Error installing impute package
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@peter-langfelder-4469
Last seen 12 months ago
United States
Hello, a user of my (CRAN) package WGCNA which depends on impute has a problem installing impute on his Mac OSX 10.8.3 under R 3.0.0. The problem seems to be loading the compiled libary impute.so. Can anyone please suggest a solution? Below is a transcript of his session. Thanks, Peter > biocLite("impute", lib = .libPaths()) BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. Installing package(s) 'impute' trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/cont rib/3.0/impute_1.34.0.tgz' Content type 'application/x-gzip' length 652872 bytes (637 Kb) opened URL ================================================== downloaded 637 Kb The downloaded binary packages are in /var/folders/x_/wps51c0n0tx33tx406_xt9n80000gn/T//Rtmpd8CN5X/d ownloaded_packages > library(impute) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute /libs/impute.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/librar y/impute/libs/impute.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/impute/ libs/impute.so Reason: image not found Error: package or namespace load failed for ?impute?
impute impute • 1.5k views
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@stephanie-m-gogarten-5121
Last seen 7 weeks ago
University of Washington
Is the error occurring just in the R GUI, or in any R session? I'm having a similar problem with DNAcopy when I try to load in the R GUI, but it works fine in the terminal or in Emacs. This is what I get with the GUI: > library(DNAcopy) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcop y/libs/DNAcopy.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ DNAcopy/libs/DNAcopy.so, 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAcopy /libs/DNAcopy.so Reason: image not found Error: package or namespace load failed for ?DNAcopy? > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.0 loaded via a namespace (and not attached): [1] tools_3.0.0 Stephanie On 4/10/13 2:41 PM, Peter Langfelder wrote: > Hello, > > a user of my (CRAN) package WGCNA which depends on impute has a > problem installing impute on his Mac OSX 10.8.3 under R 3.0.0. The > problem seems to be loading the compiled libary impute.so. Can anyone > please suggest a solution? Below is a transcript of his session. > > Thanks, > > Peter > >> biocLite("impute", lib = .libPaths()) > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. > Installing package(s) 'impute' > trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/co ntrib/3.0/impute_1.34.0.tgz' > Content type 'application/x-gzip' length 652872 bytes (637 Kb) > opened URL > ================================================== > downloaded 637 Kb > > > The downloaded binary packages are in > /var/folders/x_/wps51c0n0tx33tx406_xt9n80000gn/T//Rtmpd8CN5 X/downloaded_packages >> library(impute) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/impu te/libs/impute.so': > dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/lib rary/impute/libs/impute.so, > 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/3.0/Resources/library/imput e/libs/impute.so > Reason: image not found > Error: package or namespace load failed for ?impute? > > _______________________________________________ > 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 >
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On Wed, Apr 10, 2013 at 3:08 PM, Stephanie M. Gogarten <sdmorris at="" u.washington.edu=""> wrote: > Is the error occurring just in the R GUI, or in any R session? I'm having a > similar problem with DNAcopy when I try to load in the R GUI, but it works > fine in the terminal or in Emacs. > I have the same results; I get the error in the GUI but not in the command line. So I have two workarounds: 1) Use the command line version of R for the time being; and 2) Start the GUI R like this: Open Terminal.app (in /Applications/Utilities) then paste the following: export DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Reso urces/lib open /Applications/R.app Then loading the impute package should work. I need to get back to you with a better solution. Dan > This is what I get with the GUI: >> library(DNAcopy) > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAc opy/libs/DNAcopy.so': > > dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/librar y/DNAcopy/libs/DNAcopy.so, > 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAco py/libs/DNAcopy.so > Reason: image not found > Error: package or namespace load failed for ?DNAcopy? >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.10.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.0 > > Stephanie > > > On 4/10/13 2:41 PM, Peter Langfelder wrote: >> >> Hello, >> >> a user of my (CRAN) package WGCNA which depends on impute has a >> problem installing impute on his Mac OSX 10.8.3 under R 3.0.0. The >> problem seems to be loading the compiled libary impute.so. Can anyone >> please suggest a solution? Below is a transcript of his session. >> >> Thanks, >> >> Peter >> >>> biocLite("impute", lib = .libPaths()) >> >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. >> Installing package(s) 'impute' >> trying URL >> 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/ impute_1.34.0.tgz' >> Content type 'application/x-gzip' length 652872 bytes (637 Kb) >> opened URL >> ================================================== >> downloaded 637 Kb >> >> >> The downloaded binary packages are in >> >> /var/folders/x_/wps51c0n0tx33tx406_xt9n80000gn/T//Rtmpd8CN5X/downlo aded_packages >>> >>> library(impute) >> >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> >> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/imp ute/libs/impute.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/libra ry/impute/libs/impute.so, >> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib >> Referenced from: >> >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/impu te/libs/impute.so >> Reason: image not found >> Error: package or namespace load failed for ?impute? >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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
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Thanks Dan and Stephanie, both solutions have worked. Best, Peter On Wed, Apr 10, 2013 at 3:29 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Wed, Apr 10, 2013 at 3:08 PM, Stephanie M. Gogarten > <sdmorris at="" u.washington.edu=""> wrote: >> Is the error occurring just in the R GUI, or in any R session? I'm having a >> similar problem with DNAcopy when I try to load in the R GUI, but it works >> fine in the terminal or in Emacs. >> > > I have the same results; I get the error in the GUI but not in the > command line. So I have two workarounds: > > 1) Use the command line version of R for the time being; and > 2) Start the GUI R like this: > > Open Terminal.app (in /Applications/Utilities) > > then paste the following: > export DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Re sources/lib > open /Applications/R.app > > Then loading the impute package should work. I need to get back to you > with a better solution. > > Dan > > > >> This is what I get with the GUI: >>> library(DNAcopy) >> >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNA copy/libs/DNAcopy.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/libra ry/DNAcopy/libs/DNAcopy.so, >> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib >> Referenced from: >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/DNAc opy/libs/DNAcopy.so >> Reason: image not found >> Error: package or namespace load failed for ?DNAcopy? >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.10.0 >> >> loaded via a namespace (and not attached): >> [1] tools_3.0.0 >> >> Stephanie >> >> >> On 4/10/13 2:41 PM, Peter Langfelder wrote: >>> >>> Hello, >>> >>> a user of my (CRAN) package WGCNA which depends on impute has a >>> problem installing impute on his Mac OSX 10.8.3 under R 3.0.0. The >>> problem seems to be loading the compiled libary impute.so. Can anyone >>> please suggest a solution? Below is a transcript of his session. >>> >>> Thanks, >>> >>> Peter >>> >>>> biocLite("impute", lib = .libPaths()) >>> >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. >>> Installing package(s) 'impute' >>> trying URL >>> 'http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0 /impute_1.34.0.tgz' >>> Content type 'application/x-gzip' length 652872 bytes (637 Kb) >>> opened URL >>> ================================================== >>> downloaded 637 Kb >>> >>> >>> The downloaded binary packages are in >>> >>> /var/folders/x_/wps51c0n0tx33tx406_xt9n80000gn/T//Rtmpd8CN5X/downl oaded_packages >>>> >>>> library(impute) >>> >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> unable to load shared object >>> >>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/im pute/libs/impute.so': >>> >>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/libr ary/impute/libs/impute.so, >>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib >>> Referenced from: >>> >>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/imp ute/libs/impute.so >>> Reason: image not found >>> Error: package or namespace load failed for ?impute? >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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
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