Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9
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 doesn't really need labl-x11, this was a change to get it to compile at an earlier version that appears not to be needed now: 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. 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!
Re: [Fink-users] zsh 5.0.3 nowhere to be found?
On Dec 17, 2013, at 2:32 PM, Hanspeter Niederstrasser f...@snaggledworks.com wrote: On 12/17/2013 5:10 PM, Alexander Hansen wrote: On 12/17/13 2:03 PM, Martin Costabel wrote: On 17/12/13 17:33, Bill Waggoner wrote: fink is trying to update zsh to zsh-5.0.3-1 but it is nowhere to be found: Failed: file download failed for zsh-5.0.3.tar.bz2 of package zsh-5.0.3-1 I don't even see it on sourceforge. Has it been included by accident or mistake? Looks like a mistake. De-facto maintainer CCed. I'll redirect it to the last committer. :-) It's found in one of upstream's mirrors, but not their global SF mirror: http://www.zsh.org/ http://www.zsh.org/pub/ Hanspeter Sorry, fixed it with currently active URL. These should be mirrored on sourceforge soon, at which point I will uncomment those urls. Bill -- 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! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ 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
Re: [Fink-users] zsh 5.0.3 nowhere to be found?
Thanks, Bill. That works much better. Bill On Wed, Dec 18, 2013 at 6:16 AM, William Scott wgsc...@ucsc.edu wrote: On Dec 17, 2013, at 2:32 PM, Hanspeter Niederstrasser f...@snaggledworks.com wrote: On 12/17/2013 5:10 PM, Alexander Hansen wrote: On 12/17/13 2:03 PM, Martin Costabel wrote: On 17/12/13 17:33, Bill Waggoner wrote: fink is trying to update zsh to zsh-5.0.3-1 but it is nowhere to be found: Failed: file download failed for zsh-5.0.3.tar.bz2 of package zsh-5.0.3-1 I don't even see it on sourceforge. Has it been included by accident or mistake? Looks like a mistake. De-facto maintainer CCed. I'll redirect it to the last committer. :-) It's found in one of upstream's mirrors, but not their global SF mirror: http://www.zsh.org/ http://www.zsh.org/pub/ Hanspeter Sorry, fixed it with currently active URL. These should be mirrored on sourceforge soon, at which point I will uncomment those urls. Bill -- 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! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ 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
[Fink-users] trouble downloading/installing pymol-py27
Hi all - I'm trying to use Fink to install Pymol, and it doesn't appear to be working. (See below for config information.) I've run fink selfupdate and update-all. When I execute fink install pymol-py27 (or -py26) I successfully installed a whole bunch of Python packages the first time I ran the command. However, things run into trouble when I get to the actual Pymol code. The download of the Pymol tarball fails with a checksum error: curl --connect-timeout 30 -f -L -A 'fink/0.36.1' -O http://distfiles.master.finkmirrors.net/pymol-1.6.0-src.tar.bz2 % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total Spent Left Speed 100 8472k 100 8472k0 0 706k 0 0:00:11 0:00:11 --:--:-- 1044k The checksum of the file is incorrect. The most likely cause for this is a corrupted or incomplete download Expected: bae7424af441978fd9939ac029fdc366 Actual: MD5(1706c013269d41125ebb3bb0573300fe) SHA1(eece9a1624d2e84ea4da284ae639a79bca02c700) Downloading the file pymol-1.6.0-src.tar.bz2 failed. I have gotten the same error, with exactly the same filesize and checksum, every time I've tried, from multiple different mirrors. Therefore, I think it's not a transmission error. It's possible our firewall is messing things up, but no other fink download has had this problem. If I ignore the checksum problem, and tell fink to use the file anyway, it unpacks it OK and begins the installation process. Things start to go wrong at the file patching stage: patching file contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c patching file contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c patching file layer4/Cmd.c patching file contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp patching file contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp can't find file to patch at input line 173 Perhaps you used the wrong -p or --strip option? The text leading up to this was: -- |--- pymol-1.5/contrib/pyopengl/openglutil.c.orig 2013-06-07 20:11:42.0 -0400 |+++ pymol-1.5/contrib/pyopengl/openglutil.c2013-06-07 20:12:18.0 -0400 -- Indeed, I can't find openglutil.c anywhere in the pymol directories (or anywhere in /sw). If I skip this patch, things proceed for a little longer before failing for good: patching file layer2/RepSurface.c patching file layer3/Selector.c Hunk #1 succeeded at 8660 (offset 45 lines). patching file layer2/ObjectMolecule2.c patching file layer2/RepCylBond.c ### execution of /tmp/fink.SOSLL failed, exit code 1 ### execution of /tmp/fink.kMmYU failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-pymol-py27-1.6.0-3 (Reading database ... 36268 files and directories currently installed.) Removing fink-buildlock-pymol-py27-1.6.0-3 ... Failed: phase patching: pymol-py27-1.6.0-3 failed It looks to me like the fink installation script doesn't match the files actually present in the tarball. I imagine this is related to the checksum error. Could somebody please advise me on how to proceed? Is the problem on my end, or something the package maintainer needs to address? Thanks for any help you can provide, Matt Config information: Package manager version: 0.36.1 Distribution version: selfupdate-rsync Wed Dec 18 11:37:21 2013, 10.6, x86_64 Trees: local/main stable/main unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 pymol-py27-1.6.0-3 is set to build with only one job. Operating system is an Intel Mac Pro 5.1, running OS X 10.6.8. Fink is being run in an X11 window, XQuartz 2.3.6. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374 -- 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! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ 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
Re: [Fink-users] trouble downloading/installing pymol-py27
