 16 Dec 2013, Hanspeter Niederstrasser wrote:

> On 12/16/2013 4:55 PM, Viv Kendon wrote:
>> Apologies if this has already been reported.  Doesn't seem
>> to be a maintainer to Cc, not Cc'ing fink-devel as I'm not
>> subscribed.
>> 
>> cd Togl && make togl.o CC="ocamlc.opt -verbose" CFLAGS='-c
>> -ccopt "-c -O -I../../src -ITogl -I/sw/include -I.
>> -I/usr/X11R6/include "'
>> make[2]: Entering directory
>> `/sw/src/fink.build/lablgl-x11-1.04-1/lablGL-1.04/Togl/src/Togl'
>> ocamlc.opt -verbose -c -ccopt "-c -O -I../../src -ITogl
>> -I/sw/include -I.  -I/usr/X11R6/include " togl.c
>> + gcc -fno-defer-pop -Wall -D_FILE_OFFSET_BITS=64
>> -D_REENTRANT  -c -c -O -I../../src -ITogl -I/sw/include -I.
>> -I/usr/X11R6/include   -I'/sw/lib/ocaml' 'togl.c'
>> clang: warning: argument unused during compilation:
>> '-fno-defer-pop'
>> togl.c:162:2: error: "Sorry, you will have to edit togl.c to
>> include the right
>> tkInt.h file"
>> #error "Sorry, you will have to edit togl.c to include the
>> right tkInt.h file"
>>^
>
> Can you try the attached lablgl.info for both lablgl and lablgl-x11 ? It 
> bumps to the latest 1.05 (our current 1.04 version is from 2008). Hopefully 
> it knows how to deal with the tk used on 10.9.
>
> Hanspeter
>

case sensitive file system typo:

lablgl-1.05/LablGlut/examples/caml-images/ppm.ppm
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-lablgl-1.05-1
(Reading database ... 274908 files and directories currently 
installed.)
Removing fink-buildlock-lablgl-1.05-1 ...
Failed: directory 
/sw/src/fink.build/lablgl-1.05-1/lablGL-1.05 doesn't exist, 
check the package description

fixed that, but then I need the patch file:

lablgl-1.05/LablGlut/examples/caml-images/ppm.ppm
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-lablgl-1.05-1
(Reading database ... 274908 files and directories currently 
installed.)
Removing fink-buildlock-lablgl-1.05-1 ...
Failed: Cannot read PatchFile 
"/sw/fink/dists/local/main/finkinfo/lablgl.patch"

copied that out of the stable tree and lablgl compiles on 
10.9

then tried lablgl-x11 and it also compiles (with the same 
info file mods and patch) but I then get:

While trying to install:
   lablgl-x11-1.05-1

The following inconsistencies found:
   Unsatisfied dependency in lablgtk2: lablgl

so either I need to specify both will do in lablglgtk2.info, 
or lablgl-x11 needs to provide lablgl as well as lablgl-togl 
and I'm not sure how to fix that in the info files...

But so far so good!  Many thanks
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9

[Viv Kendon]

On Mon, 16 Dec 2013, Alexander Hansen wrote:

> On 12/16/13 3:47 PM, Viv Kendon wrote:
>> On Mon, 16 Dec 2013, Hanspeter Niederstrasser wrote:
>> 
>>> On 12/16/2013 4:55 PM, Viv Kendon wrote:
>>>> Apologies if this has already been reported.  Doesn't seem
>>>> to be a maintainer to Cc, not Cc'ing fink-devel as I'm not
>>>> subscribed.
>>>> 
>>>> cd Togl && make togl.o CC="ocamlc.opt -verbose" CFLAGS='-c
>>>> -ccopt "-c -O -I../../src -ITogl -I/sw/include -I.
>>>> -I/usr/X11R6/include "'
>>>> make[2]: Entering directory
>>>> `/sw/src/fink.build/lablgl-x11-1.04-1/lablGL-1.04/Togl/src/Togl'
>>>> ocamlc.opt -verbose -c -ccopt "-c -O -I../../src -ITogl
>>>> -I/sw/include -I.  -I/usr/X11R6/include " togl.c
>>>> + gcc -fno-defer-pop -Wall -D_FILE_OFFSET_BITS=64
>>>> -D_REENTRANT  -c -c -O -I../../src -ITogl -I/sw/include -I.
>>>> -I/usr/X11R6/include   -I'/sw/lib/ocaml' 'togl.c'
>>>> clang: warning: argument unused during compilation:
>>>> '-fno-defer-pop'
>>>> togl.c:162:2: error: "Sorry, you will have to edit togl.c to
>>>> include the right
>>>> tkInt.h file"
>>>> #error "Sorry, you will have to edit togl.c to include the
>>>> right tkInt.h file"
>>>>^
>>>> togl.c:1260:4: error: unknown type name 'TkWindow'; did you
>>>> mean 'Tk_Window'?
>>>>  TkWindow *winPtr = (TkWindow *) togl->TkWin;
>>>>  ^~~~
>>>>  Tk_Window
>>> 
>>> Can you confirm that the package 'lablgl' builds (or fails) on 10.9?
>>> 
>>> Hanspeter
>>> 
>> 
>> It builds for me on 10.9.  I substituted lablgl for lablgl-x11 in the
>> dependencies in lablgtk2.info, which is what I'm trying to install (as a
>> dependency of unison).  It built fine like this, and so did unison
>> (yay!)  Still need to test it, but it starts up with the X11 gui OK.
>> 
>> I have attached the info file for lablgtk2.info, because I think I had
>> to change a few other deps as well.  And since it now works for me,
>> unison.info also attached.
>> 
>> many thanks,
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>> 
>> 
>
> Thanks!  I'll make getting Unison back into Fink a priority.

That would be great.  I'm happy to help and test.

A warning: I'm having some sort of archive compatibility 
issue testing with my 10.6 server and this newly built 
unison.  I'll head over to the unison list to try to resolve 
it, but since unison is working on local archives, the 
changes to the build I've just made could be to blame 
somehow.  Most likely it is different versions of ocaml, it 
is 4.01.0-1 on 10.9 but only 3.12.1-1 on 10.6...tomorrow 
I'll try to test between 10.9 and 10.7 and see if I can sort 
it out.

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds



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Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9

[Viv Kendon]

On Mon, 16 Dec 2013, Hanspeter Niederstrasser wrote:


On 12/16/2013 4:55 PM, Viv Kendon wrote:

Apologies if this has already been reported.  Doesn't seem
to be a maintainer to Cc, not Cc'ing fink-devel as I'm not
subscribed.

cd Togl && make togl.o CC="ocamlc.opt -verbose" CFLAGS='-c
-ccopt "-c -O -I../../src -ITogl -I/sw/include -I.
-I/usr/X11R6/include "'
make[2]: Entering directory
`/sw/src/fink.build/lablgl-x11-1.04-1/lablGL-1.04/Togl/src/Togl'
ocamlc.opt -verbose -c -ccopt "-c -O -I../../src -ITogl
-I/sw/include -I.  -I/usr/X11R6/include " togl.c
+ gcc -fno-defer-pop -Wall -D_FILE_OFFSET_BITS=64
-D_REENTRANT  -c -c -O -I../../src -ITogl -I/sw/include -I.
-I/usr/X11R6/include   -I'/sw/lib/ocaml' 'togl.c'
clang: warning: argument unused during compilation:
'-fno-defer-pop'
togl.c:162:2: error: "Sorry, you will have to edit togl.c to
include the right
tkInt.h file"
#error "Sorry, you will have to edit togl.c to include the
right tkInt.h file"
   ^
togl.c:1260:4: error: unknown type name 'TkWindow'; did you
mean 'Tk_Window'?
 TkWindow *winPtr = (TkWindow *) togl->TkWin;
 ^~~~
 Tk_Window


Can you confirm that the package 'lablgl' builds (or fails) on 10.9?

Hanspeter



It builds for me on 10.9.  I substituted lablgl for 
lablgl-x11 in the dependencies in lablgtk2.info, which is 
what I'm trying to install (as a dependency of unison).  It 
built fine like this, and so did unison (yay!)  Still need 
to test it, but it starts up with the X11 gui OK.


I have attached the info file for lablgtk2.info, because I 
think I had to change a few other deps as well.  And since 
it now works for me, unison.info also attached.


many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds
Package: lablgtk2
Version: 2.14.2
Revision: 4
Maintainer: Corey Halpin 
BuildDepends: <<
  aspell-dev,
  atk1 (>= 1.20.0-1),
  audiofile,
  cairo (>= 1.6-1),
  esound,
  expat1,
  fink (>= 0.24.12),
  fontconfig2-dev (>= 2.4.1-1),
  freetype219 (>= 2.3.5-1),
  gconf2-dev (>= 2.20.0-1),
  gettext-tools,
  glib2-dev (>= 2.14.0-1),
  glitz,
  gnome-keyring-dev,
  gnome-panel-dev (>= 2.20.0-1),
  gnome-vfs2-unified-dev (>= 1:2.20.0-1),
  gtk+2-dev (>= 2.12.0-1),
  gtkglarea2,
  gtksourceview2-dev,
  gtkspell2-dev (>= 2.0.11-1004),
  libart2,
  libbonobo2-dev (>= 2.20.0-1),
  libbonoboui2-dev (>= 2.20.0-1),
  libgettext8-dev,
  libglade2 (>= 2.6.2-1),
  libgnome2-dev (>= 2.20.0-1),
  libgnomecanvas2-dev (>= 2.20.0-1),
  libgnomeprint2.2-dev,
  libgnomeui2-dev (>= 2.20.0-1),
  libiconv-dev,
  libpng16,
  librsvg2 (>= 2.20.0-1),
  libxml2 (>= 2.6.30-1),
  ocaml (>=3.08),
  orbit2-dev (>= 2.14.9-1),
  pango1-xft2-ft219-dev (>= 1.18.4-4),
  pixman (>= 0.10.0-1),
  pkgconfig (>= 0.21-1),
  popt,
  x11-dev,
  xft2-dev
<<
Depends: <<
  aspell-shlibs,
  atk1-shlibs (>= 1.20.0-1),
  audiofile-shlibs,
  cairo-shlibs,
  esound-shlibs,
  fontconfig2-shlibs,
  freetype219-shlibs,
  gconf2-shlibs (>= 2.20.0-1),
  gconf2-shlibs,
  glib2-shlibs (>= 2.14.0-1),
  gnome-keyring,
  gnome-panel-shlibs (>= 2.20.0-1),
  gnome-vfs2-unified-shlibs (>= 1:2.20.0-1),
  gtk+2-shlibs (>= 2.12.0-1),
  gtkglarea2-shlibs,
  gtksourceview2-shlibs,
  gtkspell2-shlibs (>= 2.0.11-1004),
  lablgl,
  libart2-shlibs,
  libbonobo2-shlibs (>= 2.20.0-1),
  libbonoboui2-shlibs (>= 2.20.0-1),
  libgettext8-shlibs,
  libglade2-shlibs (>= 2.6.2-1),
  libgnome2-shlibs (>= 2.20.0-1),
  libgnomecanvas2-shlibs (>= 2.20.0-1),
  libgnomeprint2.2-shlibs,
  libgnomeui2-shlibs (>= 2.20.0-1),
  libiconv,
  librsvg2-shlibs (>= 2.20.0-1),
  libxml2-shlibs (>= 2.6.30-1),
  ocaml (>=3.08),
  orbit2-shlibs (>= 2.14.9-1),
  pango1-xft2-ft219-shlibs (>= 1.18.4-4),
  popt-shlibs,
  x11,
  x11-shlibs
<<
CompileScript:<<
#!/bin/bash -ev
  ./configure %c
  make world
<<
InstallScript: make install DESTDIR=%d
Source: http://forge.ocamlcore.org/frs/download.php/561/lablgtk-%v.tar.gz
Source-MD5: bad77680a72dab8b915cae99d1ec9b1f
#PatchFile: %n.patch
#PatchFile-MD5: cb193aa8f99656d78aecc90e1188c2f1
ConfigureParams: --with-gnomecanvas --disable-dependency-tracking 
PKG_CONFIG_PATH="%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:$PKG_CONFIG_PATH"
 FREETYPE_CONFIG=%p/lib/freetype219/bin/freetype-config
SetLIBRARY_PATH: %b/src
DocFiles: CHANGES COPYING README
DescPackaging:<<
  Between 2.6.0-2 and 2.6.0-3 it was necessary to change one of the
dependancies of this package from labl to lablgl-x11.
Unfortunately, because of this change, the upgrade between 

[Fink-users] lablgl-x11-1.04-1 build failure on 10.9

[Viv Kendon]

#x27; (aka
   'struct Tk_Window_ *') is not a structure or union
   if (winPtr->parentPtr->window == None) {
   ~~^ ~
togl.c:1552:47: error: member reference base type 
'Tk_Window' (aka
   'struct Tk_Window_ *') is not a structure or union
  Tk_MakeWindowExist((Tk_Window) winPtr->parentPtr);
 ~~^ ~
togl.c:1554:22: error: member reference base type 
'Tk_Window' (aka
   'struct Tk_Window_ *') is not a structure or union
   parent = winPtr->parentPtr->window;
~~^ ~
fatal error: too many errors emitted, stopping now 
[-ferror-limit=]
20 errors generated.
make[2]: *** [togl.o] Error 2
make[2]: Leaving directory 
`/sw/src/fink.build/lablgl-x11-1.04-1/lablGL-1.04/Togl/src/Togl'
make[1]: *** [Togl/togl.o] Error 2
make[1]: Leaving directory 
`/sw/src/fink.build/lablgl-x11-1.04-1/lablGL-1.04/Togl/src'
make: *** [togl] Error 2
### execution of /tmp/fink.ybf2v failed, exit code 2
### execution of /tmp/fink.hCQH5 failed, exit code 2

Package manager version: 0.36.1
Distribution version: selfupdate-rsync Sun Dec 15 14:27:38 
2013, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 5.0.2
Xcode command-line tools: 5.0.1.0.1.1382131676
lablgl-x11-1.04-1 is set to build with only one job.
and case sensitive file system.

I have tcltk installed, but tkInt.h appears to live in
/sw/include/tcltk-private/tk8.6/generic/tkInt.h

Happy to supply more info if required...

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] clnum-py27-1.6-1 failed on 10.9

[Viv Kendon]

(Ahem) resending with presumed typo in maintainer's email 
address fixed -- I cut and pasted from the fink info and 
didn't notice :-)  fang...@uesrs.sourceforge.net

On Sun, 15 Dec 2013, Viv Kendon wrote:

> (maintainer Cc'd)
>
> gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv
> -O3 -Wall -Wstrict-prototypes -I/sw/include
> -I/sw/include/python2.7 -c clnum/src/clnum.cpp -o
> build/temp.macosx-10.9-x86_64-2.7/clnum/src/clnum.o
> In file included from clnum/src/clnum.cpp:30:
> In file included from /sw/include/cln/cln.h:27:
> /sw/include/cln/string.h:28:9: warning: class 'cl_string'
> was previously
>   declared as a struct [-Wmismatched-tags]
> friend class cl_string;
>^
> /sw/include/cln/string.h:13:8: note: previous use is here
> struct cl_string;
>^
> In file included from clnum/src/clnum.cpp:30:
> In file included from /sw/include/cln/cln.h:29:
> /sw/include/cln/proplist.h:41:1: warning: 'cl_property_list'
> defined as a struct
>   here but previously declared as a class
> [-Wmismatched-tags]
> struct cl_property_list {
> ^
> /sw/include/cln/proplist.h:35:9: note: did you mean struct
> here?
> friend class cl_property_list;
>^
>struct
> clnum/src/clnum.cpp:819:2: error: This routine needs to be
> fixed
> #error This routine needs to be fixed
>
>
> ...which suggests this problem might already be known?
>
>
> Package manager version: 0.36.1
> Distribution version: selfupdate-rsync Sun Dec 15 14:27:38
> 2013, 10.9, x86_64
> Trees: local/main stable/main
> Xcode.app: 5.0.2
> Xcode command-line tools: 5.0.1.0.1.1382131676
> Max. Fink build jobs:  4
>
> and case-sensitive file system
>
> many thanks,
> -- Viv
> 
> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
> tel: +44 113 343 4864  Physics and Astronomy
> Quantum Information GroupUniversity of Leeds
>
>
>
> --
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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>



Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds

I am working to contract as part of UCU's action short of a strike from
1st November in support of fair pay in HE.  It may take longer than usual
for me to respond to your message.
  For more info see http://www.ucu.org.uk/hepay13
  To join the union and the action http://www.ucu.org.uk/join


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[Fink-users] clnum-py27-1.6-1 failed on 10.9

[Viv Kendon]

(maintainer Cc'd)

gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv 
-O3 -Wall -Wstrict-prototypes -I/sw/include 
-I/sw/include/python2.7 -c clnum/src/clnum.cpp -o 
build/temp.macosx-10.9-x86_64-2.7/clnum/src/clnum.o
In file included from clnum/src/clnum.cpp:30:
In file included from /sw/include/cln/cln.h:27:
/sw/include/cln/string.h:28:9: warning: class 'cl_string' 
was previously
   declared as a struct [-Wmismatched-tags]
 friend class cl_string;
^
/sw/include/cln/string.h:13:8: note: previous use is here
struct cl_string;
^
In file included from clnum/src/clnum.cpp:30:
In file included from /sw/include/cln/cln.h:29:
/sw/include/cln/proplist.h:41:1: warning: 'cl_property_list' 
defined as a struct
   here but previously declared as a class 
[-Wmismatched-tags]
struct cl_property_list {
^
/sw/include/cln/proplist.h:35:9: note: did you mean struct 
here?
 friend class cl_property_list;
^
struct
clnum/src/clnum.cpp:819:2: error: This routine needs to be 
fixed
#error This routine needs to be fixed


...which suggests this problem might already be known?


