Error installing impute package

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Levi Waldron ▴ 80

@levi-waldron-6357

Last seen 10.2 years ago

I just noticed this problem myself - not with impute itself, but because WGCNA is not building in CRAN for Mavericks. I guess CRAN doesn't have linkable URLs, but here is the error message on the WGCNA build check for Mavericks: using R version 3.1.0 Patched (2014-06-11 r65921) using platform: x86_64-apple-darwin13.1.0 (64-bit) using session charset: UTF-8 checking for file 'WGCNA/DESCRIPTION' ... OK this is package 'WGCNA' version '1.34' checking package namespace information ... OK checking package dependencies ... ERROR Package required but not available: 'impute' Packages suggested but not available for checking: 'GO.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'AnnotationDbi' 'minet' See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. On Wed, Apr 10, 2013 at 6:55 PM, Peter Langfelder <peter.langfelder at="" gmail.com=""> wrote: > 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/R esources/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/DN Acopy/libs/DNAcopy.so': >>> >>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/libr ary/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/DNA copy/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/down loaded_packages >>>>> >>>>> library(impute) >>>> >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> unable to load shared object >>>> >>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/i mpute/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/im pute/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 > > _______________________________________________ > 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 -- Levi Waldron Assistant Professor of Biostatistics City University of New York School of Public Health, Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 phone: 212-396-7747 www.waldronlab.org

GUI impute DNAcopy GUI impute DNAcopy • 3.9k views

ADD COMMENT • link updated 10.4 years ago by Dan Tenenbaum ★ 8.2k • written 10.5 years ago by Levi Waldron ▴ 80

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 5 months ago

United States

Hi Levi, ----- Original Message ----- > From: "Levi Waldron" <levi.waldron at="" hunter.cuny.edu=""> > To: "Peter Langfelder" <peter.langfelder at="" gmail.com=""> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Stephanie M. Gogarten" <sdmorris at="" u.washington.edu="">, > bioconductor at r-project.org > Sent: Thursday, June 12, 2014 6:22:47 PM > Subject: Re: [BioC] Error installing impute package > > I just noticed this problem myself - not with impute itself, but > because WGCNA is not building in CRAN for Mavericks. I guess CRAN > doesn't have linkable URLs, but here is the error message on the > WGCNA > build check for Mavericks: > > using R version 3.1.0 Patched (2014-06-11 r65921) > using platform: x86_64-apple-darwin13.1.0 (64-bit) > using session charset: UTF-8 > checking for file 'WGCNA/DESCRIPTION' ... OK > this is package 'WGCNA' version '1.34' > checking package namespace information ... OK > checking package dependencies ... ERROR > Package required but not available: 'impute' > > Packages suggested but not available for checking: > 'GO.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'AnnotationDbi' 'minet' > > See the information on DESCRIPTION files in the chapter 'Creating R > packages' of the 'Writing R Extensions' manual. > > The url is http://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks /WGCNA-00check.html I have written to Simon Urbanek who is running the Mavericks CRAN builds and asked him about this. impute is available on all platforms so I don't think the problem is on the BioC end. That build report also says that other BioC packages in WGCNA's Suggests field are not available, but they all should be. Will let you know what I find out. Thanks, Dan > On Wed, Apr 10, 2013 at 6:55 PM, Peter Langfelder > <peter.langfelder at="" gmail.com=""> wrote: > > 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/Resour ces/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/ DNAcopy/libs/DNAcopy.so': > >>> > >>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/li brary/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/D NAcopy/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/do wnloaded_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/l ibrary/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' > >>>> > >>>> _______________________________________________ > >>>> 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 > > > > _______________________________________________ > > 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 > > > > -- > Levi Waldron > Assistant Professor of Biostatistics > City University of New York School of Public Health, Hunter College > 2180 3rd Ave Rm 538 > New York NY 10035-4003 > phone: 212-396-7747 > www.waldronlab.org >

ADD COMMENT • link 10.4 years ago Dan Tenenbaum ★ 8.2k

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Hi all, Simon already installed impute on the Mavericks machine, per my request. I just submitted a new version of WGCNA to CRAN and it should be up in a day or two, hopefully including the Mavericks binary. To the best of my knowledge Bioconductor packages are not necessarily all installed on all CRAN machines, sometimes one has to ask for it specifically. Best, Peter On Fri, Jun 13, 2014 at 5:02 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > Hi Levi, > > ----- Original Message ----- >> From: "Levi Waldron" <levi.waldron at="" hunter.cuny.edu=""> >> To: "Peter Langfelder" <peter.langfelder at="" gmail.com=""> >> Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Stephanie M. Gogarten" <sdmorris at="" u.washington.edu="">, >> bioconductor at r-project.org >> Sent: Thursday, June 12, 2014 6:22:47 PM >> Subject: Re: [BioC] Error installing impute package >> >> I just noticed this problem myself - not with impute itself, but >> because WGCNA is not building in CRAN for Mavericks. I guess CRAN >> doesn't have linkable URLs, but here is the error message on the >> WGCNA >> build check for Mavericks: >> >> using R version 3.1.0 Patched (2014-06-11 r65921) >> using platform: x86_64-apple-darwin13.1.0 (64-bit) >> using session charset: UTF-8 >> checking for file 'WGCNA/DESCRIPTION' ... OK >> this is package 'WGCNA' version '1.34' >> checking package namespace information ... OK >> checking package dependencies ... ERROR >> Package required but not available: 'impute' >> >> Packages suggested but not available for checking: >> 'GO.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'AnnotationDbi' 'minet' >> >> See the information on DESCRIPTION files in the chapter 'Creating R >> packages' of the 'Writing R Extensions' manual. >> >> > > The url is > > http://www.r-project.org/nosvn/R.check/r-release-osx- x86_64-mavericks/WGCNA-00check.html > > I have written to Simon Urbanek who is running the Mavericks CRAN builds and asked him about this. impute is available on all platforms so I don't think the problem is on the BioC end. That build report also says that other BioC packages in WGCNA's Suggests field are not available, but they all should be. > > Will let you know what I find out. > > Thanks, > Dan > > >> On Wed, Apr 10, 2013 at 6:55 PM, Peter Langfelder >> <peter.langfelder at="" gmail.com=""> wrote: >> > 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/Resou rces/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 /DNAcopy/libs/DNAcopy.so': >> >>> >> >>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/l ibrary/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/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/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/librar y/impute/libs/impute.so': >> >>>> >> >>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/ library/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' >> >>>> >> >>>> _______________________________________________ >> >>>> 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 >> > >> > _______________________________________________ >> > 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 >> >> >> >> -- >> Levi Waldron >> Assistant Professor of Biostatistics >> City University of New York School of Public Health, Hunter College >> 2180 3rd Ave Rm 538 >> New York NY 10035-4003 >> phone: 212-396-7747 >> www.waldronlab.org >>

