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Question: R error by installing the org.Hs.eg.db package
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5.8 years ago by
Guest User12k
Guest User12k wrote:
I have a question about installing a package in R. It seems to be very simple, but I can't figure out why it goes wrong. I want to install the package: org.Hs.eg.db from bioconductor. All the information about the R version and other package version are below. I hope that somebody can help me with this! > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("org.Hs.eg.db") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'org.Hs.eg.db' trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin /windows/contrib/2.15/org.Hs.eg.db_2.8.0.zip' Content type 'application/zip' length 47453600 bytes (45.3 Mb) opened URL downloaded 45.3 Mb The downloaded binary packages are in C:\Users\lsvijfhuizen\AppData\Local\Temp\RtmpUvyORM\downloaded_pac kages Old packages: 'digest' Update all/some/none? [a/s/n]: a trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/digest_0.6.1.zip' Content type 'application/zip' length 135921 bytes (132 Kb) opened URL downloaded 132 Kb package ???digest??? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\lsvijfhuizen\AppData\Local\Temp\RtmpUvyORM\downloaded_pac kages Warning message: In unzip(zipname, exdir = dest) : write error in extracting from zip file -- output of sessionInfo(): >sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) - locale: LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252 - attached base packages: stats graphics grDevices utils datasets methods base - other attached packages: BiocInstaller_1.8.3 globaltest_5.12.0 biomaRt_2.14.0 edgeR_3.0.8 limma_3.14.4 - loaded via a namespace (and not attached): annotate_1.36.0 AnnotationDbi_1.20.3 Biobase_2.18.0 BiocGenerics_0.4.0 DBI_0.2-5 IRanges_1.16.4 parallel_2.15.2 RCurl_1.95-3 RSQLite_0.11.2 splines_2.15.2 stats4_2.15.2 survival_2.37-2 tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 5.8 years ago by James W. MacDonald48k • written 5.8 years ago by Guest User12k
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5.8 years ago by
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James W. MacDonald48k wrote:
Hi Lisann, On 1/23/2013 10:32 AM, lisann [guest] wrote: > I have a question about installing a package in R. It seems to be very simple, but I can't figure out why it goes wrong. I want to install the package: org.Hs.eg.db from bioconductor. All the information about the R version and other package version are below. > > I hope that somebody can help me with this! > > > source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > > biocLite("org.Hs.eg.db") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'org.Hs.eg.db' > trying URL 'http://bioconductor.org/packages/2.11/data/annotation/ bin/windows/contrib/2.15/org.Hs.eg.db_2.8.0.zip' > Content type 'application/zip' length 47453600 bytes (45.3 Mb) > opened URL > downloaded 45.3 Mb > > > The downloaded binary packages are in > C:\Users\lsvijfhuizen\AppData\Local\Temp\RtmpUvyORM\downloaded_ packages > Old packages: 'digest' > Update all/some/none? [a/s/n]: a > trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.15/digest_0.6.1.zip' > Content type 'application/zip' length 135921 bytes (132 Kb) > opened URL > downloaded 132 Kb > > package ???digest??? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\lsvijfhuizen\AppData\Local\Temp\RtmpUvyORM\downloaded_ packages > Warning message: > In unzip(zipname, exdir = dest) : write error in extracting from zip file Have you tried again? I just installed without problems: > biocLite("org.Hs.eg.db") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'org.Hs.eg.db' trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/windows/con trib/2.15/org.Hs.eg.db_2.8.0.zip' Content type 'application/zip' length 47453600 bytes (45.3 Mb) opened URL downloaded 45.3 Mb package 'org.Hs.eg.db' successfully unpacked and MD5 sums checked Best, Jim > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > - locale: > LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252 > > - attached base packages: > > stats graphics grDevices utils datasets methods base > > - other attached packages: > > BiocInstaller_1.8.3 globaltest_5.12.0 biomaRt_2.14.0 edgeR_3.0.8 limma_3.14.4 > > - loaded via a namespace (and not attached): > > annotate_1.36.0 AnnotationDbi_1.20.3 Biobase_2.18.0 > BiocGenerics_0.4.0 DBI_0.2-5 IRanges_1.16.4 > parallel_2.15.2 RCurl_1.95-3 RSQLite_0.11.2 > splines_2.15.2 stats4_2.15.2 survival_2.37-2 > tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.8 years ago by James W. MacDonald48k
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