Package manager version: 0.36.1
Distribution version: selfupdate-rsync Sun Dec 15 14:27:38 
2013, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 5.0.2
Xcode command-line tools: 5.0.1.0.1.1382131676
Max. Fink build jobs:  4

and case-sensitive file system

many thanks,
-- Viv
____________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds



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[Fink-users] biskit-py27-2.4.0-2 missing netcdf

[Viv Kendon]

This is probably easy to fix:

Can't resolve dependency "netcdf" for package 
"biskit-py27-2.4.0-2" (no matching packages/versions found)

on 10.9 fresh install, case-sensitive file system.

thanks,
-- Viv
____________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] re-alpine build failure on 10.9

[Viv Kendon]

Apologies for missing this, I waited in case an update came 
through, then forgot to check back.

On Tue, 26 Nov 2013, Hisashi T Fujinaka wrote:

> I think fang added alpine to 10.6. Can you see if it works for you?

on my 10.6 system, fink list alpine gives
  alpine   2.00-109 OBSOLETE use package 
're-alpine' instead
  i   re-alpine2.02-2   Text based tool for 
managing emails

I don't see a newer alpine.  On 10.7 and 10.9 I have the 
newer alpine running fine, on 10.9 for example,

  alpine   2.11-1   Text based tool for 
managing emails
  i   alpine-alpha 2.19.1-1 Text based tool for 
managing emails
  re-alpine2.02-4   Text based tool for 
managing emails

many thanks,
-- Viv

> On Tue, 19 Nov 2013, Viv Kendon wrote:
>
>> OK, that sounds like good advice, and it installed fine on 10.9 -- thanks!
>>
>> But the latest alpine is not available on 10.6, and I have a system I can't
>> upgrade that I use re-alpine on regularly.  Hopefully the two versions will
>> be compatible with the same .pinerc file on a networked home dir...
>>
>> many thanks,
>> -- Viv
>>
>> On Mon, 18 Nov 2013, Hisashi T Fujinaka wrote:
>>
>>> I think alpine has leapfrogged re-alpine again and you may just want to
>>> switch.
>>>
>>> On Mon, 18 Nov 2013, Viv Kendon wrote:
>>>
>>>> trying to install re-alpine-2.02-4 on a set up from scratch
>>>> 10.9 case sensitive iMac:
>>>>
>>>> gcc -DHAVE_CONFIG_H   -I../../../include -I../../../include
>>>> -I/sw/include -I/sw/include -g -D_THREAD_SAFE  -Dbsd -g -O2
>>>> -MT alpined.o -MD -MP -MF .deps/alpined.Tpo -c -o alpined.o
>>>> alpined.c
>>>> alpined.c:763:50: error: no member named 'result' in 'struct
>>>> Tcl_Interp'
>>>>   ...case TCL_OK  : peReturn(cs, "OK",
>>>> interp->result); break;
>>>>   ~~  ^
>>>> alpined.c:764:55: error: no member named 'result' in 'struct
>>>> Tcl_Interp'
>>>>   ...case TCL_ERROR  : peReturn(cs, "ERROR",
>>>> interp->result); break;
>>>>  ~~  ^
>>>> alpined.c:765:55: error: no member named 'result' in 'struct
>>>> Tcl_Interp'
>>>>   ...case TCL_BREAK  : peReturn(cs, "BREAK",
>>>> interp->result); break;
>>>>  ~~  ^
>>>> alpined.c:766:56: error: no member named 'result' in 'struct
>>>> Tcl_Interp'
>>>>   ...case TCL_RETURN : peReturn(cs, "RETURN",
>>>> interp->result); break;
>>>>   ~~  ^
>>>> Package manager version: 0.36.1
>>>> Distribution version: selfupdate-rsync Mon Nov 18 15:38:11
>>>> 2013, 10.9, x86_64
>>>> Trees: local/main stable/main
>>>> Xcode.app: 5.0.2
>>>> Xcode command-line tools: 5.0.1.0.1.1382131676
>>>> re-alpine-2.02-4 is set to build with only one job.
>>>
>>> --
>>> Hisashi T Fujinaka - ht...@twofifty.com
>>> BSEE(6/86) + BSChem(3/95) + BAEnglish(8/95) + MSCS(8/03) + $2.50 = latte
>>>
>>>
>>> ----------
>>> Shape the Mobile Experience: Free Subscription
>>> Software experts and developers: Be at the forefront of tech innovation.
>>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
>>> conversations that shape the rapidly evolving mobile landscape. Sign up
>>> now.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>>> ___
>>> Fink-users mailing list
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>>> List archive:
>>> http://news.gmane.org/gmane.os.macosx.fink.user
>>> Subscription management:
>>> https://lists.sourceforge.net/lists/listinfo/fink-users
>>>
>>
>>
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>>
>> I am working to contract as part of UCU's action short of a strike from
>> 1st November in support of fair pay in HE.  It may take longer th

Re: [Fink-users] Using the bindist

[Viv Kendon]

On Mon, 25 Nov 2013, Martin Costabel wrote:

> Coming across the new bindist by chance (BTW, great work! My respect to
> those involved), I wanted to try and use it.
> Now during years of not using apt-get and a bindist, I all but forgot
> how to do it. It turns out I am not the only one, though... Fink itself
> seem to have forgotten.
>
> I added the line
> deb http://bindist.finkproject.org/10.9 stable main
> to the sources.list file and changed the config line UseBinaryDist: from
> false to true. Then I used `fink install` for two or three packages.
>
> The result is that Fink correctly downloaded the debs from the bindist
> server, but then went ahead and compiled them from source anyway,
> without apologizing in any way. An example output is shown below.
>
> Did I forget some additional step necessary to make this work, or has
> Fink forgotten how to use the bindist?
>
> --
> Martin
>
> Example output:
>
> costabel% fink update gnuplot
> Information about 8157 packages read in 0 seconds.
> The following package will be installed or updated:
>  gnuplot
> /sw/bin/apt-get-lockwait -q --ignore-breakage --download-only install
> gnuplot=4.6.4-4
> Reading Package Lists...
> Building Dependency Tree...
> 1 packages upgraded, 0 newly installed, 0 to remove and 21  not upgraded.
> Need to get 3343kB of archives. After unpacking 0B will be used.
> Get:1 http://bindist.finkproject.org stable/main gnuplot 4.6.4-4 [3343kB]
> Fetched 3343kB in 12s (274kB/s)
> Download complete and in download only mode
> Setting runtime build-lock...
> dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-gnuplot-4.6.4-4
> /sw/src/fink.build
> dpkg-deb: building package `fink-buildlock-gnuplot-4.6.4-4' in
> `/sw/src/fink.build/fink-buildlock-gnuplot-4.6.4-4_2013.11.25-13.01.18_darwin-x86_64.deb'.
> Installing build-lock package...
> /sw/bin/dpkg-lockwait -i
> /sw/src/fink.build/fink-buildlock-gnuplot-4.6.4-4_2013.11.25-13.01.18_darwin-x86_64.deb
> Selecting previously deselected package fink-buildlock-gnuplot-4.6.4-4.
> (Reading database ... 263568 files and directories currently installed.)
> Unpacking fink-buildlock-gnuplot-4.6.4-4 (from
> .../fink-buildlock-gnuplot-4.6.4-4_2013.11.25-13.01.18_darwin-x86_64.deb) ...
> Setting up fink-buildlock-gnuplot-4.6.4-4 (2013.11.25-13.01.18) ...
>
> sudo -u fink-bld [ENV] sh -c /tmp/fink.SZWdN
> env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner --no-same-permissions
> -xf /sw/src/gnuplot-4.6.4.tar.gz
> [and so on, goes ahead and builds and installs gnuplot from source]


Having been running my own private bindists to save 
compiling the same thing for several similar macs, I 
discovered this some years ago[*], some of the bindist code 
has been disabled or removed from fink when there was no 
official bindist.  I was advised then to use sudo apt-get 
update followed by sudo apt-get dist-upgrade after setting 
the correct lines in /sw/etc/apt/sources.list

This works, but has the undesirable effect of not updating 
the package descriptions, only the lists of available debs. 
So I do run fink selfupdate after doing the apt-get 
commands.

It would be nice to have the bindist functionality restored, 
but it does work OK with apt-get.

-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


[*]
>From: Viv Kendon 
To: Fink Users Mailing List 

Date: Tue, 15 Dec 2009 15:26:56 + (GMT)
Subject: [Fink-users] using own binary dist with 10.6
X-Spam-Status: No, score=0.2 required=5.0 
tests=AWL,DNS_FROM_RFC_ABUSE,
 FORGED_RCVD_HELO autolearn=no version=3.0.5

I have successfully run my own internal binary distribution
for 10.4 and 10.5, but I can't get it working between my two
(clean installed) 10.6 systems.  Is it something to do with
the way UseBinaryDist is automatically set to false for the
moment?  What I observe is that, even with that flag set to
true in fink.conf, and the server added to apt sources.list,
the debs are correctly pulled from the server, but then it
starts doing a compile from source instead of installing the
deb it just collected:

   fink -b install deborphan
Information about 7917 packages read in 1 seconds.
The following package will be installed or updated:
   deborphan
The following additional package will be installed:
   dialog
Do you want to continue? [Y/n]
/sw/bin/apt-get-lockwait --ignore-breakage --download-only 
install
deborphan=1.7.23-2 dialog=1.0-20060221-1002
Reading Package Lists... Done
Building Dependency Tree... Done
The following NEW packages will be installed:
deborphan dialog
0 packages upgraded, 2 newly installed, 0 to remove and 50 
not upgraded.
Need to get 168kB of archives. After unpacking 545kB will be 
used.
Get:1 

Re: [Fink-users] Failed: phase compiling: octave-atlas-x11-3.6.4-7 failed

[Viv Kendon]

On Thu, 21 Nov 2013, Alexander Hansen wrote:

> On 11/21/13 6:55 AM, Alexander Hansen wrote:
>> On 11/21/13 3:59 AM, Viv Kendon wrote:
>> 
>> 
>> 
>>>> 
>>> 
>>> logs attached as requested, having updated fink to the latest now the
>>> mirrors are back in sync.  list not CC'd as I think the attachments are
>>> too big.
>>> 
>>> many thanks,
>>> -- Viv
>>> 
>>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>>> tel: +44 113 343 4864  Physics and Astronomy
>>> Quantum Information GroupUniversity of Leeds
>>> 
>> 
>> Thanks.  Nothing obvious jumped out at me, but I think I can rule out
>> anything atlas-specific.  I'll attempt a non-atlas build on 10.7 right
>> now and see what happens.
>> 
>
> I found the problem.  I had added a flag to make the package work on 10.9 and 
> assumed unwisely that it would also work for 10.7 without having tested it.
>
> Revision 9 _should_ be available following a selfupdate soon
>
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/
>

Great, that works for me, too.  Many thanks, much 
appreciated.

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] Failed: phase compiling: octave-atlas-x11-3.6.4-7 failed

[Viv Kendon]

Apologies if this has already been on the list, I've been 
deleting everything I thought was fixed...

I _think_ this is the error, full log available if not:

mv -f .deps/liboctave_la-idx-vector.Tpo 
.deps/liboctave_la-idx-vector.Plo
/bin/sh ../libtool  --tag=CXX   --mode=compile flag-sort -r 
g++ -std=c++0x -DHAV
E_CONFIG_H -I. -I..-I../libgnu -I../libgnu 
-I../libcruft/misc -I/sw/
include -I/sw/include -O3 -MD -I/usr/X11/include 
-DHAVE_CONFIG_H -I/sw/include
-I/sw/include/freetype2 -I/sw/include -I/sw/include   -Wall 
-W -Wshadow -Wold-st
yle-cast -Wformat -Wpointer-arith -Wwrite-strings 
-Wcast-align -Wcast-qual -O3 -
MD -I/usr/X11/include -D_THREAD_SAFE -pthread -O3 -MD 
-I/usr/X11/include -MT lib
octave_la-oct-alloc.lo -MD -MP -MF 
.deps/liboctave_la-oct-alloc.Tpo -c -o liboct
ave_la-oct-alloc.lo `test -f 'oct-alloc.cc' || echo 
'./'`oct-alloc.cc
lo-specfun.cc:336:12: error: use of undeclared identifier 
'lgamma_r'; did you mean 'xgamma_'?
   result = lgamma_r (x, &sgngam);
^~~~
xgamma_
lo-specfun.cc:175:13: note: 'xgamma_' declared here
   F77_FUNC (xgamma, XGAMMA) (const float&, float&);
 ^
../config.h:86:29: note: expanded from macro 'F77_FUNC'
#define F77_FUNC(name,NAME) name ## _
 ^
:245:1: note: expanded from macro 'xgamma'
xgamma_
^
lo-specfun.cc:336:25: error: non-const lvalue reference to 
type 'float' cannot bind to a temporary of type 'int *'
   result = lgamma_r (x, &sgngam);
 ^~~
lo-specfun.cc:175:50: note: passing argument to parameter 
here
   F77_FUNC (xgamma, XGAMMA) (const float&, float&);
  ^
lo-specfun.cc:401:12: error: use of undeclared identifier 
'lgammaf_r'; did you mean 'xgamma_'?
   result = lgammaf_r (x, &sgngam);
^
xgamma_
lo-specfun.cc:175:13: note: 'xgamma_' declared here
   F77_FUNC (xgamma, XGAMMA) (const float&, float&);
 ^
../config.h:86:29: note: expanded from macro 'F77_FUNC'
#define F77_FUNC(name,NAME) name ## _
 ^
:245:1: note: expanded from macro 'xgamma'
xgamma_
^
lo-specfun.cc:401:26: error: non-const lvalue reference to 
type 'float' cannot bind to a temporary of type 'int *'
   result = lgammaf_r (x, &sgngam);
  ^~~
lo-specfun.cc:175:50: note: passing argument to parameter 
here
   F77_FUNC (xgamma, XGAMMA) (const float&, float&);
  ^
libtool: compile:  flag-sort -r g++ -std=c++0x 
-DHAVE_CONFIG_H -I. -I.. -I../libgnu -I../libgnu 
-I../libcruft/misc -I/sw/include -I/sw/include -O3 -MD 
-I/usr/X11/include -DHAVE_CONFIG_H -I/sw/include 
-I/sw/include/freetype2 -I/sw/include -I/sw/include -Wall -W 
-Wshadow -Wold-style-cast -Wformat -Wpointer-arith 
-Wwrite-strings -Wcast-align -Wcast-qual -O3 -MD 
-I/usr/X11/include -D_THREAD_SAFE -pthread -O3 -MD 
-I/usr/X11/include -MT liboctave_la-mach-info.lo -MD -MP -MF 
.deps/liboctave_la-mach-info.Tpo -c mach-info.cc 
-fno-common -DPIC -o .libs/liboctave_la-mach-info.o
libtool: compile:  flag-sort -r g++ -std=c++0x 
-DHAVE_CONFIG_H -I. -I.. -I../libgnu -I../libgnu 
-I../libcruft/misc -I/sw/include -I/sw/include -O3 -MD 
-I/usr/X11/include -DHAVE_CONFIG_H -I/sw/include 
-I/sw/include/freetype2 -I/sw/include -I/sw/include -Wall -W 
-Wshadow -Wold-style-cast -Wformat -Wpointer-arith 
-Wwrite-strings -Wcast-align -Wcast-qual -O3 -MD 
-I/usr/X11/include -D_THREAD_SAFE -pthread -O3 -MD 
-I/usr/X11/include -MT liboctave_la-oct-alloc.lo -MD -MP -MF 
.deps/liboctave_la-oct-alloc.Tpo -c oct-alloc.cc 
-fno-common -DPIC -o .libs/liboctave_la-oct-alloc.o
4 errors generated.
make[1]: *** [liboctave_la-lo-specfun.lo] Error 1
make[1]: *** Waiting for unfinished jobs
mv -f .deps/liboctave_la-oct-alloc.Tpo 
.deps/liboctave_la-oct-alloc.Plo
lo-utils.cc:358:56: warning: unused parameter 'sign' 
[-Wunused-parameter]
read_float_inf_nan_na (std::istream& is, char c0, char sign 
= '+')



Package manager version: 0.36.0
Distribution version: selfupdate-rsync Wed Nov 20 18:47:26 
2013, 10.7, x86_64
Trees: local/main stable/main
Xcode.app: 4.6.1
Xcode command-line tools: 4.6.0.0.1.1362189000
Max. Fink build jobs:  4

and case sensitive file system.

