Re: [Fink-devel] tk file dialogs broken?
Jack Howarth wrote: [] > ImportError: dlopen(/sw/lib/pymol-py25/modules/pymol/_cmd.so, 2): Symbol not > found: __cg_jpeg_CreateCompress > Referenced from: > /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO > Expected in: /sw/lib/libJPEG.dylib > > I find this last error rather strange. It is a classical error that appears whenever DYLD_LIBRARY_PATH is set to /sw/lib and the ApplicationServices framework is invoked. Instead of /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib, the linker then loads /sw/lib/libJPEG.dylib (which doea not exist, but on a case-insensitive file system, /sw/lib/libjpeg.dylib will do) and finds to its surprise that it does not contain the right symbols. If things are compiled correctly, DYLD_LIBRARY_PATH and LD_LIBRARY_PATH are *never* necessary. -- Martin -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] tk file dialogs broken?
After looking over NMRPipe, it would require a major
structural overhaul in order to pass all of its components
through shell wrappers to set DYLD_LIBRARY_PATH and
LD_LIBRARY_PATH. Fortunately, only a few components really
need those set. The attached changes to the NMRPipe install.com
script eliminates the issue by resetting the RPATHs and
eliminates the breakage NMRPipe causes to fink. I'm am
trying to get upstream to adopt this change to their
installer (although it will require Xcode to be installed).
Jack
--- install.com.org 2009-11-11 12:17:48.0 -0500
+++ install.com 2009-11-11 12:59:53.0 -0500
@@ -516,11 +516,33 @@
endif
endif
+set binDir = nmrbin.$binType
+
+# fix RPATH settings for Darwin
+if ($binType == mac) then
+ if (-e /usr/bin/install_name_tool) then
+ set origLibDir = "/net/space/delaglio/local/mac/lib"
+ set origLibDir2 = "/usr/openwin/lib"
+ install_name_tool -change "$origLibDir/libtk8.4.dylib"
"$baseDir/$binDir/lib/libtk8.4.dylib" $baseDir/$binDir/nmrWish
+ install_name_tool -change "$origLibDir/libtcl8.4.dylib"
"$baseDir/$binDir/lib/libtcl8.4.dylib" $baseDir/$binDir/nmrWish
+ install_name_tool -change "$origLibDir2/libxview.dylib"
"$baseDir/$binDir/lib/libxview.dylib" $baseDir/$binDir/nmrdraw.app
+ install_name_tool -change "$origLibDir2/libolgx.dylib"
"$baseDir/$binDir/lib/libolgx.dylib" $baseDir/$binDir/nmrdraw.app
+ install_name_tool -change "$origLibDir2/libxview.dylib"
"$baseDir/$binDir/lib/libxview.dylib" $baseDir/$binDir/xnotify.app
+ install_name_tool -change "$origLibDir2/libolgx.dylib"
"$baseDir/$binDir/lib/libolgx.dylib" $baseDir/$binDir/xnotify.app
+ install_name_tool -id "$baseDir/$binDir/lib/libxview.dylib"
$baseDir/$binDir/lib/libxview.dylib
+ install_name_tool -change "$origLibDir2/libolgx.dylib"
"$baseDir/$binDir/lib/libolgx.dylib" $baseDir/$binDir/lib/libxview.dylib
+ install_name_tool -id "$baseDir/$binDir/lib/libolgx.dylib"
$baseDir/$binDir/lib/libolgx.dylib
+ install_name_tool -change "$origLibDir2/libxview.dylib"
"$baseDir/$binDir/lib/libxview.dylib" $baseDir/$binDir/lib/libolgx.dylib
+ install_name_tool -id "$baseDir/$binDir/lib/libtk8.4.dylib"
$baseDir/$binDir/lib/libtk8.4.dylib
+ install_name_tool -id "$baseDir/$binDir/lib/libtcl8.4.dylib"
$baseDir/$binDir/lib/libtcl8.4.dylib
+else
+ echo "Darwin users must have Xcode installed..."
