shared object ‘mzR.so’ not found after mzR update
1
0
Entering edit mode
@alejandra-gonzalez-beltran-5863
Last seen 7.1 years ago
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 mzR • 1.3k views
ADD COMMENT
0
Entering edit mode
@steve-lianoglou-2771
Last seen 5 hours ago
Denali
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 COMMENT
0
Entering edit mode
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]]

Login before adding your answer.

Traffic: 241 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6