  My latest selfupdate was with the mirror
   rsync://ber.de.eu.finkmirrors.net/finkinfo/
  in case the problem is that it isn't up to date.

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Shape the Mobile Experie

Re: [Fink-users] re-alpine build failure on 10.9

[Viv Kendon]

OK, that sounds like good advice, and it installed fine on 
10.9 -- thanks!

But the latest alpine is not available on 10.6, and I 
have a system I can't upgrade that I use re-alpine on 
regularly.  Hopefully the two versions will be compatible 
with the same .pinerc file on a networked home dir...

many thanks,
-- Viv

On Mon, 18 Nov 2013, Hisashi T Fujinaka wrote:

> I think alpine has leapfrogged re-alpine again and you may just want to
> switch.
>
> On Mon, 18 Nov 2013, Viv Kendon wrote:
>
>> trying to install re-alpine-2.02-4 on a set up from scratch
>> 10.9 case sensitive iMac:
>>
>> gcc -DHAVE_CONFIG_H   -I../../../include -I../../../include
>> -I/sw/include -I/sw/include -g -D_THREAD_SAFE  -Dbsd -g -O2
>> -MT alpined.o -MD -MP -MF .deps/alpined.Tpo -c -o alpined.o
>> alpined.c
>> alpined.c:763:50: error: no member named 'result' in 'struct
>> Tcl_Interp'
>>   ...case TCL_OK  : peReturn(cs, "OK",
>> interp->result); break;
>>   ~~  ^
>> alpined.c:764:55: error: no member named 'result' in 'struct
>> Tcl_Interp'
>>   ...case TCL_ERROR  : peReturn(cs, "ERROR",
>> interp->result); break;
>>  ~~  ^
>> alpined.c:765:55: error: no member named 'result' in 'struct
>> Tcl_Interp'
>>   ...case TCL_BREAK  : peReturn(cs, "BREAK",
>> interp->result); break;
>>  ~~  ^
>> alpined.c:766:56: error: no member named 'result' in 'struct
>> Tcl_Interp'
>>   ...case TCL_RETURN : peReturn(cs, "RETURN",
>> interp->result); break;
>>   ~~  ^
>> Package manager version: 0.36.1
>> Distribution version: selfupdate-rsync Mon Nov 18 15:38:11
>> 2013, 10.9, x86_64
>> Trees: local/main stable/main
>> Xcode.app: 5.0.2
>> Xcode command-line tools: 5.0.1.0.1.1382131676
>> re-alpine-2.02-4 is set to build with only one job.
>
> -- 
> Hisashi T Fujinaka - ht...@twofifty.com
> BSEE(6/86) + BSChem(3/95) + BAEnglish(8/95) + MSCS(8/03) + $2.50 = latte
>
> --
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> conversations that shape the rapidly evolving mobile landscape. Sign up now.
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Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds

I am working to contract as part of UCU's action short of a strike from
1st November in support of fair pay in HE.  It may take longer than usual
for me to respond to your message.
  For more info see http://www.ucu.org.uk/hepay13
  To join the union and the action http://www.ucu.org.uk/join


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[Fink-users] re-alpine build failure on 10.9

[Viv Kendon]

trying to install re-alpine-2.02-4 on a set up from scratch 
10.9 case sensitive iMac:

gcc -DHAVE_CONFIG_H   -I../../../include -I../../../include 
-I/sw/include -I/sw/include -g -D_THREAD_SAFE  -Dbsd -g -O2 
-MT alpined.o -MD -MP -MF .deps/alpined.Tpo -c -o alpined.o 
alpined.c
alpined.c:763:50: error: no member named 'result' in 'struct 
Tcl_Interp'
   ...case TCL_OK  : peReturn(cs, "OK", 
interp->result); break;
   ~~  ^
alpined.c:764:55: error: no member named 'result' in 'struct 
Tcl_Interp'
   ...case TCL_ERROR  : peReturn(cs, "ERROR", 
interp->result); break;
  ~~  ^
alpined.c:765:55: error: no member named 'result' in 'struct 
Tcl_Interp'
   ...case TCL_BREAK  : peReturn(cs, "BREAK", 
interp->result); break;
  ~~  ^
alpined.c:766:56: error: no member named 'result' in 'struct 
Tcl_Interp'
   ...case TCL_RETURN : peReturn(cs, "RETURN", 
interp->result); break;
   ~~  ^
Package manager version: 0.36.1
Distribution version: selfupdate-rsync Mon Nov 18 15:38:11 
2013, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 5.0.2
Xcode command-line tools: 5.0.1.0.1.1382131676
re-alpine-2.02-4 is set to build with only one job.

can provide more output if needed.

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] nan-atlas-oct364 glitch

[Viv Kendon]

On Thu, 3 Oct 2013, Alexander Hansen wrote:

> On 10/3/13 9:26 AM, Viv Kendon wrote:
>> On Thu, 3 Oct 2013, Alexander Hansen wrote:
>> 
>>> On 10/3/13 4:40 AM, Viv Kendon wrote:
>>>> almost there on my octave udpates.  Just nan-atlas-octave364 isn't
>>>> playing nicely.  Output below, not sure what is going wrong, could it be
>>>> a case-sensitive file system problem??
>>>> 
>>>> many thanks,
>>>> -- Viv
>>>> 
>>>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>>>> tel: +44 113 343 4864  Physics and Astronomy
>>>> Quantum Information GroupUniversity of Leeds
>>>> 
>>>> 
>>> 
>>> 
>>> 
>>>> if [ type_pkg[oct] -ge 343 ]
>>>>   then pkgsrc=NaN
>>>>   else pkgsrc=nan
>>>> fi
>>>> /tmp/fink.ytRj1: line 3: [: type_pkg[oct]: integer expression expected
>>> 
>>> 
>>> 
>>> Thanks!
>>> 
>>> It's a typo which happens still to give the desired outcome on a
>>> case-insensitive system, which is why I didn't catch it.  I just uploaded 
>>> the
>>> fix.
>>> 
>>> --
>>> Alexander Hansen, Ph.D.
>>> Fink User Liaison
>>> My package updates: http://finkakh.wordpress.com/
>>> 
>> 
>> OK, thanks, I just saw a nan-oct.info update come through,
>> tried again, but it still fails with almost the same error:
>> 
>> if [ type_pkg[-oct] -ge 343 ]
>>       then pkgsrc=NaN
>>   else pkgsrc=nan
>> fi
>> /tmp/fink.n8lJr: line 3: [: type_pkg[-oct]: integer
>> expression expected
>> 
>> (spot the - sign difference).  And it is in fact why I can't
>> install bundle-octave on the other machine, it can't yet
>> find nan-atlas-oct364 to complete the bundle...after the
>> apt-get update the rest were resolved.
>> 
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>> 
>> 
>
> Oops.  I should have waited until after I had some coffee. :-)  "oct" was 
> right, but "type_pkg" should be "%type_pkg".
>
> The new fix is on the way.
>
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/

Great, that worked, and octave364 is now fully installed on 
both machines.

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] nan-atlas-oct364 glitch

[Viv Kendon]

On Thu, 3 Oct 2013, Alexander Hansen wrote:

> On 10/3/13 4:40 AM, Viv Kendon wrote:
>> almost there on my octave udpates.  Just nan-atlas-octave364 isn't
>> playing nicely.  Output below, not sure what is going wrong, could it be
>> a case-sensitive file system problem??
>> 
>> many thanks,
>> -- Viv
>> ________
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>> 
>> 
>
> 
>
>> if [ type_pkg[oct] -ge 343 ]
>>  then pkgsrc=NaN
>>  else pkgsrc=nan
>> fi
>> /tmp/fink.ytRj1: line 3: [: type_pkg[oct]: integer expression expected
>
> 
>
> Thanks!
>
> It's a typo which happens still to give the desired outcome on a 
> case-insensitive system, which is why I didn't catch it.  I just uploaded the 
> fix.
>
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/
>

OK, thanks, I just saw a nan-oct.info update come through,
tried again, but it still fails with almost the same error:

if [ type_pkg[-oct] -ge 343 ]
 then pkgsrc=NaN
 else pkgsrc=nan
fi
/tmp/fink.n8lJr: line 3: [: type_pkg[-oct]: integer 
expression expected

(spot the - sign difference).  And it is in fact why I can't 
install bundle-octave on the other machine, it can't yet 
find nan-atlas-oct364 to complete the bundle...after the 
apt-get update the rest were resolved.

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] bundle-octave364-atlas problem?

[Viv Kendon]

I now want to install the octave364-atlas-x11 I just 
compiled on one machine over on a similar machine that has 
access to the deb files and is set up to see them as a 
binary repositary...  so I tried

sudo apt-get install bundle-octave364-atlas
Reading Package Lists... Done
Building Dependency Tree... Done
Some packages could not be installed. This may mean that you 
have
requested an impossible situation or if you are using the 
unstable
distribution that some required packages have not yet been 
created
or been moved out of Incoming.

Since you only requested a single operation it is extremely 
likely that
the package is simply not installable and a bug report 
against
that package should be filed.
The following information may help to resolve the situation:

Sorry, but the following packages have unmet dependencies:
   bundle-octave364-atlas: Depends: communications-oct364 but 
it is not going to be installed
   Depends: control-atlas-oct364 but 
it is not going to be installed
   Depends: data-smoothing-oct364 but 
it is not going to be installed
   Depends: econometrics-oct364 but 
it is not going to be installed
   Depends: ga-oct364 but it is not 
going to be installed
   Depends: image-oct364 but it is 
not going to be installed
   Depends: 
linear-algebra-atlas-oct364 but it is not going to be 
installed
   Depends: mechanics-oct364 but it 
is not going to be installed
   Depends: nan-atlas-oct364 but it 
is not going to be installed
   Depends: ocs-oct364 but it is not 
going to be installed
   Depends: octgpr-atlas-oct364 but 
it is not going to be installed
   Depends: odepkg-atlas-oct364 but 
it is not going to be installed
   Depends: optim-atlas-oct364 but it 
is not going to be installed
   Depends: optiminterp-atlas-oct364 
but it is not going to be installed
   Depends: signal-oct364 but it is 
not going to be installed
   Depends: vrml-oct364 but it is not 
going to be installed
E: Sorry, broken packages


Now, this may not work the way I want, there is no "x11" 
variant of the bundles.  But the error isn't about that...

Meanwhile, I can go about installing the debs 
individually.

many thanks,
-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


--
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[Fink-users] nan-atlas-oct364 glitch

[Viv Kendon]

almost there on my octave udpates.  Just nan-atlas-octave364 
isn't playing nicely.  Output below, not sure what is going 
wrong, could it be a case-sensitive file system problem??

many thanks,
-- Viv
____
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


The following package will be installed or updated:
  nan-atlas-oct364
Setting runtime build-lock...
dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-nan-atlas-oct364-2.5.5-8 
/sw/src/fink.build
dpkg-deb: building package `fink-buildlock-nan-atlas-oct364-2.5.5-8' in 
`/sw/src/fink.build/fink-buildlock-nan-atlas-oct364-2.5.5-8_2013.10.03-12.36.13_darwin-x86_64.deb'.
Installing build-lock package...
/sw/bin/dpkg-lockwait -i 
/sw/src/fink.build/fink-buildlock-nan-atlas-oct364-2.5.5-8_2013.10.03-12.36.13_darwin-x86_64.deb
Selecting previously deselected package fink-buildlock-nan-atlas-oct364-2.5.5-8.
(Reading database ... 266034 files and directories currently installed.)
Unpacking fink-buildlock-nan-atlas-oct364-2.5.5-8 (from 
.../fink-buildlock-nan-atlas-oct364-2.5.5-8_2013.10.03-12.36.13_darwin-x86_64.deb)
 ...
Setting up fink-buildlock-nan-atlas-oct364-2.5.5-8 (2013.10.03-12.36.13) ...

env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner --no-same-permissions -xvf 
/sw/src/nan-2.5.5.tar.gz
NaN/
NaN/inst/
NaN/inst/hist2res.m
NaN/inst/moment.m
NaN/inst/mean.m
NaN/inst/xval.m
NaN/inst/classify.m
NaN/inst/geomean.m
NaN/inst/nantest.m
NaN/inst/var.m
NaN/inst/nanfft.m
NaN/inst/zscore.m
NaN/inst/tcdf.m
NaN/inst/statistic.m
NaN/inst/norminv.m
NaN/inst/spearman.m
NaN/inst/median.m
NaN/inst/normpdf.m
NaN/inst/meansq.m
NaN/inst/naninsttest.m
NaN/inst/kurtosis.m
NaN/inst/trimean.m
NaN/inst/tinv.m
NaN/inst/range.m
NaN/inst/ranks.m
NaN/inst/ttest.m
NaN/inst/meandev.m
NaN/inst/normcdf.m
NaN/inst/nansum.m
NaN/inst/row_col_deletion.m
NaN/inst/train_lda_sparse.m
NaN/inst/rms.m
NaN/inst/cov.m
NaN/inst/flag_implicit_skip_nan.m
NaN/inst/cdfplot.m
NaN/inst/nanstd.m
NaN/inst/nanmean.m
NaN/inst/harmmean.m
NaN/inst/nanconv.m
NaN/inst/corrcoef.m
NaN/inst/nanfilter.m
NaN/inst/cat2bin.m
NaN/inst/sem.m
NaN/inst/ecdf.m
NaN/inst/flag_nans_occured.m
NaN/inst/test_sc.m
NaN/inst/std.m
NaN/inst/train_sc.m
NaN/inst/covm.m
NaN/inst/partcorrcoef.m
NaN/inst/decovm.m
NaN/inst/mad.m
NaN/inst/rankcorr.m
NaN/inst/trimmean.m
NaN/inst/mahal.m
NaN/inst/cumsumskipnan.m
NaN/inst/coefficient_of_variation.m
NaN/inst/prctile.m
NaN/inst/flag_implicit_significance.m
NaN/inst/tpdf.m
NaN/inst/tiedrank.m
NaN/inst/cor.m
NaN/inst/xptopen.m
NaN/inst/bland_altman.m
NaN/inst/load_fisheriris.m
NaN/inst/center.m
NaN/inst/flag_accuracy_level.m
NaN/inst/gscatter.m
NaN/inst/iqr.m
NaN/inst/zScoreMedian.m
NaN/inst/skewness.m
NaN/inst/detrend.m
NaN/inst/percentile.m
NaN/inst/medAbsDev.m
NaN/inst/fss.m
NaN/inst/quantile.m
NaN/inst/xcovf.m
NaN/inst/ttest2.m
NaN/inst/sumsq.m
NaN/inst/sumskipnan.m
NaN/inst/nanfilter1uc.m
NaN/inst/kappa.m
NaN/DESCRIPTION
NaN/INDEX
NaN/src/
NaN/src/kth_element.mexa64
NaN/src/make.m
NaN/src/kth_element.mexw32
NaN/src/train.mexa64
NaN/src/histo_mex.cpp
NaN/src/xptopen.cpp
NaN/src/str2array.mexw64
NaN/src/linear.cpp
NaN/src/svm_model_matlab.c
NaN/src/svmpredict_mex.mexw32
NaN/src/svmpredict_mex.cpp
NaN/src/str2array.mexw32
NaN/src/covm_mex.mexw32
NaN/src/train.mexw64
NaN/src/svmtrain_mex.mexw32
NaN/src/str2array.mexa64
NaN/src/covm_mex.mexa64
NaN/src/sumskipnan_mex.cpp
NaN/src/svm.cpp
NaN/src/covm_mex.mexw64
NaN/src/kth_element.mexw64
NaN/src/str2array.cpp
NaN/src/svmpredict_mex.mexw64
NaN/src/sumskipnan_mex.mexa64
NaN/src/svm_model_matlab.h
NaN/src/svmpredict_mex.mexa64
NaN/src/predict.c
NaN/src/sumskipnan_mex.mexw32
NaN/src/linear.h
NaN/src/kth_element.cpp
NaN/src/svmtrain_mex.cpp
NaN/src/linear_model_matlab.h
NaN/src/tron.h
NaN/src/svmtrain_mex.mexw64
NaN/src/histo_mex.mexw64
NaN/src/svmtrain_mex.mexa64
NaN/src/train.mexw32
NaN/src/train.c
NaN/src/Makefile
NaN/src/xptopen.mexw32
NaN/src/histo_mex.mexa64
NaN/src/histo_mex.mexw32
NaN/src/xptopen.mexw64
NaN/src/sumskipnan_mex.mexw64
NaN/src/svm.h
NaN/src/tron.cpp
NaN/src/covm_mex.cpp
NaN/src/xptopen.mexa64
NaN/src/linear_model_matlab.c
NaN/COPYING
NaN/doc/
NaN/doc/INSTALL
NaN/doc/README.TXT
NaN/test/
NaN/test/test_mex_accuracy.m
NaN/test/test_classify.m
NaN/test/test_perf_skipnan.m
NaN/test/test_xval.m
NaN/test/test_fss.m
NaN/test/test_train_sc.m
NaN/test/test_xptopen.m
NaN/VERSION
[ -r /sw/fink/dists/stable/main/finkinfo/sci/nan-oct.patch ]
/tmp/fink.1wFDF
#!/bin/sh -ev
sed -e 's|@FINKPREFIX@|/sw|g' \
-e 's|@OCTVERSION@|3.6.4|g' \
-e "s|@BLAS_LIBS@|`mkoctfile -p BLAS_LIBS`|" \
-e 's|@GCC@|4.7|' \

/sw/fink/dists/stable/main/finkinfo/sci/nan-oct.patch | patch -p1
mkoctfile -p BLAS_LIBS
patching file src/xptopen.cpp
patching file s

Re: [Fink-users] octave364 dependency problems?