On 12/18/13 1:45 PM, Matthew Franklin wrote: Hi all - I'm trying to use Fink to install Pymol, and it doesn't appear to be working. (See below for config information.) I've run fink selfupdate and update-all. When I execute fink install pymol-py27 (or -py26) I successfully installed a whole bunch of Python packages the first time I ran the command. However, things run into trouble when I get to the actual Pymol code. The download of the Pymol tarball fails with a checksum error: curl --connect-timeout 30 -f -L -A 'fink/0.36.1' -O http://distfiles.master.finkmirrors.net/pymol-1.6.0-src.tar.bz2 % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total Spent Left Speed 100 8472k 100 8472k0 0 706k 0 0:00:11 0:00:11 --:--:-- 1044k The checksum of the file is incorrect. The most likely cause for this is a corrupted or incomplete download Expected: bae7424af441978fd9939ac029fdc366 Actual: MD5(1706c013269d41125ebb3bb0573300fe) SHA1(eece9a1624d2e84ea4da284ae639a79bca02c700) Downloading the file pymol-1.6.0-src.tar.bz2 failed. I have gotten the same error, with exactly the same filesize and checksum, every time I've tried, from multiple different mirrors. Therefore, I think it's not a transmission error. It's possible our firewall is messing things up, but no other fink download has had this problem. If I ignore the checksum problem, and tell fink to use the file anyway, it unpacks it OK and begins the installation process. Things start to go wrong at the file patching stage: patching file contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c patching file contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c patching file layer4/Cmd.c patching file contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp patching file contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp can't find file to patch at input line 173 Perhaps you used the wrong -p or --strip option? The text leading up to this was: -- |--- pymol-1.5/contrib/pyopengl/openglutil.c.orig 2013-06-07 20:11:42.0 -0400 |+++ pymol-1.5/contrib/pyopengl/openglutil.c2013-06-07 20:12:18.0 -0400 -- Indeed, I can't find openglutil.c anywhere in the pymol directories (or anywhere in /sw). If I skip this patch, things proceed for a little longer before failing for good: patching file layer2/RepSurface.c patching file layer3/Selector.c Hunk #1 succeeded at 8660 (offset 45 lines). patching file layer2/ObjectMolecule2.c patching file layer2/RepCylBond.c ### execution of /tmp/fink.SOSLL failed, exit code 1 ### execution of /tmp/fink.kMmYU failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-pymol-py27-1.6.0-3 (Reading database ... 36268 files and directories currently installed.) Removing fink-buildlock-pymol-py27-1.6.0-3 ... Failed: phase patching: pymol-py27-1.6.0-3 failed It looks to me like the fink installation script doesn't match the files actually present in the tarball. I imagine this is related to the checksum error. Could somebody please advise me on how to proceed? Is the problem on my end, or something the package maintainer needs to address? Thanks for any help you can provide, Matt Config information: Package manager version: 0.36.1 Distribution version: selfupdate-rsync Wed Dec 18 11:37:21 2013, 10.6, x86_64 Trees: local/main stable/main unstable/main unstable/crypto Xcode.app: 3.2.6 Xcode command-line tools: 3.2.6 pymol-py27-1.6.0-3 is set to build with only one job. Operating system is an Intel Mac Pro 5.1, running OS X 10.6.8. Fink is being run in an X11 window, XQuartz 2.3.6. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374 The tarball got updated without a corresponding version change. Unfortunately the packaging for 10.6 wasn't updated correspondingly. How to handle that is up to the maintainer. Since _we_ generate those tarballs, I might advocate that we either include a revision number in the filename--maybe the first package revision for which the tarball is valid--or have the package use SourceRename so that we mirror valid past snapshots so that folks aren't left high and dry. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- 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!
Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9
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 -- 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! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ 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
Re: [Fink-users] lablgl-x11-1.04-1 build failure on 10.9
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 -- 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! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ 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
[Fink-users] Problem compiling with gcc-4, missing library
Hi, I have a rather old fortran code that I want to compile on a Mac OS 10.9. It seems a needed library is no longer available that prevent the compilation. Here are the errors I got when launching gcc-4 my code.f90: Undefined symbols for architecture x86_64: __gfortran_compare_string, referenced from: _writedown_ in ccKb9lV8.o _initial_ in ccKb9lV8.o _psf_ in ccKb9lV8.o _MAIN__ in ccKb9lV8.o __gfortran_concat_string, referenced from: _k2_ in ccKb9lV8.o _initial_ in ccKb9lV8.o __gfortran_pause_string, referenced from: _svd_ in ccKb9lV8.o __gfortran_set_args, referenced from: _main in ccKb9lV8.o __gfortran_set_options, referenced from: _main in ccKb9lV8.o …. ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status I have also tried with ifort (v11), for which the error is similar, but may be a little bit more clear : [Emmanuels-MacBook-Pro:~/Divers/CG/Owens] caux% ifort Owens.f90 ld: library not found for -lSystemStubs Browsing the web, it seems this library that was available with Xcode until 10.6 is not anymore from 10.7. It could be working with fort v12, but I do not have this version to test, and anyway I would prefer to have this code running on a standard fink install, rather than only with ifort. I tried a fink list lSystemStubs, but this library is not listed, maybe I should use another name, but have no idea which one. Does somebody know what can I do ? Many thanks, !! PLEASE NOTE MY NEW EMAIL ADDRESS !! -- Emmanuel Caux, emmanuel.c...@irap.omp.eu DR2 CNRS - Departement MICMAC Institut de Recherche en Astrophysique et Planétologie (IRAP formerly CESR) BP 44346, 31028 Toulouse Cedex 4, France Phone : (+33) 561 556 689 Fax : (+33) 561 556 651 -- -- 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! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ 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
