problem installing S.cerevisiae genome
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Entering edit mode
ealopera • 0
@ealopera-14681
Last seen 3.4 years ago

Hello, I have been trying to isntall S.cerevisiae genome, but it just does not work, and I cannot figureout why. This is the compelte output:

biocLite("BSgenome.Scerevisiae.UCSC.sacCer2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
Installing package(s) ‘BSgenome.Scerevisiae.UCSC.sacCer2’
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES'
installing the source package ‘BSgenome.Scerevisiae.UCSC.sacCer2’
trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz'
Content type 'application/x-gzip' length 2967843 bytes (2.8 MB)
downloaded 2.8 MB
'\\servidordc\documentos$\investigador1\Mis documentos'
CMD.EXE se inici¢ con esta ruta como el directorio actual. No se permiten
rutas UNC. Regresando de manera predeterminada al directorio Windows.
* installing *source* package 'BSgenome.Scerevisiae.UCSC.sacCer2' ...
** R

** inst
** preparing package for lazy loading
`Warning: package 'BSgenome' was built under R version 3.4.1`
Warning: package 'BiocGenerics' was built under R version 3.4.1
`Warning: package 'S4Vectors' was built under R version 3.4.1`
`Warning: package 'IRanges' was built under R version 3.4.1`
`Warning: package 'GenomeInfoDb' was built under R version 3.4.2`
`Warning: package 'GenomicRanges' was built under R version 3.4.2`
`Warning: package 'Biostrings' was built under R version 3.4.1`
`Warning: package 'rtracklayer' was built under R version 3.4.2`
`** help`
`*** installing help indices`
`** building package indices`
`** testing if installed package can be loaded`
`*** arch - i386`
`Warning: package 'BSgenome' was built under R version 3.4.1`
`Warning: package 'BiocGenerics' was built under R version 3.4.1`
`Warning: package 'S4Vectors' was built under R version 3.4.1`
`Warning: package 'IRanges' was built under R version 3.4.1`
`Warning: package 'GenomeInfoDb' was built under R version 3.4.2`
`Warning: package 'GenomicRanges' was built under R version 3.4.2`
`Warning: package 'Biostrings' was built under R version 3.4.1`
`Warning: package 'rtracklayer' was built under R version 3.4.2`
`Error: package or namespace load failed for 'BSgenome.Scerevisiae.UCSC.sacCer2':`
` .onLoad failed in loadNamespace() for 'BSgenome.Scerevisiae.UCSC.sacCer2', details:`
`  call: system.file("extdata", package = pkgname, lib.loc = libname, `
`  error: no file found`
`Error: loading failed`
`Ejecución interrumpida`
`*** arch - x64`
`Warning: package 'BSgenome' was built under R version 3.4.1`
`Warning: package 'BiocGenerics' was built under R version 3.4.1`
`Warning: package 'S4Vectors' was built under R version 3.4.1`
`Warning: package 'IRanges' was built under R version 3.4.1`
`Warning: package 'GenomeInfoDb' was built under R version 3.4.2`
`Warning: package 'GenomicRanges' was built under R version 3.4.2`
`Warning: package 'Biostrings' was built under R version 3.4.1`
`Warning: package 'rtracklayer' was built under R version 3.4.2`
`Error: package or namespace load failed for 'BSgenome.Scerevisiae.UCSC.sacCer2':`
` .onLoad failed in loadNamespace() for 'BSgenome.Scerevisiae.UCSC.sacCer2', details:`
`  call: system.file("extdata", package = pkgname, lib.loc = libname, `
`  error: no file found`
`Error: loading failed`
`Ejecución interrumpida`
`ERROR: loading failed for 'i386', 'x64'`
`* removing '\\servidordc/documentos$/investigador1/Mis documentos/R/win-library/3.4/BSgenome.Scerevisiae.UCSC.sacCer2'`
`The downloaded source packages are in`
`‘C:\Users\investigador1\AppData\Local\Temp\RtmpWQCOIp\downloaded_packages’`
`Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:`
`  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'`
`installation path not writeable, unable to update packages: boot, coin,`
`  cubature, data.table, digest, dplyr, foreign, glue, gWidgetsRGtk2, lazyeval,`
`  Matrix, mgcv, multcomp, plotrix, Rcpp, reshape, reshape2, rlang, sandwich,`
`  scales, sciplot, stringi, survey, tibble, tidyr`
`Warning messages:`
`1: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "\\servidordc\documentos$\investigador1\Mis documentos\R\win-library\3.4" C:\Users\INVEST~1\AppData\Local\Temp\RtmpWQCOIp/downloaded_packages/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz' had status 1 `
`2: In install.packages(pkgs = doing, lib = lib, ...) :`
`  installation of package ‘BSgenome.Scerevisiae.UCSC.sacCer2’ had non-zero exit status`

 

any help woul be great.

thank you

software error • 846 views
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0
Entering edit mode
@martin-morgan-1513
Last seen 5 days ago
United States

Try mapping the network drive \servidordc\docmentos$\... to a drive letter w:\ or similar, ad arranging for R to use the mapped drive.

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