[Viv Kendon]

On Wed, 2 Oct 2013, Alexander Hansen wrote:

> On 10/2/13 10:28 AM, Viv Kendon wrote:
>> (maintainer Cc'd)
>> 
>> I tried to update octave364 separately while waiting for a reply to my
>> questions about removal:
>> 
>> fink install octave364-atlas-x11
>> Information about 7988 packages read in 0 seconds.
>> The following package will be installed or updated:
>>   octave364-atlas-x11
>> The following additional package will be installed:
>>   octave364-atlas-x11-shlibs
>> Do you want to continue? [Y/n]
>> Reading buildlock packages...
>>  All buildlocks accounted for.
>> 
>> While trying to install:
>>octave364-atlas-x11-3.6.4-5
>>octave364-atlas-x11-shlibs-3.6.4-5
>> 
>> The following inconsistencies found:
>>Unsatisfied dependency in octgpr-atlas-oct364:
>> octave364-interpreter-ptatlas
>>Unsatisfied dependency in control-atlas-oct364:
>> octave364-interpreter-ptatlas
>>Unsatisfied dependency in optim-atlas-oct364:
>> octave364-interpreter-ptatlas
>>Unsatisfied dependency in nan-atlas-oct364:
>> octave364-interpreter-ptatlas
>>Unsatisfied dependency in octave-atlas-x11: octave364-atlas-x11 (=
>> 3.6.4-2)
>>Unsatisfied dependency in odepkg-atlas-oct364:
>> octave364-interpreter-ptatlas
>>Unsatisfied dependency in optiminterp-atlas-oct364:
>> octave364-interpreter-ptatlas
>>Unsatisfied dependency in octave364-atlas-x11-dev:
>> octave364-atlas-x11-shlibs
>> (= 3.6.4-2)
>>Unsatisfied dependency in octave364-atlas-x11-dev:
>> octave364-atlas-x11 (=
>> 3.6.4-2)
>>Unsatisfied dependency in linear-algebra-atlas-oct364:
>> octave364-interpreter-ptatlas
>> 
>> Trying to resolve dependencies...
>> Could not resolve inconsistent dependencies!
>> 
>> Fink isn't sure how to install the above packages safely. You may be
>> able to
>> fix things by running:
>>
>>fink scanpackages
>>sudo apt-get update
>>    sudo apt-get install octave364-atlas-x11=3.6.4-5
>> octave364-atlas-x11-shlibs=3.6.4-5
>> 
>> Failed: Fink::SysState: Could not resolve inconsistent dependencies
>> 
>> I'm not sure whether this is related to my removal problems or not...
>> 
>> many thanks,
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>> 
>
> This is completely unrelated to your other problem, as it is due to 
> dependency changes rather than missing files.
>
> If you follow the "fix things" instruction above, that will remove the 
> relevant -oct364 modules and install your updated octave364-atlas-x11*. 
> After you do that, you can install newer versions of those modules which 
> expect "octave364-interpreter-newatlas".
> 
> The issues that lead to this are:
>
> 1)  The new atlas maintainer decided to make an incompatible change in the 
> libraries installed by the atlas-shlibs package; this normally is supposed to 
> require a new package name but it's too late for that now.
>
> 2)  Because of 1) Octave needed to be rebuilt to use the new libraries.
>
> 3)  I use a virtual package to track the Octave version and what provides 
> BLAS/LAPACK for it, in order to simplify maintenance of the Octave Forge 
> modules.  Due to the incompatible atlas change and the fact that the virtual 
> packages can't have versions, I had to change the name to denote the change 
> in the version of atlas against which Octave was built.  Unfortunately, this 
> precluded a clean upgrade path.
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/
>

...and that problem is fixed now as well.  Still have a 
second machine that is going to hit the same problems (it is 
slower at building so didn't get to octave yet) but now I 
know what to do...

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] removing old versions of octave...

[Viv Kendon]

On Wed, 2 Oct 2013, Alexander Hansen wrote:

> On 10/2/13 10:22 AM, Viv Kendon wrote:
>> (maintainer Cc'd)
>> 
>> help, how do you remove old versions of octave?
>> 
>> I tried fink remove bundle-octave362-atlas and that didn't remove very
>> much.
>> 
>> I tried (several times, and installed xvfb-run along the way; this is
>> the current version of the output):
>> 
>> fink remove --recursive octave362-atlas-x11
>> Information about 7988 packages read in 0 seconds.
>> WARNING: communications-oct362 is not installed, skipping.
>> Fink will attempt to remove --recursive 1 package
>> 
>> Do you want to continue? [Y/n]
>> /sw/bin/apt-get-lockwait remove octave362-atlas-x11
>> Reading Package Lists... Done
>> Building Dependency Tree... Done
>> You might want to run `apt-get -f install' to correct these:
>> Sorry, but the following packages have unmet dependencies:
>>actuarial-oct362: Depends: octave362-interpreter
>>audio-oct362: Depends: octave362-interpreter
>>benchmark-oct362: Depends: octave362-interpreter
>>bim-oct362: Depends: octave362-interpreter
>>bioinfo-oct362: Depends: octave362-interpreter
>>cgi-oct362: Depends: octave362-interpreter
>>civil-engineering-oct362: Depends: octave362-interpreter
>>communications-oct362: Depends: octave362-interpreter
>>   Depends: signal-oct362 (>= 1.1.3-1) but it is
>> not going to be installed
>>control-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>data-smoothing-oct362: Depends: octave362-interpreter
>>dataframe-oct362: Depends: octave362-interpreter
>>dicom-oct362: Depends: octave362-interpreter
>>econometrics-oct362: Depends: octave362-interpreter
>>engine-oct362: Depends: octave362-interpreter
>>fenv-oct362: Depends: octave362-interpreter
>>financial-oct362: Depends: octave362-interpreter
>>fits-oct362: Depends: octave362-interpreter
>>fl-core-oct362: Depends: octave362-interpreter
>>fpl-oct362: Depends: octave362-interpreter
>>fuzzy-logic-toolkit-oct362: Depends: octave362-interpreter
>>ga-oct362: Depends: octave362-interpreter
>>general-oct362: Depends: octave362-interpreter
>>generate-html-oct362: Depends: octave362-interpreter
>>geometry-oct362: Depends: octave362-interpreter
>>gnuplot-oct362: Depends: octave362-interpreter
>>gsl-oct362: Depends: octave362-interpreter
>>ident-oct362: Depends: octave362-interpreter
>>image-oct362: Depends: octave362-interpreter
>>  Depends: signal-oct362 (>= 1.2.0-1) but it is not going
>> to be installed
>>informationtheory-oct362: Depends: octave362-interpreter
>>integration-oct362: Depends: octave362-interpreter
>>io-oct362: Depends: octave362-interpreter
>>irsa-oct362: Depends: octave362-interpreter
>>linear-algebra-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>lssa-oct362: Depends: octave362-interpreter
>>mapping-oct362: Depends: octave362-interpreter
>>mechanics-oct362: Depends: octave362-interpreter
>>miscellaneous-oct362: Depends: octave362-interpreter
>>missing-functions-oct362: Depends: octave362-interpreter
>>msh-oct362: Depends: octave362-interpreter
>>multicore-oct362: Depends: octave362-interpreter
>>nan-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>ncarray-oct362: Depends: octave362-interpreter
>>nlwing2-oct362: Depends: octave362-interpreter
>>nnet-oct362: Depends: octave362-interpreter
>>nurbs-oct362: Depends: octave362-interpreter
>>ocs-oct362: Depends: octave362-interpreter
>>octcdf-nc4-oct362: Depends: octave362-interpreter
>>octclip-oct362: Depends: octave362-interpreter
>>octgpr-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>octproj-oct362: Depends: octave362-interpreter
>>odebvp-oct362: Depends: octave362-interpreter
>>odepkg-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>openmpi-ext-oct362: Depends: octave362-interpreter
>>optim-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>optiminterp-atlas-oct362: Depends: octave362-interpreter-ptatlas
>>outliers-oct362: Depends: octave362-interpreter
>>parallel-oct362: Depends: octave362-interpreter
>>pdb-oct362: Depends: octave362-interpreter
>>plot-oct362: Depends: octave362-interpreter
>>quaternion-oct362: Depends: octave362-interpreter
>>secs1d-oct362: Depends: octave362-interpreter
>>se

[Fink-users] octave364 dependency problems?

[Viv Kendon]

(maintainer Cc'd)

I tried to update octave364 separately while waiting for a 
reply to my questions about removal:

fink install octave364-atlas-x11
Information about 7988 packages read in 0 seconds.
The following package will be installed or updated:
  octave364-atlas-x11
The following additional package will be installed:
  octave364-atlas-x11-shlibs
Do you want to continue? [Y/n]
Reading buildlock packages...
 All buildlocks accounted for.

While trying to install:
   octave364-atlas-x11-3.6.4-5
   octave364-atlas-x11-shlibs-3.6.4-5

The following inconsistencies found:
   Unsatisfied dependency in octgpr-atlas-oct364: 
octave364-interpreter-ptatlas
   Unsatisfied dependency in control-atlas-oct364: 
octave364-interpreter-ptatlas
   Unsatisfied dependency in optim-atlas-oct364: 
octave364-interpreter-ptatlas
   Unsatisfied dependency in nan-atlas-oct364: 
octave364-interpreter-ptatlas
   Unsatisfied dependency in octave-atlas-x11: 
octave364-atlas-x11 (= 3.6.4-2)
   Unsatisfied dependency in odepkg-atlas-oct364: 
octave364-interpreter-ptatlas
   Unsatisfied dependency in optiminterp-atlas-oct364:
octave364-interpreter-ptatlas
   Unsatisfied dependency in octave364-atlas-x11-dev: 
octave364-atlas-x11-shlibs
(= 3.6.4-2)
   Unsatisfied dependency in octave364-atlas-x11-dev: 
octave364-atlas-x11 (=
3.6.4-2)
   Unsatisfied dependency in linear-algebra-atlas-oct364:
octave364-interpreter-ptatlas

Trying to resolve dependencies...
Could not resolve inconsistent dependencies!

Fink isn't sure how to install the above packages safely. 
You may be able to
fix things by running:

   fink scanpackages
   sudo apt-get update
   sudo apt-get install octave364-atlas-x11=3.6.4-5
octave364-atlas-x11-shlibs=3.6.4-5

Failed: Fink::SysState: Could not resolve inconsistent 
dependencies

I'm not sure whether this is related to my removal problems 
or not...

many thanks,
-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


--
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[Fink-users] removing old versions of octave...

[Viv Kendon]

y 'apt-get -f install' with no 
packages (or specify a solution).
### execution of /sw/bin/apt-get-lockwait failed, exit code 
100
Failed: can't remove package octave362-atlas-x11

I've tried removing packages separately, but that fails, and 
the suggested fix also fails:

sudo apt-get -f install
Reading Package Lists... Done
Building Dependency Tree... Done
Correcting dependencies... Done
The following packages will be REMOVED:
   communications-oct362 ga-oct362 image-oct362
0 packages upgraded, 0 newly installed, 3 to remove and 0 
not upgraded.
52 packages not fully installed or removed.
Need to get 0B of archives. After unpacking 4354kB will be 
freed.
Do you want to continue? [Y/n]
(Reading database ... 276462 files and directories currently 
installed.)
Removing ga-oct362 ...
dyld: Library not loaded: /sw/lib/libqrupdate.1.dylib
   Referenced from: /sw/lib/octave/3.6.2/liboctave.1.dylib
   Reason: image not found
/sw/bin/xvfb-run: line 172: 87346 Trace/BPT trap: 5 
DISPLAY=:$SERVERNUM XAUTHORITY=$AUTHFILE "$@" 2>&1
/sw/bin/dpkg: error processing ga-oct362 (--remove):
  subprocess pre-removal script returned error exit status 
133
dyld: Library not loaded: /sw/lib/libqrupdate.1.dylib
   Referenced from: /sw/lib/octave/3.6.2/liboctave.1.dylib
   Reason: image not found
/sw/bin/xvfb-run: line 172: 87397 Trace/BPT trap: 5 
DISPLAY=:$SERVERNUM XAUTHORITY=$AUTHFILE "$@" 2>&1
dpkg: error while cleaning up:
  subprocess post-installation script returned error exit 
status 133
Removing communications-oct362 ...
dyld: Library not loaded: /sw/lib/libqrupdate.1.dylib
   Referenced from: /sw/lib/octave/3.6.2/liboctave.1.dylib
   Reason: image not found
/sw/bin/xvfb-run: line 172: 87447 Trace/BPT trap: 5 
DISPLAY=:$SERVERNUM XAUTHORITY=$AUTHFILE "$@" 2>&1
/sw/bin/dpkg: error processing communications-oct362 
(--remove):
  subprocess pre-removal script returned error exit status 
133
Removing image-oct362 ...
dyld: Library not loaded: /sw/lib/libqrupdate.1.dylib
   Referenced from: /sw/lib/octave/3.6.2/liboctave.1.dylib
   Reason: image not found
/sw/bin/xvfb-run: line 172: 87497 Trace/BPT trap: 5 
DISPLAY=:$SERVERNUM XAUTHORITY=$AUTHFILE "$@" 2>&1
/sw/bin/dpkg: error processing image-oct362 (--remove):
  subprocess pre-removal script returned error exit status 
133
Errors were encountered while processing:
  ga-oct362
  communications-oct362
  image-oct362
E: Sub-process /sw/bin/dpkg returned an error code (1)


How do I get out of this mess?!  Help much appreciated!

And then how do I avoid a new mess when removing octave363?

(The aim is to end up with just octave364 installed.)

