problem installing S.cerevisiae genome
1
0
Entering edit mode
ealopera • 0
@ealopera-14681
Last seen 4.0 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 • 957 views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 4 months 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.

ADD COMMENT

Login before adding your answer.

Traffic: 656 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