[BioC] R error by installing the org.Hs.eg.db package

[James W. MacDonald]

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/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

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