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Question: shared object ‘mzR.so’ not found after mzR update
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gravatar for Alejandra Gonzalez-Beltran
5.7 years ago by
Dear all, After I updated the mzR package, I am unable to check or install my package due to 'shared object ‘mzR.so’ not found' . I am including the whole error and my sessionInfo() below. I thought it could be related to the recent changes as discussed in the thread entitled "mzR crashes R" and I have followed the discussion and tried to re-install mzR in different ways (e.g. indicating the mirror site, from source) but the problem persists. I will be grateful to get some guidance on how to solve this issue. Best regards, Alejandra ___ * installing *source* package ‘Risa’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes 'Risa.Rnw' ** testing if installed package can be loaded *** arch - i386 Error in library.dynam(lib, package, package.lib) : shared object ‘mzR.so’ not found Calls: sys.load.image ... tryCatch -> tryCatchList -> tryCatchOne -> <anonymous> Execution halted *** arch - x86_64 During startup - Warning message: Class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’ ERROR: loading failed for 'i386' ___ ___ sessionInfo() > sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Risa_1.1.0 biocViews_1.26.0 Rcpp_0.10.3 Biobase_2.18.0 BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] codetools_0.2-8 graph_1.36.2 mzR_1.4.7 RBGL_1.34.0 RCurl_1.95-4.1 RUnit_0.4.26 stats4_2.15.3 [8] tools_2.15.3 xcms_1.34.0 XML_3.95-0.2 ____ [[alternative HTML version deleted]]
mzr
ADD COMMENTlink modified 5.7 years ago by Steve Lianoglou12k • written 5.7 years ago by Alejandra Gonzalez-Beltran20
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gravatar for Steve Lianoglou
5.7 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, The errors you paste below suggest that you likely only have the 64bit version of mzR installed. Assuming that R is set to run in 64bit mode by default, if you try to install your package from the command line like so: R CMD INSTALL --no-multiarch /path/to/yourPackage Does it work? HTH, -steve On Thu, Mar 28, 2013 at 2:36 AM, Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran at="" gmail.com=""> wrote: > Dear all, > > After I updated the mzR package, I am unable to check or install my package > due to 'shared object ?mzR.so? not found' . I am including the whole error > and my sessionInfo() below. > > I thought it could be related to the recent changes as discussed in the > thread entitled "mzR crashes R" and I have followed the discussion and > tried to re-install mzR in different ways (e.g. indicating the mirror site, > from source) but the problem persists. > > I will be grateful to get some guidance on how to solve this issue. > > Best regards, > > Alejandra > > ___ > * installing *source* package ?Risa? ... > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** installing vignettes > 'Risa.Rnw' > ** testing if installed package can be loaded > *** arch - i386 > Error in library.dynam(lib, package, package.lib) : > shared object ?mzR.so? not found > Calls: sys.load.image ... tryCatch -> tryCatchList -> tryCatchOne -> > <anonymous> > Execution halted > *** arch - x86_64 > During startup - Warning message: > Class "C++Object" is defined (with package slot ?Rcpp?) but no metadata > object found to revise subclass information---not exported? Making a copy > in package ?.GlobalEnv? > ERROR: loading failed for 'i386' > ___ > > ___ sessionInfo() >> sessionInfo() > R version 2.15.3 (2013-03-01) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Risa_1.1.0 biocViews_1.26.0 Rcpp_0.10.3 > Biobase_2.18.0 BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] codetools_0.2-8 graph_1.36.2 mzR_1.4.7 RBGL_1.34.0 > RCurl_1.95-4.1 RUnit_0.4.26 stats4_2.15.3 > [8] tools_2.15.3 xcms_1.34.0 XML_3.95-0.2 > ____ > > [[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 -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 5.7 years ago by Steve Lianoglou12k
Hi Steve, Yes, it worked. Thank you very much for your help. Alejandra On 28 March 2013 06:51, Steve Lianoglou <mailinglist.honeypot@gmail.com>wrote: > Hi, > > The errors you paste below suggest that you likely only have the 64bit > version of mzR installed. Assuming that R is set to run in 64bit mode > by default, if you try to install your package from the command line > like so: > > R CMD INSTALL --no-multiarch /path/to/yourPackage > > Does it work? > > HTH, > > -steve > > On Thu, Mar 28, 2013 at 2:36 AM, Alejandra Gonzalez-Beltran > <alejandra.gonzalez.beltran@gmail.com> wrote: > > Dear all, > > > > After I updated the mzR package, I am unable to check or install my > package > > due to 'shared object ‘mzR.so’ not found' . I am including the whole > error > > and my sessionInfo() below. > > > > I thought it could be related to the recent changes as discussed in the > > thread entitled "mzR crashes R" and I have followed the discussion and > > tried to re-install mzR in different ways (e.g. indicating the mirror > site, > > from source) but the problem persists. > > > > I will be grateful to get some guidance on how to solve this issue. > > > > Best regards, > > > > Alejandra > > > > ___ > > * installing *source* package ‘Risa’ ... > > ** R > > ** inst > > ** preparing package for lazy loading > > ** help > > *** installing help indices > > ** building package indices > > ** installing vignettes > > 'Risa.Rnw' > > ** testing if installed package can be loaded > > *** arch - i386 > > Error in library.dynam(lib, package, package.lib) : > > shared object ‘mzR.so’ not found > > Calls: sys.load.image ... tryCatch -> tryCatchList -> tryCatchOne -> > > <anonymous> > > Execution halted > > *** arch - x86_64 > > During startup - Warning message: > > Class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata > > object found to revise subclass information---not exported? Making a > copy > > in package ‘.GlobalEnv’ > > ERROR: loading failed for 'i386' > > ___ > > > > ___ sessionInfo() > >> sessionInfo() > > R version 2.15.3 (2013-03-01) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] Risa_1.1.0 biocViews_1.26.0 Rcpp_0.10.3 > > Biobase_2.18.0 BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > > > loaded via a namespace (and not attached): > > [1] codetools_0.2-8 graph_1.36.2 mzR_1.4.7 RBGL_1.34.0 > > RCurl_1.95-4.1 RUnit_0.4.26 stats4_2.15.3 > > [8] tools_2.15.3 xcms_1.34.0 XML_3.95-0.2 > > ____ > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Steve Lianoglou > Defender of The Thesis > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]]
ADD REPLYlink written 5.7 years ago by Alejandra Gonzalez-Beltran20
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