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


--
October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
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Re: [Fink-users] arpack-ng-mpi-atlas-3.1.3-1 failed on 10.7

[Viv Kendon]

On Tue, 9 Apr 2013, Alexander Hansen wrote:

> On 4/9/13 9:41 AM, Viv Kendon wrote:
>> On Tue, 9 Apr 2013, Alexander Hansen wrote:
>>
>>> On 4/9/13 8:04 AM, Viv Kendon wrote:
>>>> On Tue, 9 Apr 2013, Alexander Hansen wrote:
>>>>
>>>>> On 4/9/13 3:42 AM, Viv Kendon wrote:
>>>>>> On Sun, 7 Apr 2013, Alexander Hansen wrote:
>>>>>>
>>>>>>> On 4/7/13 1:51 PM, Viv Kendon wrote:
>>>>>>>> I think this is the relevant part of the logs, if not, I have the
>>>>>>>> rest
>>>>>>>> of it.
>>>>>>>>
>>>>>>>> make[2]: Entering directory
>>>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpa
>>>>>>>> ck-ng-3.1.3/PARPACK'
>>>>>>>> /bin/sh ../libtool --tag=F77   --mode=link /sw/bin/mpif77 -g -O2
>>>>>>>> -no-undefined
>>>>>>>> -version-info 2:0 -Wl,-dead_strip_dylibs -L/sw/lib
>>>>>>>> -L/sw/lib/openmpi -o
>>>>>>>> libparpa
>>>>>>>> ck.la -rpath /sw/lib  ../SRC/libarpacksrc.la
>>>>>>>> ../UTIL/libarpackutil.la
>>>>>>>> ../PARPACK
>>>>>>>> /SRC/MPI/libparpacksrcmpi.la
>>>>>>>> ../PARPACK/UTIL/MPI/libparpackutilmpi.la
>>>>>>>> -ltatlas -
>>>>>>>> ltatlas
>>>>>>>> libtool: link: /sw/bin/gfortran-fsf-4.8 -dynamiclib  -o
>>>>>>>> .libs/libparpack.2.dylib
>>>>>>>> -Wl,-force_load ../SRC/.libs/libarpacksrc.a -Wl,-force_load
>>>>>>>> ../UTIL/.libs/lib
>>>>>>>> arpackutil.a -Wl,-force_load
>>>>>>>> ../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a
>>>>>>>> -Wl,-fo
>>>>>>>> rce_load ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a -L/sw/lib
>>>>>>>> -L/sw/lib/open
>>>>>>>> mpi -ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name
>>>>>>>> /sw/lib/libparpack.2.d
>>>>>>>> ylib -compatibility_version 3 -current_version 3.0
>>>>>>>> -Wl,-single_module
>>>>>>>> Undefined symbols for architecture x86_64:
>>>>>>>>"_mpi_allreduce_", referenced from:
>>>>>>>>_psgetv0_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
>>>>>>>>_psnaitr_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
>>>>>>>>_psnaup2_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
>>>>>>>>_pssaitr_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
>>>>>>>>_pssaup2_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
>>>>>>>>_psnorm2_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
>>>>>>>>_pdgetv0_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
>>>>>>>>...
>>>>>>>>"_mpi_comm_rank_", referenced from:
>>>>>>>>_psnaupd_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
>>>>>>>>_pssaupd_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
>>>>>>>>_pdnaupd_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
>>>>>>>>_pdsaupd_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
>>>>>>>>_pcnaupd_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
>>>>>>>>_pcgetv0_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
>>>>>>>>_pznaupd_ in
>>>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
>>>>>>>>...
>>>>>>>> ld: symbol(s) not found for architecture x86_64
>>>>>>>> collect2: error: ld returned 1 exit status
>>>>>>>> make[2]: *** [libparpack.la] Error

Re: [Fink-users] arpack-ng-mpi-atlas-3.1.3-1 failed on 10.7

[Viv Kendon]

On Tue, 9 Apr 2013, Alexander Hansen wrote:

> On 4/9/13 8:04 AM, Viv Kendon wrote:
>> On Tue, 9 Apr 2013, Alexander Hansen wrote:
>> 
>>> On 4/9/13 3:42 AM, Viv Kendon wrote:
>>>> On Sun, 7 Apr 2013, Alexander Hansen wrote:
>>>> 
>>>>> On 4/7/13 1:51 PM, Viv Kendon wrote:
>>>>>> I think this is the relevant part of the logs, if not, I have the rest
>>>>>> of it.
>>>>>> 
>>>>>> make[2]: Entering directory
>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpa
>>>>>> ck-ng-3.1.3/PARPACK'
>>>>>> /bin/sh ../libtool --tag=F77   --mode=link /sw/bin/mpif77 -g -O2
>>>>>> -no-undefined
>>>>>> -version-info 2:0 -Wl,-dead_strip_dylibs -L/sw/lib
>>>>>> -L/sw/lib/openmpi -o
>>>>>> libparpa
>>>>>> ck.la -rpath /sw/lib  ../SRC/libarpacksrc.la ../UTIL/libarpackutil.la
>>>>>> ../PARPACK
>>>>>> /SRC/MPI/libparpacksrcmpi.la ../PARPACK/UTIL/MPI/libparpackutilmpi.la
>>>>>> -ltatlas -
>>>>>> ltatlas
>>>>>> libtool: link: /sw/bin/gfortran-fsf-4.8 -dynamiclib  -o
>>>>>> .libs/libparpack.2.dylib
>>>>>> -Wl,-force_load ../SRC/.libs/libarpacksrc.a -Wl,-force_load
>>>>>> ../UTIL/.libs/lib
>>>>>> arpackutil.a -Wl,-force_load
>>>>>> ../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a
>>>>>> -Wl,-fo
>>>>>> rce_load ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a -L/sw/lib
>>>>>> -L/sw/lib/open
>>>>>> mpi -ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name
>>>>>> /sw/lib/libparpack.2.d
>>>>>> ylib -compatibility_version 3 -current_version 3.0 -Wl,-single_module
>>>>>> Undefined symbols for architecture x86_64:
>>>>>>"_mpi_allreduce_", referenced from:
>>>>>>_psgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
>>>>>>_psnaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
>>>>>>_psnaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
>>>>>>_pssaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
>>>>>>_pssaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
>>>>>>_psnorm2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
>>>>>>_pdgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
>>>>>>...
>>>>>>"_mpi_comm_rank_", referenced from:
>>>>>>_psnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
>>>>>>_pssaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
>>>>>>_pdnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
>>>>>>_pdsaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
>>>>>>_pcnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
>>>>>>_pcgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
>>>>>>_pznaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
>>>>>>...
>>>>>> ld: symbol(s) not found for architecture x86_64
>>>>>> collect2: error: ld returned 1 exit status
>>>>>> make[2]: *** [libparpack.la] Error 1
>>>>>> make[2]: Leaving directory
>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
>>>>>> 
>>>>>> make[1]: *** [all-recursive] Error 1
>>>>>> make[1]: Leaving directory
>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
>>>>>> 
>>>>>> make: *** [all-recursive] Error 1
>>>>>> ### execution of /tmp/fink.ZL1fo failed, exit code 2
>>>>>> 
>>>>>> Package manager version: 0.34.7
>>>>>> Distribution version: selfupdate-rsync Sun Apr  7 20:33:31 2013, 10.7,
>>>>>> x86_64
>>>>>> Trees: local/main stable/main
>>>>>> Xcode.app: 4.6.1
>>>>>> Xcode command-line tools: 4.6.0.0.1.1362189000
>>>>>> Max. Fink build jobs:  4
>>>>>> 
>>>>>> 
>>>>>> open-mpi updated to 1.6.4-2 just prior to this failure.
>>>>>&g

Re: [Fink-users] arpack-ng-mpi-atlas-3.1.3-1 failed on 10.7

[Viv Kendon]

On Tue, 9 Apr 2013, Alexander Hansen wrote:

> On 4/9/13 3:42 AM, Viv Kendon wrote:
>> On Sun, 7 Apr 2013, Alexander Hansen wrote:
>> 
>>> On 4/7/13 1:51 PM, Viv Kendon wrote:
>>>> I think this is the relevant part of the logs, if not, I have the rest
>>>> of it.
>>>> 
>>>> make[2]: Entering directory
>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpa
>>>> ck-ng-3.1.3/PARPACK'
>>>> /bin/sh ../libtool --tag=F77   --mode=link /sw/bin/mpif77 -g -O2
>>>> -no-undefined
>>>> -version-info 2:0 -Wl,-dead_strip_dylibs -L/sw/lib -L/sw/lib/openmpi -o
>>>> libparpa
>>>> ck.la -rpath /sw/lib  ../SRC/libarpacksrc.la ../UTIL/libarpackutil.la
>>>> ../PARPACK
>>>> /SRC/MPI/libparpacksrcmpi.la ../PARPACK/UTIL/MPI/libparpackutilmpi.la
>>>> -ltatlas -
>>>> ltatlas
>>>> libtool: link: /sw/bin/gfortran-fsf-4.8 -dynamiclib  -o
>>>> .libs/libparpack.2.dylib
>>>> -Wl,-force_load ../SRC/.libs/libarpacksrc.a -Wl,-force_load
>>>> ../UTIL/.libs/lib
>>>> arpackutil.a -Wl,-force_load ../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a
>>>> -Wl,-fo
>>>> rce_load ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a -L/sw/lib
>>>> -L/sw/lib/open
>>>> mpi -ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name
>>>> /sw/lib/libparpack.2.d
>>>> ylib -compatibility_version 3 -current_version 3.0 -Wl,-single_module
>>>> Undefined symbols for architecture x86_64:
>>>>"_mpi_allreduce_", referenced from:
>>>>_psgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
>>>>_psnaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
>>>>_psnaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
>>>>_pssaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
>>>>_pssaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
>>>>_psnorm2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
>>>>_pdgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
>>>>...
>>>>"_mpi_comm_rank_", referenced from:
>>>>_psnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
>>>>_pssaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
>>>>_pdnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
>>>>_pdsaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
>>>>_pcnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
>>>>_pcgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
>>>>_pznaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
>>>>...
>>>> ld: symbol(s) not found for architecture x86_64
>>>> collect2: error: ld returned 1 exit status
>>>> make[2]: *** [libparpack.la] Error 1
>>>> make[2]: Leaving directory
>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
>>>> make[1]: *** [all-recursive] Error 1
>>>> make[1]: Leaving directory
>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
>>>> make: *** [all-recursive] Error 1
>>>> ### execution of /tmp/fink.ZL1fo failed, exit code 2
>>>> 
>>>> Package manager version: 0.34.7
>>>> Distribution version: selfupdate-rsync Sun Apr  7 20:33:31 2013, 10.7,
>>>> x86_64
>>>> Trees: local/main stable/main
>>>> Xcode.app: 4.6.1
>>>> Xcode command-line tools: 4.6.0.0.1.1362189000
>>>> Max. Fink build jobs:  4
>>>> 
>>>> 
>>>> open-mpi updated to 1.6.4-2 just prior to this failure.
>>>> 
>>>> TIA,
>>>> -- Viv
>>>> 
>>>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>>>> tel: +44 113 343 4864  Physics and Astronomy
>>>> Quantum Information GroupUniversity of Leeds
>>>> 
>>> 
>>> Thanks for the report.  It looks like arpack-ng upstream tweaked the
>>> parallel library build, and I naively didn't test that.  A fixed
>>> version should be available shortly via selfupdate.
>> 
>> I think what is failing now is that it is looking for the wrong source
>> package name?
>> 
>> curl --connect-timeout 30 -f -L -A 'fink/0.34.7' -O
>&

Re: [Fink-users] arpack-ng-mpi-atlas-3.1.3-1 failed on 10.7

[Viv Kendon]

On Sun, 7 Apr 2013, Alexander Hansen wrote:

> On 4/7/13 1:51 PM, Viv Kendon wrote:
>> I think this is the relevant part of the logs, if not, I have the rest
>> of it.
>> 
>> make[2]: Entering directory
>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpa
>> ck-ng-3.1.3/PARPACK'
>> /bin/sh ../libtool --tag=F77   --mode=link /sw/bin/mpif77 -g -O2
>> -no-undefined
>> -version-info 2:0 -Wl,-dead_strip_dylibs -L/sw/lib -L/sw/lib/openmpi -o
>> libparpa
>> ck.la -rpath /sw/lib  ../SRC/libarpacksrc.la ../UTIL/libarpackutil.la
>> ../PARPACK
>> /SRC/MPI/libparpacksrcmpi.la ../PARPACK/UTIL/MPI/libparpackutilmpi.la
>> -ltatlas -
>> ltatlas
>> libtool: link: /sw/bin/gfortran-fsf-4.8 -dynamiclib  -o
>> .libs/libparpack.2.dylib
>> -Wl,-force_load ../SRC/.libs/libarpacksrc.a -Wl,-force_load
>> ../UTIL/.libs/lib
>> arpackutil.a -Wl,-force_load ../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a
>> -Wl,-fo
>> rce_load ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a -L/sw/lib
>> -L/sw/lib/open
>> mpi -ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name
>> /sw/lib/libparpack.2.d
>> ylib -compatibility_version 3 -current_version 3.0 -Wl,-single_module
>> Undefined symbols for architecture x86_64:
>>"_mpi_allreduce_", referenced from:
>>_psgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
>>_psnaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
>>_psnaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
>>_pssaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
>>_pssaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
>>_psnorm2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
>>_pdgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
>>...
>>"_mpi_comm_rank_", referenced from:
>>_psnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
>>_pssaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
>>_pdnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
>>_pdsaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
>>_pcnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
>>_pcgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
>>_pznaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
>>...
>> ld: symbol(s) not found for architecture x86_64
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [libparpack.la] Error 1
>> make[2]: Leaving directory
>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory
>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
>> make: *** [all-recursive] Error 1
>> ### execution of /tmp/fink.ZL1fo failed, exit code 2
>> 
>> Package manager version: 0.34.7
>> Distribution version: selfupdate-rsync Sun Apr  7 20:33:31 2013, 10.7,
>> x86_64
>> Trees: local/main stable/main
>> Xcode.app: 4.6.1
>> Xcode command-line tools: 4.6.0.0.1.1362189000
>> Max. Fink build jobs:  4
>> 
>> 
>> open-mpi updated to 1.6.4-2 just prior to this failure.
>> 
>> TIA,
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>> 
>
> Thanks for the report.  It looks like arpack-ng upstream tweaked the parallel 
> library build, and I naively didn't test that.  A fixed version should be 
> available shortly via selfupdate.

I think what is failing now is that it is looking for the 
wrong source package name?

curl --connect-timeout 30 -f -L -A 'fink/0.34.7' -O 
http://distfiles.master.finkmirrors.net/arpack-ng-mpi-3.1.3.tar.gz
   % Total% Received % Xferd  Average Speed   Time 
Time Time  Current
  Dload  Upload   Total 
SpentLeft  Speed
   0 00 00 0  0  0 --:--:-- 
--:--:-- --:--:-- 0
curl: (22) The requested URL returned error: 404

i.e., -mpi shouldn't be in there?

TIA,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] atlas-3.10.1-1 failed on 10.6 server

[Viv Kendon]

On Sun, 7 Apr 2013, Jack Howarth wrote:

> On Sun, Apr 07, 2013 at 11:22:08PM +0100, Viv Kendon wrote:
>> On Sun, 7 Apr 2013, Jack Howarth wrote:
>>
>>> On Sun, Apr 07, 2013 at 10:21:25PM +0100, Viv Kendon wrote:
>>>> ...but it worked on 10.7 client.  I tried to diff the two build logs, but
>>>> that's messy, and I'm still not sure what the failure actually is.
>>>> Ostensibly it is:
>>>>
>>>>  chmod -R a-x /sw/src/fink.build/root-atlas-3.10.1-1/sw/lib/*
>>>> chmod: cannot operate on dangling symlink
>>>> `/sw/src/fink.build/root-atlas-3.10.1-
>>>> 1/sw/lib/libcblas.dylib'
>>>> chmod: cannot operate on dangling symlink
>>>> `/sw/src/fink.build/root-atlas-3.10.1-
>>>> 1/sw/lib/libf77blas.dylib'
>>>> chmod: cannot operate on dangling symlink
>>>> `/sw/src/fink.build/root-atlas-3.10.1-
>>>> 1/sw/lib/liblapack.dylib'
>>>> chmod: cannot operate on dangling symlink
>>>> `/sw/src/fink.build/root-atlas-3.10.1-
>>>> 1/sw/lib/libptcblas.dylib'
>>>> chmod: cannot operate on dangling symlink
>>>> `/sw/src/fink.build/root-atlas-3.10.1-
>>>> 1/sw/lib/libptf77blas.dylib'
>>>> chmod: cannot operate on dangling symlink
>>>> `/sw/src/fink.build/root-atlas-3.10.1-
>>>> 1/sw/lib/libptlapack.dylib'
>>>> ### execution of /tmp/fink.zzyP6 failed, exit code 1
>>>> ### execution of /tmp/fink.JV6pj failed, exit code 1
>>>>
>>>> but obviously this means something went wrong earlier.

Actually, for once, this really is the error, not the 
symptom!

>> 
>>>>
>>>> I can supply the whole log if necessary, let me know.
>>>
>>> You will have to provide the full compressed log. The atlas build is quite
>>> ugly as it's makfiles often try compiles and copies that will fail until
>>> it the appropriate one succeeds. I suspect you will find some sort of
>>> error in the linkages of libsatlas.dylib and libtatlas.dylib. Afterwards
>>> you might also try removing the atlas package before you build the newer one
>>> and see if that helps.
>>>   Jack
>>>
>>>> Package manager version: 0.34.7
>>>> Distribution version: selfupdate-rsync Sun Apr  7 20:26:24 2013, 10.6,
>>>> x86_64
>>>> Trees: local/main local/crypto stable/main stable/crypto unstable/main
>>>> unstable/crypto
>>>> Xcode.app: 3.2.6
>>>> Xcode command-line tools: 3.2.6
>>>> atlas-3.10.1-1 is set to build with only one job.
>>
>> I already removed the atlas (but not atlas-shlibs) before running this
>> attempt: log attached.
>
> Do you happen to have coreutils installed on the machine 
> that completes the packaging but not on the other? If so, 
> does installing coreutils solve the problem? From your 
> log, the libstatlas.dylib and libtatlas.dylib files are 
> copied without complaint into destroot for packaging. 
> However when chomd is run on the symlinks (which point 
> these files in %p/lib), the chmod errors occur.

both had coreutils installed, the one that failed also had 
coreutils-default.  I removed coreutils-default, and it 
worked.  It then fails to install, but trying again works 
(because the offending file has been removed in the 
successful atlas-shlibs install):

Unpacking atlas (from .../atlas_3.10.1-1_darwin-x86_64.deb) 
...
/sw/bin/dpkg: error processing 
/sw/fink/dists/stable/main/binary-darwin-x86_64/sci/atlas_3.10.1-1_darwin-x86_64.deb
 
(--install):
  trying to overwrite `/sw/lib/libcblas.dylib', which is also 
in package atlas-shlibs
Preparing to replace atlas-shlibs 3.9.76-3 (using 
.../atlas-shlibs_3.10.1-1_darwin-x86_64.deb) ...
Unpacking replacement atlas-shlibs ...
Setting up atlas-shlibs (3.10.1-1) ...