ADD REPLY • link 10.4 years ago Peter Langfelder ★ 3.0k

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Entering edit mode

----- Original Message ----- > From: "Peter Langfelder" <peter.langfelder at="" gmail.com=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Levi Waldron" <levi.waldron at="" hunter.cuny.edu="">, "Stephanie M. Gogarten" <sdmorris at="" u.washington.edu="">, > bioconductor at r-project.org > Sent: Friday, June 13, 2014 5:35:38 PM > Subject: Re: [BioC] Error installing impute package > > Hi all, > > Simon already installed impute on the Mavericks machine, per my > request. I just submitted a new version of WGCNA to CRAN and it > should > be up in a day or two, hopefully including the Mavericks binary. > > To the best of my knowledge Bioconductor packages are not necessarily > all installed on all CRAN machines, sometimes one has to ask for it > specifically. > Normally any dependency you specify in your DESCRIPTION file will be installed by both the BioC and CRAN build machines. Because we didn't have Mavericks builds at the beginning of our devel cycle, Simon has been installing some packages by hand, and not installing others (such as packages in Suggests). Most BioC packages are now building on Mavericks, and I'll contact the maintainers of the remaining ones to see how we can get them green. It's better for all concerned if packages are installed automatically and we don't have to make special requests. Dan > Best, > > Peter > > > > On Fri, Jun 13, 2014 at 5:02 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > wrote: > > Hi Levi, > > > > ----- Original Message ----- > >> From: "Levi Waldron" <levi.waldron at="" hunter.cuny.edu=""> > >> To: "Peter Langfelder" <peter.langfelder at="" gmail.com=""> > >> Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Stephanie M. Gogarten" > >> <sdmorris at="" u.washington.edu="">, > >> bioconductor at r-project.org > >> Sent: Thursday, June 12, 2014 6:22:47 PM > >> Subject: Re: [BioC] Error installing impute package > >> > >> I just noticed this problem myself - not with impute itself, but > >> because WGCNA is not building in CRAN for Mavericks. I guess CRAN > >> doesn't have linkable URLs, but here is the error message on the > >> WGCNA > >> build check for Mavericks: > >> > >> using R version 3.1.0 Patched (2014-06-11 r65921) > >> using platform: x86_64-apple-darwin13.1.0 (64-bit) > >> using session charset: UTF-8 > >> checking for file 'WGCNA/DESCRIPTION' ... OK > >> this is package 'WGCNA' version '1.34' > >> checking package namespace information ... OK > >> checking package dependencies ... ERROR > >> Package required but not available: 'impute' > >> > >> Packages suggested but not available for checking: > >> 'GO.db' 'org.Hs.eg.db' 'org.Mm.eg.db' 'AnnotationDbi' 'minet' > >> > >> See the information on DESCRIPTION files in the chapter 'Creating > >> R > >> packages' of the 'Writing R Extensions' manual. > >> > >> > > > > The url is > > > > http://www.r-project.org/nosvn/R.check/r-release-osx- x86_64-mavericks/WGCNA-00check.html > > > > I have written to Simon Urbanek who is running the Mavericks CRAN > > builds and asked him about this. impute is available on all > > platforms so I don't think the problem is on the BioC end. That > > build report also says that other BioC packages in WGCNA's > > Suggests field are not available, but they all should be. > > > > Will let you know what I find out. > > > > Thanks, > > Dan > > > > > >> On Wed, Apr 10, 2013 at 6:55 PM, Peter Langfelder > >> <peter.langfelder at="" gmail.com=""> wrote: > >> > 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/Res ources/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/libra ry/DNAcopy/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/librar y/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/contr ib/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 /downloaded_packages > >> >>>>> > >> >>>>> library(impute) > >> >>>> > >> >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : > >> >>>> unable to load shared object > >> >>>> > >> >>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/libr ary/impute/libs/impute.so': > >> >>>> > >> >>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resource s/library/impute/libs/impute.so, > >> >>>> 6): Library not loaded: /usr/local/lib/libgfortran.2.dylib > >> >>>> Referenced from: > >> >>>> > >> >>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/libra ry/impute/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 > >> > > >> > _______________________________________________ > >> > 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 > >> > >> > >> > >> -- > >> Levi Waldron > >> Assistant Professor of Biostatistics > >> City University of New York School of Public Health, Hunter > >> College > >> 2180 3rd Ave Rm 538 > >> New York NY 10035-4003 > >> phone: 212-396-7747 > >> www.waldronlab.org > >> >

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