+ endif
+endif
+
#
# Check for nmrbin nmrtxt nmrtcl com:
-set binDir = nmrbin.$binType
-
foreach i ($binDir nmrtxt nmrtcl com)
if (!(-d $i)) then
echo "Error: Failed to find software directory $i"
@@ -828,15 +850,17 @@
endif
if ($binType != hp) then
- set val = "LD_LIBRARY_PATH $baseDir/$binDir/lib"
+ if ($binType != mac) then
+ set val = "LD_LIBRARY_PATH $baseDir/$binDir/lib"
- echo "" >> $scriptName
- echo "if ("'$?LD_LIBRARY_PATH'") then" >> $scriptName
- echo " setenv $val"':${LD_LIBRARY_PATH}' >> $scriptName
- echo "else" >> $scriptName
- echo " setenv $val" >> $scriptName
- echo "endif" >> $scriptName
- echo "" >> $scriptName
+ echo "" >> $scriptName
+ echo "if ("'$?LD_LIBRARY_PATH'") then" >> $scriptName
+ echo " setenv $val"':${LD_LIBRARY_PATH}' >> $scriptName
+ echo "else" >> $scriptName
+ echo " setenv $val" >> $scriptName
+ echo "endif" >> $scriptName
+ echo "" >> $scriptName
+ endif
else
set val = "SHLIB_PATH $baseDir/$binDir/lib"
echo "" >> $scriptName
@@ -848,17 +872,6 @@
echo "" >> $scriptName
endif
-if ($binType == mac) then
- set val = "DYLD_LIBRARY_PATH"
- echo "" >> $scriptName
- echo "if ("'$?DYLD_LIBRARY_PATH'") then" >> $scriptName
- echo " setenv $val "'${DYLD_LIBRARY_PATH}:${LD_LIBRARY_PATH}' >>
$scriptName
- echo "else" >> $scriptName
- echo " setenv $val "'${LD_LIBRARY_PATH}' >> $scriptName
- echo "endif" >> $scriptName
- echo "" >> $scriptName
-endif
-
echo "" >> $scriptName
echo "if ("'!($?OPENWINHOME)'") then" >> $scriptName
echo " if (-d $baseDir/$binDir/openwin) then" >> $scriptName
--
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Re: [Fink-devel] tk file dialogs broken?
I puzzled this one out. The culprit is the setup script for
NMPPipe (http://spin.niddk.nih.gov/NMRPipe/) which executes...
if ($?LD_LIBRARY_PATH) then
setenv LD_LIBRARY_PATH /usr/local/NMRPipe/nmrbin.mac/lib:${LD_LIBRARY_PATH}
else
setenv LD_LIBRARY_PATH /usr/local/NMRPipe/nmrbin.mac/lib
endif
if ($?DYLD_LIBRARY_PATH) then
setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${LD_LIBRARY_PATH}
else
setenv DYLD_LIBRARY_PATH ${LD_LIBRARY_PATH}
endif
Do we have a convention on how to fix this sort of problem?
I would assume that since /usr/local/NMRPipe/nmrbin.mac/lib
contains...
ibBLT24.a libtcl8.4.dylib libxview.dylib tcl.timestamp
libolgx.dylib libtk8.4.dylib savexv.timestamp
that their tcltk is older than the 8.4.19 in fink and their
binaries should tolerate the newer tcltk shared libraries.
So far adding...
if ($?LD_LIBRARY_PATH) then
setenv LD_LIBRARY_PATH /sw/lib:$LD_LIBRARY_PATH
endif
if ($?DYLD_LIBRARY_PATH) then
setenv DYLD_LIBRARY_PATH /sw/lib:${LD_LIBRARY_PATH}
endif
to .cshrc seems to solve the issue in sparky but seems to
break pymol...
Traceback (most recent call last):
File "/sw/lib/pymol-py25/modules/pymol/__init__.py", line 184, in
import pymol
File "/sw/lib/pymol-py25/modules/pymol/__init__.py", line 472, in
import _cmd
ImportError: dlopen(/sw/lib/pymol-py25/modules/pymol/_cmd.so, 2): Symbol not
found: __cg_jpeg_CreateCompress
Referenced from:
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
Expected in: /sw/lib/libJPEG.dylib
I find this last error rather strange. If I remove the proposed lines above
that reset
LD_LIBRARY_PATH and DYLD_LIBRARY_PATH then execute...
cd /usr/local/NMRPipe/nmrbin.mac/lib
mv libtcl8.4.dylib libtcl8.4.dylib.off
mv libtk8.4.dylib libtk8.4.dylib.off
I find pymol runs fine with .cshrc setting...
LD_LIBRARY_PATH=/usr/local/NMRPipe/nmrbin.mac/lib
DYLD_LIBRARY_PATH=/usr/local/NMRPipe/nmrbin.mac/lib
however if I execute...
setenv LD_LIBRARY_PATH /sw/lib
setenv DYLD_LIBRARY_PATH /sw/lib
pymol fails as above. It seems really weird that LD_LIBRARY_PATH and
DYLD_LIBRARY_PATH
can be set to a path outside of the fink lib directory and pymol runs fine but
when
pointed to /sw/lib, pymol crashes. Does anyone understand this error?
Jack
--
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[Fink-devel] tk file dialogs broken?
Is anyone else seeing this problem in current fink 10.5 unstable on powerpc-apple-darwin9.8.0? I am finding that both pymol-py25 and sparky-py25 are both producing tk file dialogs which contain no files or folders (for the open dialogs in both programs). I don't believe this is a system problem as the obsolete pymol-x11 binary from pymol.org works fine. I have another dual G5 which hasn't been updated as recently which isn't showing the problem. Both are running Xquartz 2.4.0. The only other difference is that the problem machine has Xcode 3.1.4 and the working machine has Xcode 3.1.3. Jack -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