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] atlas-3.10.1-1 failed on 10.6 server

[Viv Kendon]

-pointer -O3 -m64 -mfpm
ath=sse -m64 -fPIC'
./xuserflag -i ATL_tMpFiLe -o zcases.flg
gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' 
or '-march=' instead
FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= 
switch
  int main(){}
  ^
cc1: error: unrecognized command line option "-maltivec"
cc1: error: unrecognized command line option "-mabi=altivec"
gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' 
or '-march=' instead
FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= 
switch
  int main(){}
  ^
gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' 
or '-march=' instead
FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= 
switch
  int main(){}
  ^
gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' 
or '-march=' instead
FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= 
switch
  int main(){}
  ^
gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' 
or '-march=' instead
FlagCheck.c:1:0: error: bad value (970) for -mtune= switch
  int main(){}
  ^
gcc-fsf-4.8: error: unrecognized command line option 
'-mips4'
gcc-fsf-4.8: error: unrecognized command line option 
'-mips4'
gcc-fsf-4.8: error: unrecognized command line option 
'-mips4'
gcc-fsf-4.8: error: unrecognized command line option 
'-mips4'
gcc-fsf-4.8: error: unrecognized command line option '-mvsx'
gcc-fsf-4.8: error: unrecognized command line option 
'-mfpu=vfpv3'

But I think they almost all occur in the successful build 
log as well.

I can supply the whole log if necessary, let me know.

Package manager version: 0.34.7
Distribution version: selfupdate-rsync Sun Apr  7 20:26:24 
2013, 10.6, x86_64
Trees: local/main local/crypto stable/main stable/crypto 
unstable/main unstable/crypto
Xcode.app: 3.2.6
Xcode command-line tools: 3.2.6
atlas-3.10.1-1 is set to build with only one job.

TIA,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] arpack-ng-mpi-atlas-3.1.3-1 failed on 10.7

[Viv Kendon]

I think this is the relevant part of the logs, if not, I 
have the rest of it.

make[2]: Entering directory 
`/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpa
ck-ng-3.1.3/PARPACK'
/bin/sh ../libtool --tag=F77   --mode=link /sw/bin/mpif77 
-g -O2 -no-undefined
-version-info 2:0 -Wl,-dead_strip_dylibs -L/sw/lib 
-L/sw/lib/openmpi -o libparpa
ck.la -rpath /sw/lib  ../SRC/libarpacksrc.la 
../UTIL/libarpackutil.la ../PARPACK
/SRC/MPI/libparpacksrcmpi.la 
../PARPACK/UTIL/MPI/libparpackutilmpi.la -ltatlas -
ltatlas
libtool: link: /sw/bin/gfortran-fsf-4.8 -dynamiclib  -o 
.libs/libparpack.2.dylib
-Wl,-force_load ../SRC/.libs/libarpacksrc.a 
-Wl,-force_load ../UTIL/.libs/lib
arpackutil.a -Wl,-force_load 
../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a -Wl,-fo
rce_load ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a 
-L/sw/lib -L/sw/lib/open
mpi -ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name 
/sw/lib/libparpack.2.d
ylib -compatibility_version 3 -current_version 3.0 
-Wl,-single_module
Undefined symbols for architecture x86_64:
   "_mpi_allreduce_", referenced from:
   _psgetv0_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
   _psnaitr_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
   _psnaup2_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
   _pssaitr_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
   _pssaup2_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
   _psnorm2_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
   _pdgetv0_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
   ...
   "_mpi_comm_rank_", referenced from:
   _psnaupd_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
   _pssaupd_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
   _pdnaupd_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
   _pdsaupd_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
   _pcnaupd_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
   _pcgetv0_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
   _pznaupd_ in 
libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
   ...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [libparpack.la] Error 1
make[2]: Leaving directory 
`/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory 
`/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK'
make: *** [all-recursive] Error 1
### execution of /tmp/fink.ZL1fo failed, exit code 2

Package manager version: 0.34.7
Distribution version: selfupdate-rsync Sun Apr  7 20:33:31 
2013, 10.7, x86_64
Trees: local/main stable/main
Xcode.app: 4.6.1
Xcode command-line tools: 4.6.0.0.1.1362189000
Max. Fink build jobs:  4


open-mpi updated to 1.6.4-2 just prior to this failure.

TIA,
-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] maxima-5.29.1-5 update problems...

[Viv Kendon]

On Fri, 5 Apr 2013, Alexander Hansen wrote:

> On 4/5/13 10:48 AM, Viv Kendon wrote:
>> I'm seeing the same error on 10.6 server and 10.7 client:
>> 
>> compilation of maxima stops here:
>> 
>> ; compiling (DEFUN GF-X^P-POWERS ...)
>> debugger invoked on a TYPE-ERROR in thread
>> #:
>>The value #> {100332D8E3}>
>>is not of type
>>  SB-C::LAMBDA-VAR.
>> 
>> Type HELP for debugger help, or (SB-EXT:EXIT) to exit from SBCL.
>> 
>> restarts (invokable by number or by possibly-abbreviated name):
>>0: [CONTINUE] Ignore runtime option --eval "(progn (load
>> \"../lisp-utils/defsystem.lisp\") (funcall (intern (symbol-name
>> :operate-on-system) :mk) \"maxima\" :compile :verbose t) (sb-ext:quit))".
>>1: [ABORT   ] Skip rest of --eval and --load options.
>>2:Skip to toplevel READ/EVAL/PRINT loop.
>>3: [EXIT] Exit SBCL (calling #'EXIT, killing the process).
>> 
>> ((LAMBDA (#:WHOLE-VAR-781 &AUX (#:N-ENV-782 SB-C:*LEXENV*)) :IN
>> "/sw/src/fink.build/sbcl-116-maxima-1.1.6-1/sbcl-1.1.6/src/cold/compile-cold-sbcl.lisp")
>> (SB-KERNEL:%SVSET A 0 (LIST 1 1)))
>> 0]
>> 
>> 
>> I choose 3 and it aborts...
>> 
>> ; compilation aborted after 0:00:19.721
>> ;
>> ; compilation unit aborted
>> ;   caught 2 fatal ERROR conditions
>> ;   caught 3 WARNING conditions
>> ;   caught 45 STYLE-WARNING conditions
>> ;   printed 33 notes
>> make[1]: *** [binary-sbcl/maxima.core] Error 1
>> make[1]: Leaving directory
>> `/sw/src/fink.build/maxima-5.29.1-5/maxima-5.29.1/src'
>> make: *** [all-recursive] Error 1
>> ### execution of /tmp/fink.iWA46 failed, exit code 2
>> ### execution of /tmp/fink.yaecP failed, exit code 2
>> 
>> I removed everything maxima related that wasn't up to date and tried
>> again, but no change in the error.  I only have
>>
>>   i   sbcl-116-maxima  1.1.6-1  ANSI Common Lisp implementation
>> 
>> installed and I'm running "fink install bundle-maxima-x11"
>> 
>> System info:
>> 
>> Package manager version: 0.34.7
>> Distribution version: selfupdate-rsync Fri Apr  5 12:54:03 2013, 10.6,
>> x86_64
>> Trees: local/main local/crypto stable/main stable/crypto unstable/main
>> unstable/crypto
>> Xcode.app: 3.2.6
>> Xcode command-line tools: 3.2.6
>> Max. Fink build jobs:  4
>> 
>> and
>> 
>> Package manager version: 0.34.7
>> Distribution version: selfupdate-rsync Fri Apr  5 12:54:37 2013, 10.7,
>> x86_64
>> Trees: local/main stable/main
>> Xcode.app: 4.6.1
>> Xcode command-line tools: 4.6.0.0.1.1362189000
>> Max. Fink build jobs:  4
>> 
> Woops.  I thought I did a test build, but apparently I missed doing that.  It 
> didn't work for me on 10.8, either, so maybe upstream did something bad for 
> all OS X.
>
> Look for a new  maxima which reverts to SBCL-1.1.5 (known to work) shortly. 
> If "fink show-deps maxima" has sbcl-115-maxima in it, then you have the right 
> one.

Many thanks, maxima 5.30.0-1 successfully installed with 
sbcl-115-maxima on 10.7.  (I'm having atlas update problems 
on 10.6 and haven't got to maxima yet...)

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] maxima-5.29.1-5 update problems...

[Viv Kendon]

I'm seeing the same error on 10.6 server and 10.7 client:

compilation of maxima stops here:

; compiling (DEFUN GF-X^P-POWERS ...)
debugger invoked on a TYPE-ERROR in thread
#:
   The value #
   is not of type
 SB-C::LAMBDA-VAR.

Type HELP for debugger help, or (SB-EXT:EXIT) to exit from 
SBCL.

restarts (invokable by number or by possibly-abbreviated 
name):
   0: [CONTINUE] Ignore runtime option --eval "(progn (load 
\"../lisp-utils/defsystem.lisp\") (funcall (intern 
(symbol-name :operate-on-system) :mk) \"maxima\" :compile 
:verbose t) (sb-ext:quit))".
   1: [ABORT   ] Skip rest of --eval and --load options.
   2:Skip to toplevel READ/EVAL/PRINT loop.
   3: [EXIT] Exit SBCL (calling #'EXIT, killing the 
process).

((LAMBDA (#:WHOLE-VAR-781 &AUX (#:N-ENV-782 SB-C:*LEXENV*)) 
:IN 
"/sw/src/fink.build/sbcl-116-maxima-1.1.6-1/sbcl-1.1.6/src/cold/compile-cold-sbcl.lisp")
 
(SB-KERNEL:%SVSET A 0 (LIST 1 1)))
0]


I choose 3 and it aborts...

; compilation aborted after 0:00:19.721
;
; compilation unit aborted
;   caught 2 fatal ERROR conditions
;   caught 3 WARNING conditions
;   caught 45 STYLE-WARNING conditions
;   printed 33 notes
make[1]: *** [binary-sbcl/maxima.core] Error 1
make[1]: Leaving directory 
`/sw/src/fink.build/maxima-5.29.1-5/maxima-5.29.1/src'
make: *** [all-recursive] Error 1
### execution of /tmp/fink.iWA46 failed, exit code 2
### execution of /tmp/fink.yaecP failed, exit code 2

I removed everything maxima related that wasn't up to date 
and tried again, but no change in the error.  I only have

  i   sbcl-116-maxima  1.1.6-1  ANSI Common Lisp 
implementation

installed and I'm running "fink install bundle-maxima-x11"

System info:

Package manager version: 0.34.7
Distribution version: selfupdate-rsync Fri Apr  5 12:54:03 
2013, 10.6, x86_64
Trees: local/main local/crypto stable/main stable/crypto 
unstable/main unstable/crypto
Xcode.app: 3.2.6
Xcode command-line tools: 3.2.6
Max. Fink build jobs:  4

and

Package manager version: 0.34.7
Distribution version: selfupdate-rsync Fri Apr  5 12:54:37 
2013, 10.7, x86_64
Trees: local/main stable/main
Xcode.app: 4.6.1
Xcode command-line tools: 4.6.0.0.1.1362189000
Max. Fink build jobs:  4


many TIA,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] image-oct362-2.0.0-1 failure on 10.6 server

[Viv Kendon]

On Sat, 16 Mar 2013, Alexander Hansen wrote:

> On 3/16/13 10:13 AM, Viv Kendon wrote:
>> Many thanks, nearly there...new error below, old error snipped:
>>
>> On Sat, 16 Mar 2013, Alexander Hansen wrote:
>>
>>> On 3/16/13 5:00 AM, Viv Kendon wrote:
>>>> I am not sure when image-oct362 last built for me, I have been updating
>>>> the rest by hand for a while.  Should I perhaps just update to octave
>>>> 364 instead?
>>>>
>>>> 
>>>>
>>> Oops.  That was supposed to be "mkoctfile-gcc4.7"--it's autogenerated
>>> and I picked the wrong format.   A fixed has been sent out, and it will
>>> be available via selfupdate shortly.
>>
>> And after it arrived, I tried again. Now I get (on a headless server):
>>
>> Preparing to replace image-oct362 1.0.15-4 (using
>> .../image-oct362_2.0.0-1_darwin-x86_64.deb) ...
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> dpkg: warning - old pre-removal script returned error exit status 1
>> dpkg - trying script from the new package instead ...
>> /sw/bin/xvfb-run: line 172:
>> /sw/share/octave/3.6.2/image-2.0.0/octave-forge-prerm: No such file or
>> directory
>> /sw/bin/dpkg: error processing
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/image-oct362_2.0.0-1_darwin-x86_64.deb
>> (--install):
>>  subprocess new pre-removal script returned error exit status 127
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> dpkg: error while cleaning up:
>>  subprocess post-installation script returned error exit status 1
>> Errors were encountered while processing:
>>
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/image-oct362_2.0.0-1_darwin-x86_64.deb
>>
>> ### execution of /sw/bin/dpkg-lockwait failed, exit code 1
>> Updating the list of locally available binary packages.
>> Scanning dists/stable/main/binary-darwin-x86_64
>> New package:
>> dists/stable/main/binary-darwin-x86_64/sci/image-oct362_2.0.0-1_darwin-x86_64.deb
>>
>> Failed: can't install package image-oct362-2.0.0-1
>>
>>
>> The rest of octave 362 has updated without problem...
>>
>> many thanks,
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>>
>
> [ The optional use of "xvfb-run" is common to all of the Octave Forge
> packages, and was motivated by a prior bug report from you. :-) ]
>
> I probably should have put the "octave-forge-prerm" and
> "octave-forge-postinst" scripts in a directory that doesn't have the
> package version, since that makes the new and old versions incompatible.
> Sorry about that.
>
> See if you can use "xvfb-run fink update image-oct362" to work around this.

Nope, I get:

/sw/bin/xvfb-run: line 164: 25297 Trace/BPT trap 
XAUTHORITY=$AUTHFILE Xvfb ":$SERVERNUM" $XVFBARGS $LISTENTCP 
>> "$ERRORFILE" 2>&1
Xvfb failed to start

even after removing my .Xauthority file.

> If not, try editing /sw/var/lib/dpkg/info/image-oct362 as a superuser

  -- added .prerm to that

> and change
>
> /sw/share/octave/3.6.2/image-1.0.15/octave-forge-prerm
>
> to
>
> xvfb-run /sw/share/octave/3.6.2/image-1.0.15/octave-forge-prerm

and that worked -- many thanks!

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] image-oct362-2.0.0-1 failure on 10.6 server

[Viv Kendon]

Many thanks, nearly there...new error below, old error 
snipped:

On Sat, 16 Mar 2013, Alexander Hansen wrote:

> On 3/16/13 5:00 AM, Viv Kendon wrote:
>> I am not sure when image-oct362 last built for me, I have been updating
>> the rest by hand for a while.  Should I perhaps just update to octave
>> 364 instead?
>>
>> 
>>
> Oops.  That was supposed to be "mkoctfile-gcc4.7"--it's autogenerated
> and I picked the wrong format.   A fixed has been sent out, and it will
> be available via selfupdate shortly.

And after it arrived, I tried again. Now I get (on a 
headless server):

Preparing to replace image-oct362 1.0.15-4 (using 
.../image-oct362_2.0.0-1_darwin-x86_64.deb) ...
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
dpkg: warning - old pre-removal script returned error exit 
status 1
dpkg - trying script from the new package instead ...
/sw/bin/xvfb-run: line 172: 
/sw/share/octave/3.6.2/image-2.0.0/octave-forge-prerm: No 
such file or directory
/sw/bin/dpkg: error processing 
/sw/fink/dists/stable/main/binary-darwin-x86_64/sci/image-oct362_2.0.0-1_darwin-x86_64.deb
 
(--install):
  subprocess new pre-removal script returned error exit 
status 127
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
dpkg: error while cleaning up:
  subprocess post-installation script returned error exit 
status 1
Errors were encountered while processing:

/sw/fink/dists/stable/main/binary-darwin-x86_64/sci/image-oct362_2.0.0-1_darwin-x86_64.deb
### execution of /sw/bin/dpkg-lockwait failed, exit code 1
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-x86_64
New package: 
dists/stable/main/binary-darwin-x86_64/sci/image-oct362_2.0.0-1_darwin-x86_64.deb
Failed: can't install package image-oct362-2.0.0-1


The rest of octave 362 has updated without problem...

