problem with 'biomaRt' package installation: Error in loadNamespace(i, c(lib.loc, .libPaths()))
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@glazko-galina-v-4557
Last seen 7.0 years ago
United States
Dear list, I was trying to install biomaRt package. > biocLite('biomaRt') Everything worked, but I had this warning: Warning: unable to move temporary installation 'C:\Program Files\R\R-2.15.0\library\file77847d9453b\XML' to 'C:\Program Files\R\R-2.15.0\library\XML' However,: package 'biomaRt' successfully unpacked and MD5 sums checked Then, when I was trying to load the library I had the following error: > library(biomaRt) Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'XML' Error: package/namespace load failed for 'biomaRt' Enigmatically, there is no such directory 'file77847d9453b' in 'C:\Program Files\R\R-2.15.0\library' I would appreciate an advise how to fix this error! Best regards Galina > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome_1.24.0 GenomicRanges_1.8.3 Biostrings_2.24.1 IRanges_1.14.2 BiocGenerics_0.2.0 edgeR_2.6.0 limma_3.12.0 [8] BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] RCurl_1.91-1.1 stats4_2.15.0 tools_2.15.0 Confidentiality Notice: This e-mail message, including a...{{dropped:10}}
biomaRt biomaRt • 3.7k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 8 months ago
United States
On Wed, Apr 11, 2012 at 6:54 AM, Glazko, Galina V <gvglazko at="" uams.edu=""> wrote: > Dear list, > > I was trying to install biomaRt package. >> ?biocLite('biomaRt') > > Everything worked, but I had this warning: > > Warning: unable to move temporary installation 'C:\Program Files\R\R-2.15.0\library\file77847d9453b\XML' to 'C:\Program Files\R\R-2.15.0\library\XML' > > However,: > package 'biomaRt' successfully unpacked and MD5 sums checked > > Then, when I was trying to load the library I had the following error: >> ?library(biomaRt) > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > ?there is no package called 'XML' > Error: package/namespace load failed for 'biomaRt' > > Enigmatically, there is no such directory 'file77847d9453b' in 'C:\Program Files\R\R-2.15.0\library' > I would appreciate an advise how to fix this error! > > Best regards > Galina Try starting a fresh R session with R --vanilla then library(BiocInstaller) biocLite(c("XML","biomaRt")) Dan >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 ? ?LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United States.1252 > > attached base packages: > [1] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BSgenome_1.24.0 ? ? GenomicRanges_1.8.3 Biostrings_2.24.1 ? IRanges_1.14.2 ? ? ?BiocGenerics_0.2.0 ?edgeR_2.6.0 ? ? ? ? limma_3.12.0 > [8] BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] RCurl_1.91-1.1 stats4_2.15.0 ?tools_2.15.0 > Confidentiality Notice: This e-mail message, including a...{{dropped:10}} > > _______________________________________________ > 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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Dan, Genius! Thank you, it worked fine! Though do not understand why. Best regards Galina -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wednesday, April 11, 2012 9:59 AM To: Glazko, Galina V Cc: bioconductor at r-project.org Subject: Re: [BioC] problem with 'biomaRt' package installation: Error in loadNamespace(i, c(lib.loc, .libPaths())) On Wed, Apr 11, 2012 at 6:54 AM, Glazko, Galina V <gvglazko at="" uams.edu=""> wrote: > Dear list, > > I was trying to install biomaRt package. >> ?biocLite('biomaRt') > > Everything worked, but I had this warning: > > Warning: unable to move temporary installation 'C:\Program Files\R\R-2.15.0\library\file77847d9453b\XML' to 'C:\Program Files\R\R-2.15.0\library\XML' > > However,: > package 'biomaRt' successfully unpacked and MD5 sums checked > > Then, when I was trying to load the library I had the following error: >> ?library(biomaRt) > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > ?there is no package called 'XML' > Error: package/namespace load failed for 'biomaRt' > > Enigmatically, there is no such directory 'file77847d9453b' in 'C:\Program Files\R\R-2.15.0\library' > I would appreciate an advise how to fix this error! > > Best regards > Galina Try starting a fresh R session with R --vanilla then library(BiocInstaller) biocLite(c("XML","biomaRt")) Dan >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 ? ?LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_United States.1252 > > attached base packages: > [1] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BSgenome_1.24.0 ? ? GenomicRanges_1.8.3 Biostrings_2.24.1 ? IRanges_1.14.2 ? ? ?BiocGenerics_0.2.0 ?edgeR_2.6.0 ? ? ? ? limma_3.12.0 > [8] BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] RCurl_1.91-1.1 stats4_2.15.0 ?tools_2.15.0 > Confidentiality Notice: This e-mail message, including a...{{dropped:10}} > > _______________________________________________ > 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 Confidentiality Notice: This e-mail message, including a...{{dropped:8}}
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