Question: rsbml installation fails on MacOS with libsbml 3
0
gravatar for Guest User
6.5 years ago by
Guest User12k
Guest User12k wrote:
Dear all, we have a problem with installing rsbml on MacOS using libsbml 3.4.1. The error message (pasted below) is similar to the one in an older post: http://article.gmane.org/gmane.science.biology.informatics.conductor/3 3187/match=rsbml Error : .onLoad failed in loadNamespace() for 'rsbml', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework /Versions/2.15/Resources/library/rsbml/libs/x86_64/rsbml.so': dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/libra ry/rsbml/libs/x86_64/rsbml.so, 6): Symbol not found: _ASTNode_addChild Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resou rces/library/rsbml/libs/x86_64/rsbml.so Expected in: dynamic lookup We set the environment variables LIBSBML3_CFLAGS=/usr/local/lib/ and LIBSBML3_LIBS=/usr/local/include/ and the directories contain the library files and the headers, respectively. Unfortunately, we are not able to build the package from source, since we cannot get access to Xcode (development tools) on that machine. With which sbml version was the current macos rsbml package compiled? Hope someone can help us, many thanks in advance, Farah and Hannes -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] graph_1.36.2 stats4_2.15.1 tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.
rsbml • 792 views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Guest User12k
Answer: rsbml installation fails on MacOS with libsbml 3
0
gravatar for Guest User
6.5 years ago by
Guest User12k
Guest User12k wrote:
Dear all, we have a problem with installing rsbml on MacOS using libsbml 3.4.1. The error message (pasted below) is similar to the one in an older post: http://article.gmane.org/gmane.science.biology.informatics.conductor/3 3187/match=rsbml Error : .onLoad failed in loadNamespace() for 'rsbml', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework /Versions/2.15/Resources/library/rsbml/libs/x86_64/rsbml.so': dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/libra ry/rsbml/libs/x86_64/rsbml.so, 6): Symbol not found: _ASTNode_addChild Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resou rces/library/rsbml/libs/x86_64/rsbml.so Expected in: dynamic lookup We set the environment variables LIBSBML3_CFLAGS=/usr/local/lib/ and LIBSBML3_LIBS=/usr/local/include/ and the directories contain the library files and the headers, respectively. Unfortunately, we are not able to build the package from source, since we cannot get access to Xcode (development tools) on that machine. With which sbml version was the current macos rsbml package compiled? Hope someone can help us, many thanks in advance, Farah and Hannes -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] graph_1.36.2 stats4_2.15.1 tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 6.5 years ago by Guest User12k
This is probably an incompatibility between the version of libsbml used by the build machines for compiling the package and the version installed on your system. Maybe Dan can figure out the version on the build machines? Michael On Wed, May 29, 2013 at 6:32 AM, Hannes Hettling [guest] < guest@bioconductor.org> wrote: > > Dear all, > > we have a problem with installing rsbml on MacOS using libsbml 3.4.1. > > The error message (pasted below) is similar to the one in an older post: > > http://article.gmane.org/gmane.science.biology.informatics.conductor /33187/match=rsbml > > Error : .onLoad failed in loadNamespace() for 'rsbml', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rsb ml/libs/x86_64/rsbml.so': > > dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/libra ry/rsbml/libs/x86_64/rsbml.so, > 6): Symbol not found: _ASTNode_addChild > Referenced from: > /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rsbm l/libs/x86_64/rsbml.so > Expected in: dynamic lookup > > We set the environment variables LIBSBML3_CFLAGS=/usr/local/lib/ and > LIBSBML3_LIBS=/usr/local/include/ and the directories contain the library > files and the headers, respectively. > > Unfortunately, we are not able to build the package from source, since we > cannot get access to Xcode (development tools) on that machine. > > With which sbml version was the current macos rsbml package compiled? > > Hope someone can help us, > many thanks in advance, > > Farah and Hannes > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] graph_1.36.2 stats4_2.15.1 tools_2.15.1 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
ADD REPLYlink written 6.5 years ago by Michael Lawrence11k
Hi all, On Wed, May 29, 2013 at 7:25 AM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > This is probably an incompatibility between the version of libsbml used by > the build machines for compiling the package and the version installed on > your system. Maybe Dan can figure out the version on the build machines? > OK. Hannes, it would help to know the output of sessionInfo() on your machine. Both our release and devel build machines use libsbml 3.4.1. Dan > Michael > > > > > On Wed, May 29, 2013 at 6:32 AM, Hannes Hettling [guest] < > guest at bioconductor.org> wrote: > >> >> Dear all, >> >> we have a problem with installing rsbml on MacOS using libsbml 3.4.1. >> >> The error message (pasted below) is similar to the one in an older post: >> >> http://article.gmane.org/gmane.science.biology.informatics.conducto r/33187/match=rsbml >> >> Error : .onLoad failed in loadNamespace() for 'rsbml', details: >> call: dyn.load(file, DLLpath = DLLpath, ...) >> error: unable to load shared object >> '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rs bml/libs/x86_64/rsbml.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/libr ary/rsbml/libs/x86_64/rsbml.so, >> 6): Symbol not found: _ASTNode_addChild >> Referenced from: >> /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rsb ml/libs/x86_64/rsbml.so >> Expected in: dynamic lookup >> >> We set the environment variables LIBSBML3_CFLAGS=/usr/local/lib/ and >> LIBSBML3_LIBS=/usr/local/include/ and the directories contain the library >> files and the headers, respectively. >> >> Unfortunately, we are not able to build the package from source, since we >> cannot get access to Xcode (development tools) on that machine. >> >> With which sbml version was the current macos rsbml package compiled? >> >> Hope someone can help us, >> many thanks in advance, >> >> Farah and Hannes >> >> -- output of sessionInfo(): >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C/UTF-8/C/C/C/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocGenerics_0.4.0 BiocInstaller_1.8.3 >> >> loaded via a namespace (and not attached): >> [1] graph_1.36.2 stats4_2.15.1 tools_2.15.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.5 years ago by Dan Tenenbaum8.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 224 users visited in the last hour