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] image-oct362-2.0.0-1 failure on 10.6 server

[Viv Kendon]

I am not sure when image-oct362 last built for me, I have 
been updating the rest by hand for a while.  Should I 
perhaps just update to octave 364 instead?



image/inst/wavelength2rgb.m
perl -pi -e 's/^(MKOCTFILE.*mkoctfile)/\1-gcc47/' 
src/Makefile
/tmp/fink.UTOy7
#!/bin/sh -ev
 if [ $UID -ne 0 ]
 then
 echo "image-oct362 cannot be built with 
--build-as-nobody"
 exit 1
 fi
 export OCTAVE=/sw/bin/octave-3.6.2
 # repack tarball, since octave-3.4.3 appears not to 
want to install
 # from directories
 cd src
 ./configure --prefix=/sw
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out



configure: creating ./config.status
config.status: creating config.h
make
mkoctfile-gcc47 -Wall __spatial_filtering__.cc
make: mkoctfile-gcc47: Command not found
make: *** [__spatial_filtering__.oct] Error 127
### execution of /tmp/fink.UTOy7 failed, exit code 2



Package manager version: 0.34.6
Distribution version: selfupdate-rsync Sat Mar 16 10:19:19 
2013, 10.6, x86_64
Trees: local/main local/crypto stable/main stable/crypto 
unstable/main unstable/crypto
Xcode.app: 3.2.6
Xcode command-line tools: 3.2.6
image-oct362-2.0.0-1 is set to build with only one job.

and the contents of  /tmp/fink.UTOy7 are:
(indented by one space to avoid spurious line wrapping in 
email)

  #!/bin/sh -ev
  if [ $UID -ne 0 ]
  then
  echo "image-oct362 cannot be built with --build-as-nobody"
  exit 1
  fi
  export OCTAVE=/sw/bin/octave-3.6.2
  # repack tarball, since octave-3.4.3 appears not to want to install
  # from directories
  cd src
  ./configure --prefix=/sw
  make
  cd ../..
  tar -cf image-2.0.0.tar image
  cd /sw/src/fink.build/image-oct362-2.0.0-1/image
  pkgsrc=image-2.0.0.tar

  /sw/share/octave/3.6.2/scripts/octave-forge-compile.sh $pkgsrc

I have more of the build log if you need it, let me know.

tia,
-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] poppler4 patch checksum mismatch on 10.6

[Viv Kendon]

(Maintainer Cc'd)  I'm getting

Failed: PatchFile 
"/sw/fink/dists/stable/main/finkinfo/libs/poppler4.patch" 
checksum does not match!
Actual: 7a749c622a60ff1c7948d87aaf3de01f
Expected: 1e09765ff4ec9bf41bfc4776906c2ba4

on my 10.6 server, which is stopping poppler4-glib-shlibs 
from updating...

tia,
-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] dependency problems bundle-maxima-x11-20120812-2

[Viv Kendon]

Many thanks, seems to be OK now.
-- Viv

On Wed, 21 Nov 2012, Alexander Hansen wrote:

> On 11/21/12 9:30 AM, Viv Kendon wrote:
>>
>> Can't resolve dependency "gnuplot-bin (-x11 = -x11) xmaxima-x11" for
>> package
>> "bundle-maxima-x11-20120812-2" (no matching packages/versions found)
>>
>> on 10.6 and 10.7
>>
>> I've tried various combinations of removing everything maxima related
>> and updating gnuplot, to no avail.
>>
>> fink list -ti gnuplot
>>  i  gnuplot 4.6.1-1 Command-driven interactive plotting program
>>  p  gnuplot-bin     [virtual package]
>>
>> TIA
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>>
>
> Oops.  There was a missing comma after gnuplot-bin in the Depends list.
> I was just now able to upload a fix, so you should see that via
> selfupdate soon.
>
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/
>
> --
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tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] dependency problems bundle-maxima-x11-20120812-2

[Viv Kendon]

Can't resolve dependency "gnuplot-bin (-x11 = -x11) 
xmaxima-x11" for package
"bundle-maxima-x11-20120812-2" (no matching 
packages/versions found)

on 10.6 and 10.7

I've tried various combinations of removing everything 
maxima related and updating gnuplot, to no avail.

fink list -ti gnuplot
  i  gnuplot 4.6.1-1 Command-driven interactive plotting program
  p  gnuplot-bin [virtual package]

TIA
-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] dependency problem for openmpi-ext-oct362-1.1.0-1

[Viv Kendon]

On Fri, 28 Sep 2012, Alexander Hansen wrote:

> On 9/28/12 9:17 AM, Viv Kendon wrote:
>> On Fri, 28 Sep 2012, Alexander Hansen wrote:
>>
>>> On 9/28/12 5:58 AM, Viv Kendon wrote:
>>>> On Thu, 27 Sep 2012, Alexander Hansen wrote:
>>>>
>>>>> On 9/27/12 8:16 AM, Viv Kendon wrote:
>>>>>>
>>>>>> 10.6.8 server; update-all complains
>>>>>>
>>>>>> Can't resolve dependency "liboctave362-gcc46-dev" for package
>>>>>> "openmpi-ext-oct362-1.1.0-1" (no matching packages/versions found)
>>>>>>
>>>>>> TIA
>>>>>> -- Viv
>>>>>
>>>>> Thanks.  A fix should be available shortly via "fink selfupdate"
>>>>>
>>>>> --
>>>>> Alexander Hansen, Ph.D.
>>>>> Fink User Liaison
>>>>> My package updates: http://finkakh.wordpress.com/
>>>>
>>>> I have a slightly stranger error now:
>>>>
>>>> /sw/bin/dpkg-lockwait -i
>>>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/ope
>>>> nmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb
>>>> Selecting previously deselected package openmpi-ext-oct362.
>>>> (Reading database ... 350602 files and directories currently installed.)
>>>> Preparing to replace openmpi-ext-oct362 1.0.2-104 (using
>>>> .../openmpi-ext-oct362_
>>>> 1.1.0-1_darwin-x86_64.deb) ...
>>>> XIO:  fatal IO error 54 (Connection reset by peer) on X server
>>>> "localhost:10.0"
>>>>   after 0 requests (0 known processed) with 0 events remaining.
>>>> X connection to localhost:10.0 broken (explicit kill or server
>>>> shutdown).
>>>> dpkg: warning - old pre-removal script returned error exit status 1
>>>> dpkg - trying script from the new package instead ...
>>>> /sw/var/lib/dpkg/tmp.ci/prerm: line 6:
>>>> /sw/share/octave/3.6.2/openmpi_ext-1.1.0/
>>>> octave-forge-prerm: No such file or directory
>>>> /sw/bin/dpkg: error processing
>>>> /sw/fink/dists/stable/main/binary-darwin-x86_64/s
>>>> ci/openmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb (--install):
>>>>  subprocess new pre-removal script returned error exit status 1
>>>> X connection to localhost:10.0 broken (explicit kill or server
>>>> shutdown).
>>>> X connection to localhost:10.0 broken (explicit kill or server
>>>> shutdown).
>>>> dpkg: error while cleaning up:
>>>>  subprocess post-installation script returned error exit status 1
>>>> Errors were encountered while processing:
>>>>
>>>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/openmpi-ext-oct362_1.1.0-1_
>>>>
>>>>
>>>> darwin-x86_64.deb
>>>> ### execution of /sw/bin/dpkg-lockwait failed, exit code 1
>>>>
>>>> Now, that X error _might_ be a red herring, I was running this over an
>>>> ssh session to the server (that wasn't broken, I was still logged
>>>> in...)  I've never seen something like this find its way into the saved
>>>> log from a fink update before.  But I don't think it is the actual
>>>> problem with the package??
>>>>
>>>> TIA,
>>>> -- VIv
>>>
>>> The X error does indeed appear to be a red herring.
>>>
>>> The missing octave-forge-prerm is the problem.  This is supposed to have
>>> been copied into the package as part of the build process.  Please run
>>>
>>> dpkg -c
>>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/openmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb
>>>
>>> | grep forge
>>>
>>> If that, in fact, does not show octave-forge-prerm then something may be
>>> amiss in how the package is getting generated for you and I'll want to
>>> see a build log from "fink rebuild openmpi-ext-oct362.
>>>
>>> The octave-forge-prerm and octave-forge-postinst scripts for the
>>> individual Octave Forge packages are generated by copying the respective
>>> template files from the Octave versioned runtime package (e.g.
>>> octave362) and editing them.
>>
>> dpkg -c etc returns
>>
>> -rwxr-xr-x root/admin  287 2012-09-28 10:46
>> ./sw/share/octave/3.6.2/openmpi_ext-1.1.0/octave-forge-postinst
>> -rwxr-xr-x root/admin  271 2012-09-28 10:46
>> ./sw/share/octave/3.6.2/open

Re: [Fink-users] dependency problem for openmpi-ext-oct362-1.1.0-1

[Viv Kendon]

On Fri, 28 Sep 2012, Alexander Hansen wrote:

> On 9/28/12 5:58 AM, Viv Kendon wrote:
>> On Thu, 27 Sep 2012, Alexander Hansen wrote:
>>
>>> On 9/27/12 8:16 AM, Viv Kendon wrote:
>>>>
>>>> 10.6.8 server; update-all complains
>>>>
>>>> Can't resolve dependency "liboctave362-gcc46-dev" for package
>>>> "openmpi-ext-oct362-1.1.0-1" (no matching packages/versions found)
>>>>
>>>> TIA
>>>> -- Viv
>>>
>>> Thanks.  A fix should be available shortly via "fink selfupdate"
>>>
>>> --
>>> Alexander Hansen, Ph.D.
>>> Fink User Liaison
>>> My package updates: http://finkakh.wordpress.com/
>>
>> I have a slightly stranger error now:
>>
>> /sw/bin/dpkg-lockwait -i
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/ope
>> nmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb
>> Selecting previously deselected package openmpi-ext-oct362.
>> (Reading database ... 350602 files and directories currently installed.)
>> Preparing to replace openmpi-ext-oct362 1.0.2-104 (using
>> .../openmpi-ext-oct362_
>> 1.1.0-1_darwin-x86_64.deb) ...
>> XIO:  fatal IO error 54 (Connection reset by peer) on X server
>> "localhost:10.0"
>>   after 0 requests (0 known processed) with 0 events remaining.
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> dpkg: warning - old pre-removal script returned error exit status 1
>> dpkg - trying script from the new package instead ...
>> /sw/var/lib/dpkg/tmp.ci/prerm: line 6:
>> /sw/share/octave/3.6.2/openmpi_ext-1.1.0/
>> octave-forge-prerm: No such file or directory
>> /sw/bin/dpkg: error processing
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/s
>> ci/openmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb (--install):
>>  subprocess new pre-removal script returned error exit status 1
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> X connection to localhost:10.0 broken (explicit kill or server shutdown).
>> dpkg: error while cleaning up:
>>  subprocess post-installation script returned error exit status 1
>> Errors were encountered while processing:
>>
>> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/openmpi-ext-oct362_1.1.0-1_
>>
>> darwin-x86_64.deb
>> ### execution of /sw/bin/dpkg-lockwait failed, exit code 1
>>
>> Now, that X error _might_ be a red herring, I was running this over an
>> ssh session to the server (that wasn't broken, I was still logged
>> in...)  I've never seen something like this find its way into the saved
>> log from a fink update before.  But I don't think it is the actual
>> problem with the package??
>>
>> TIA,
>> -- VIv
>
> The X error does indeed appear to be a red herring.
>
> The missing octave-forge-prerm is the problem.  This is supposed to have
> been copied into the package as part of the build process.  Please run
>
> dpkg -c
> /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/openmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb
> | grep forge
>
> If that, in fact, does not show octave-forge-prerm then something may be
> amiss in how the package is getting generated for you and I'll want to
> see a build log from "fink rebuild openmpi-ext-oct362.
>
> The octave-forge-prerm and octave-forge-postinst scripts for the
> individual Octave Forge packages are generated by copying the respective
> template files from the Octave versioned runtime package (e.g.
> octave362) and editing them.

dpkg -c etc returns

-rwxr-xr-x root/admin  287 2012-09-28 10:46 
./sw/share/octave/3.6.2/openmpi_ext-1.1.0/octave-forge-postinst
-rwxr-xr-x root/admin  271 2012-09-28 10:46 
./sw/share/octave/3.6.2/openmpi_ext-1.1.0/octave-forge-prerm

The X error is connected to whatever the problem is somehow, 
it repeatably shows up when running

fink reinstall openmpi-ext-oct362

whereupon it tried to unpack the deb as above.  I checked 
what is in that location currently, and it is:

/sw/share/octave/3.6.2/openmpi_ext-1.0.2/octave-forge-prerm

which contains

#!/sw/bin/octave-3.6.2 -q
load /sw/var/octave/3.6.2/octave_packages
for i = 1:length(global_packages)
   if strcmp(global_packages{i}.name,'openmpi_ext')
 global_packages(i) = [];
 break
   endif
endfor
save -text /sw/var/octave/3.6.2/octave_packages 
global_packages

So is it trying to call the old prerm script with the new 
name?  openmpi-ext-1.1.0 vs openmpi-ext-1.0.2?

TIA,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864 

Re: [Fink-users] dependency problem for openmpi-ext-oct362-1.1.0-1

[Viv Kendon]

On Thu, 27 Sep 2012, Alexander Hansen wrote:

> On 9/27/12 8:16 AM, Viv Kendon wrote:
>>
>> 10.6.8 server; update-all complains
>>
>> Can't resolve dependency "liboctave362-gcc46-dev" for package
>> "openmpi-ext-oct362-1.1.0-1" (no matching packages/versions found)
>>
>> TIA
>> -- Viv
>
> Thanks.  A fix should be available shortly via "fink selfupdate"
>
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/

I have a slightly stranger error now:

/sw/bin/dpkg-lockwait -i 
/sw/fink/dists/stable/main/binary-darwin-x86_64/sci/ope
nmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb
Selecting previously deselected package openmpi-ext-oct362.
(Reading database ... 350602 files and directories currently 
installed.)
Preparing to replace openmpi-ext-oct362 1.0.2-104 (using 
.../openmpi-ext-oct362_
1.1.0-1_darwin-x86_64.deb) ...
XIO:  fatal IO error 54 (Connection reset by peer) on X 
server "localhost:10.0"
   after 0 requests (0 known processed) with 0 events 
remaining.
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
dpkg: warning - old pre-removal script returned error exit 
status 1
dpkg - trying script from the new package instead ...
/sw/var/lib/dpkg/tmp.ci/prerm: line 6: 
/sw/share/octave/3.6.2/openmpi_ext-1.1.0/
octave-forge-prerm: No such file or directory
/sw/bin/dpkg: error processing 
/sw/fink/dists/stable/main/binary-darwin-x86_64/s
ci/openmpi-ext-oct362_1.1.0-1_darwin-x86_64.deb (--install):
  subprocess new pre-removal script returned error exit 
status 1
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
X connection to localhost:10.0 broken (explicit kill or 
server shutdown).
dpkg: error while cleaning up:
  subprocess post-installation script returned error exit 
status 1
Errors were encountered while processing:

/sw/fink/dists/stable/main/binary-darwin-x86_64/sci/openmpi-ext-oct362_1.1.0-1_
darwin-x86_64.deb
### execution of /sw/bin/dpkg-lockwait failed, exit code 1

Now, that X error _might_ be a red herring, I was running 
this over an ssh session to the server (that wasn't broken, 
I was still logged in...)  I've never seen something like 
this find its way into the saved log from a fink update 
before.  But I don't think it is the actual problem with the 
package??

TIA,
-- VIv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] dependency problem for openmpi-ext-oct362-1.1.0-1

[Viv Kendon]

10.6.8 server; update-all complains

Can't resolve dependency "liboctave362-gcc46-dev" for 
package
"openmpi-ext-oct362-1.1.0-1" (no matching packages/versions 
found)

TIA
-- Viv
____________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] Binary dist functionality on 10.7

[Viv Kendon]

On Thu, 30 Aug 2012, Alexander Hansen wrote:

> On 8/30/12 6:40 AM, Viv Kendon wrote:
>> I have set up one of my macs to serve binary packages for
>> the rest, to save recompiling the same thing over again.
>>
>> I've been using apt-get {upgrade/dist-update} and that works
>> with the appropriate lines added to /sw/etc/apt/source.list
>>
>> However, I turned on the "UseBinaryDist" flag in fink.conf,
>> and that doesn't work:
>>
>> Downloading the indexes of available packages in the binary
>> distribution.
>> /sw/bin/apt-get-lockwait -q update
>> Err http://quince.leeds.ac.uk stable/main Packages
>>Cannot initiate the connection to 3128:80 (0.0.12.56). -
>> connect (65 No route to host)
>> Err http://quince.leeds.ac.uk stable/main Release
>>Cannot initiate the connection to 3128:80 (0.0.12.56). -
>> connect (65 No route to host)
>> Err http://quince.leeds.ac.uk stable/crypto Packages
>>Cannot initiate the connection to 3128:80 (0.0.12.56). -
>> connect (65 No route to host)
>>
>> I have "ProxyHTTP" set using port 3128, and clearly
>> something isn't parsing this correctly.  Everything else
>> works as it should, so I don't think it is the proxy
>> setting, which in full is:
>>
>> ProxyHTTP: http://www-cache.leeds.ac.uk:3128



>>
>> Running sudo /sw/bin/apt-get-lockwait -q update
>>
>> by hand does work as expected.  I think this only broke
>> recently, but I'm not sure when.
>>
>> Obviously I can live without it and keep using apt-get
>> directly, but I thought I'd report it in case it is easy to
>> fix.
>>
>> -- Viv
>> 
>> Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
>> tel: +44 113 343 4864  Physics and Astronomy
>> Quantum Information GroupUniversity of Leeds
>>
>>
>
> What, literally, is your setting for the ProxyHTTP flag in fink.conf?
> According to the fink.conf manpage:
>
>ProxyHTTP: url
>   If you use a HTTP proxy then you should enter its address
> here, for example:
> ProxyHTTP: http://yourhost.com:3128/
>   Leave if blank if you do not use a HTTP proxy.
>
>
> The error message above suggests that the host portion is missing and
> only the port is getting passed along to apt-get, which therefore
> assumes that this is a hostname.

Yes, it does look like that, but I didn't hand edit this, 
fink generated the entry from what I entered at the prompts 
during fink configure (which I gave above, here it is again:

ProxyHTTP: http://www-cache.leeds.ac.uk:3128

-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] meep/meep-mpi work on 10.7

[Viv Kendon]

I upgraded one of my computers from 10.5 to 10.7, found out 
that meep wasn't in 10.7 yet, so I tried just copying over 
all the info files into my local tree.  It worked, once I 
updated a few dependencies:

in h5utils.info, hdf5 -> hdf5.7

in libctl.info, gmp -> gmp5

in meep.info, openmpi-dev -> openmpi

also, I think meep needs guile18-shlibs and libctl added to 
the Depends, because when I used apt-get to install it on a 
second machine, it didn't also install those two and gave me 
errors on start up.  It has been tested (not by me) and 
reported to "work nicely".

cheers,
-- Viv
____________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] Binary dist functionality on 10.7

[Viv Kendon]

I have set up one of my macs to serve binary packages for 
the rest, to save recompiling the same thing over again.

I've been using apt-get {upgrade/dist-update} and that works 
with the appropriate lines added to /sw/etc/apt/source.list

However, I turned on the "UseBinaryDist" flag in fink.conf, 
and that doesn't work:

Downloading the indexes of available packages in the binary 
distribution.
/sw/bin/apt-get-lockwait -q update
Err http://quince.leeds.ac.uk stable/main Packages
   Cannot initiate the connection to 3128:80 (0.0.12.56). - 
connect (65 No route to host)
Err http://quince.leeds.ac.uk stable/main Release
   Cannot initiate the connection to 3128:80 (0.0.12.56). - 
connect (65 No route to host)
Err http://quince.leeds.ac.uk stable/crypto Packages
   Cannot initiate the connection to 3128:80 (0.0.12.56). - 
connect (65 No route to host)

I have "ProxyHTTP" set using port 3128, and clearly 
something isn't parsing this correctly.  Everything else 
works as it should, so I don't think it is the proxy 
setting, which in full is:

ProxyHTTP: http://www-cache.leeds.ac.uk:3128

Running sudo /sw/bin/apt-get-lockwait -q update

by hand does work as expected.  I think this only broke 
recently, but I'm not sure when.

Obviously I can live without it and keep using apt-get 
directly, but I thought I'd report it in case it is easy to 
fix.

-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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[Fink-users] qtoctave-x11 works for me on 10.7

[Viv Kendon]

In case it is useful for anyone else:

I copied the qtoctave.info and .patch files to my 10.7 local 
tree and tried installing the x11 variant.  It built, 
installed, and seems to run OK (once you tell it the name of 
the octave executable via the config menu).

The build issues lots of warnings like this:
In file included from 
/sw/src/fink.build/qtoctave-x11-0.9.1-1006/qtoctave-0.9.1/qtoctave/src/moc_session.cxx:10:
In file included from 
/sw/src/fink.build/qtoctave-x11-0.9.1-1006/qtoctave-0.9.1/qtoctave/src/session.h:4:
In file included from 
/sw/lib/qt4-x11/include/QtCore/QObject:1:
In file included from 
/sw/lib/qt4-x11/include/QtCore/qobject.h:47:
In file included from 
/sw/lib/qt4-x11/include/QtCore/qobjectdefs.h:45:
In file included from 
/sw/lib/qt4-x11/include/QtCore/qnamespace.h:45:
/sw/lib/qt4-x11/include/QtCore/qglobal.h:327:6: warning: 
#warning "This version
   of Mac OS X is unsupported" [-W#warnings]
#warning "This version of Mac OS X is unsupported"
  ^
1 warning generated.

My kit:

Package manager version: 0.34.2
Distribution version: selfupdate-rsync Wed Aug  8 15:38:03 
2012, 10.7, x86_64
Trees: local/main stable/main

Darwin Kernel Version 11.4.0: Mon Apr  9 19:32:15 PDT 2012; 
root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64

i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple 
Inc. build 5658) (LLVM build 2336.9.00)

and a case-sensitive file system.

I did not change anything in the info/patch files.

-- Viv
________
Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] wxmaxima-gtk runtime issue was Re: Failed: phase installing: wxmaxima-gtk-12.04.0-4 failed

[Viv Kendon]

On Tue, 7 Aug 2012, Alexander Hansen wrote:

> On 8/1/12 12:14 AM, Viv Kendon wrote:
>
> 
>
>>>> Many thanks for the help, it all built and installed without further
>>>> problems (bundle-maxima-x11).  xmaxima appears to work fine, but
>>>> wxmaxima cannot start/connect to the server no matter what I've tried to
>>>> reconfigure.  It looks OK apart from that, but obviously I can't test it
>>>> very much in its serverless state. I can't get any more useful debug
>>>> messages out of it either.
>>>
>>> I've tried checking the maxima mailing list archives on this issue, too,
>>> but nothing jumped out at me.
>>>
>>> wxmaxima-mac gives me the following processes:
>>>
>>> $ wxmaxima
>>> $ ps ax | grep maxima
>>> 18126   ??  U  0:00.47
>>> /sw/Applications/wxMaxima.app/Contents/MacOS/wxmaxima -psn_0_3961799
>>> 18154   ??  S  0:00.11 /sw/opt/sbcl-1.0.57/lib/sbcl/sbcl --core
>>> /sw/lib/maxima/5.27.0/binary-sbcl/maxima.core --noinform
>>> --end-runtime-options --eval (cl-user::run) --end-toplevel-options -r
>>> :lisp (setup-client 4010)
>>> 18172 s001  S+ 0:00.00 grep maxima
>>>
>>> Maybe wxmaxima isn't waiting long enough to connect in the gtk case.
>>
>> I get only
>>
>>  ps ax | grep maxima
>> 64767   ??  S  0:00.64
>> /sw/Applications/wxMaxima.app/Contents/MacOS/wxmaxima -psn_0_10295761
>> 64802 s000  R+ 0:00.00 grep maxima
>>
>> and I see nothing appear even transiently when I try "restart Maxima"
>> from the Maxima menu.  I don't think the right comands are even getting
>> as far as the OS.  Could it be using the wrong command to exec
>> something?  A linux only one perhaps?  How does the mac version launch
>> Maxima compared to the x11 version?
>>
> Had a little time to look into this:
>
> The commands _do_ get to the OS.  I had a GTK wxMaxima window open and I
> ran "sudo fs_usage | grep bin/maxima in a terminal window to catch any
> invocations of /sw/bin/maxima.  When I tried to restart it from
> wxMaxima, I got:
>
> $ sudo fs_usage | grep bin/maxima
> Password:
> 14:38:33  execve/sw/bin/maxima
> 0.000520   wxmaxima.bin
> 14:38:33  open  /sw/bin/maxima
> 0.14   sh
> 14:40:51  execve/sw/bin/maxima
> 0.000332   wxmaxima.bin
> 14:40:51  open  /sw/bin/maxima
> 0.06   sh
>
> i.e. wxMaxima would try to launch maxima, but it would die.
>
> However, restarting maxima from wxMaxima hasn't worked for the recent
> GTK versions for me in any case.
>
> Up until recently, I had to restart wxMaxima over and over, and
> eventually it would start up in communication with an instance of
> maxima, but now even that doesn't work.
>
> I've discontinued wxmaxima-gtk until I find a fix to make it work at
> least part of the time.

OK, I'll keep an eye out for an update appearing at some 
point...

many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] ncarray-oct362 case sensitive problem

[Viv Kendon]

On Sat, 4 Aug 2012, Alexander Hansen wrote:

> On 8/4/12 2:14 PM, Viv Kendon wrote:
>> On Sat, 4 Aug 2012, Alexander Hansen wrote:
>>
>>> On 8/4/12 12:34 AM, Viv Kendon wrote:
>>>> On Fri, 3 Aug 2012, Alexander Hansen wrote:
>>>>
>>>>> On 8/3/12 2:39 PM, Viv Kendon wrote:
>>>>>> One more:
>>>>>>
>>>>>> 
>>>>>> ncArray/DESCRIPTION
>>>>>> Removing runtime build-lock...
>>>>>> Removing build-lock package...
>>>>>> /sw/bin/dpkg-lockwait -r fink-buildlock-ncarray-oct362-1.0.0-1
>>>>>> (Reading database ... 337903 files and directories currently
>>>>>> installed.)
>>>>>> Removing fink-buildlock-ncarray-oct362-1.0.0-1 ...
>>>>>> Failed: directory /sw/src/fink.build/ncarray-oct362-1.0.0-1/ncarray
>>>>>> doesn't exist, check the package description
>>>>>>
>>>>>> I'm using a case-sensitive file system, so ncArray and ncarray don't
>>>>>> match...
>>>>>
>>>>> Oops.  Yeah, that would be problematic.  Now fixed in CVS.
>>>>
>>>> Not quite, I now get:
>>>>
>>>> ncArray/DESCRIPTION
>>>> /tmp/fink._tcKo
>>>> #!/bin/sh -ev
>>>> #--build-as-nobody blocker
>>>> if [ $UID -ne 0 ]
>>>> then
>>>> echo "ncarray-oct362 cannot be built with
>>>> --build-as-nobody"
>>>> exit 1
>>>> fi
>>>> export OCTAVE=/sw/bin/octave-3.6.2
>>>> srcdir=ncarray
>>>> # repack tarball, since octave-3.4.3+ appears not to want to
>>>> install
>>>> # from directories
>>>> cd ..
>>>> tar -cvf $srcdir-1.0.0.tar $srcdir
>>>> tar: ncarray: Cannot stat: No such file or directory
>>>> tar: Exiting with failure status due to previous errors
>>>> ### execution of /tmp/fink._tcKo failed, exit code 2
>>>>
>>> Oops. That's fixed now.
>>>
>> It is still fighting back, now octave is unhappy about it:
>>
>> ans =
>> /sw/src/fink.build/ncarray-oct362-1.0.0-1/bld/share/octave/3.6.2/packages
>> mkdir (/var/tmp/oct-ErNDwI)
>> untar (./ncArray-1.0.0.tar, /var/tmp/oct-ErNDwI)
>> package name 'ncarray' doesn't correspond to its filename 'ncArray-1.0.0'
>> error: called from `pkg>install' in file
>> /sw/share/octave/3.6.2/m/pkg/pkg.m near line 745, column 11
>> error: called from:
>> error:   /sw/share/octave/3.6.2/m/pkg/pkg.m at line 773, column 5
>> error:   /sw/share/octave/3.6.2/m/pkg/pkg.m at line 383, column 9
>> error: /sw/src/fink.build/ncarray-oct362-1.0.0-1/bld/octave-forge-comp
>> at line 4, column 1
>> ### execution of /tmp/fink.ZHNGL failed, exit code 1
>>
> Sorry about that.  I just sent a fix that works on a case-sensitive
> filesystem to CVS, so you should be able to get that via selfupdate soon.

And it does indeed work on my system.

Many thanks,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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Re: [Fink-users] ncarray-oct362 case sensitive problem

[Viv Kendon]

On Sat, 4 Aug 2012, Alexander Hansen wrote:

> On 8/4/12 12:34 AM, Viv Kendon wrote:
>> On Fri, 3 Aug 2012, Alexander Hansen wrote:
>>
>>> On 8/3/12 2:39 PM, Viv Kendon wrote:
>>>> One more:
>>>>
>>>> 
>>>> ncArray/DESCRIPTION
>>>> Removing runtime build-lock...
>>>> Removing build-lock package...
>>>> /sw/bin/dpkg-lockwait -r fink-buildlock-ncarray-oct362-1.0.0-1
>>>> (Reading database ... 337903 files and directories currently installed.)
>>>> Removing fink-buildlock-ncarray-oct362-1.0.0-1 ...
>>>> Failed: directory /sw/src/fink.build/ncarray-oct362-1.0.0-1/ncarray
>>>> doesn't exist, check the package description
>>>>
>>>> I'm using a case-sensitive file system, so ncArray and ncarray don't
>>>> match...
>>>
>>> Oops.  Yeah, that would be problematic.  Now fixed in CVS.
>>
>> Not quite, I now get:
>>
>> ncArray/DESCRIPTION
>> /tmp/fink._tcKo
>> #!/bin/sh -ev
>> #--build-as-nobody blocker
>> if [ $UID -ne 0 ]
>> then
>> echo "ncarray-oct362 cannot be built with
>> --build-as-nobody"
>> exit 1
>> fi
>> export OCTAVE=/sw/bin/octave-3.6.2
>> srcdir=ncarray
>> # repack tarball, since octave-3.4.3+ appears not to want to
>> install
>> # from directories
>> cd ..
>> tar -cvf $srcdir-1.0.0.tar $srcdir
>> tar: ncarray: Cannot stat: No such file or directory
>> tar: Exiting with failure status due to previous errors
>> ### execution of /tmp/fink._tcKo failed, exit code 2
>>
> Oops. That's fixed now.
>
It is still fighting back, now octave is unhappy about it:

ans = /sw/src/fink.build/ncarray-oct362-1.0.0-1/bld/share/octave/3.6.2/packages
mkdir (/var/tmp/oct-ErNDwI)
untar (./ncArray-1.0.0.tar, /var/tmp/oct-ErNDwI)
package name 'ncarray' doesn't correspond to its filename 'ncArray-1.0.0'
error: called from `pkg>install' in file 
/sw/share/octave/3.6.2/m/pkg/pkg.m near line 745, column 11
error: called from:
error:   /sw/share/octave/3.6.2/m/pkg/pkg.m at line 773, 
column 5
error:   /sw/share/octave/3.6.2/m/pkg/pkg.m at line 383, 
column 9
error: 
/sw/src/fink.build/ncarray-oct362-1.0.0-1/bld/octave-forge-comp 
at line 4, column 1
### execution of /tmp/fink.ZHNGL failed, exit code 1

TIA,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


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threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: [Fink-users] ncarray-oct362 case sensitive problem

[Viv Kendon]

On Fri, 3 Aug 2012, Alexander Hansen wrote:

> On 8/3/12 2:39 PM, Viv Kendon wrote:
>> One more:
>>
>> 
>> ncArray/DESCRIPTION
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-ncarray-oct362-1.0.0-1
>> (Reading database ... 337903 files and directories currently installed.)
>> Removing fink-buildlock-ncarray-oct362-1.0.0-1 ...
>> Failed: directory /sw/src/fink.build/ncarray-oct362-1.0.0-1/ncarray
>> doesn't exist, check the package description
>>
>> I'm using a case-sensitive file system, so ncArray and ncarray don't
>> match...
>
> Oops.  Yeah, that would be problematic.  Now fixed in CVS.
>

Not quite, I now get:

ncArray/DESCRIPTION
/tmp/fink._tcKo
#!/bin/sh -ev
 #--build-as-nobody blocker
 if [ $UID -ne 0 ]
 then
 echo "ncarray-oct362 cannot be built with --build-as-nobody"
 exit 1
 fi
 export OCTAVE=/sw/bin/octave-3.6.2
 srcdir=ncarray
 # repack tarball, since octave-3.4.3+ appears not to want to install
 # from directories
 cd ..
 tar -cvf $srcdir-1.0.0.tar $srcdir
tar: ncarray: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
### execution of /tmp/fink._tcKo failed, exit code 2

TIA,
-- Viv

Dr Viv Kendonhttp://quantum.leeds.ac.uk/~viv
tel: +44 113 343 4864  Physics and Astronomy
Quantum Information GroupUniversity of Leeds


--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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