Trouble installing DESeq / GenomeInfoDb
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@nathanmedd-13641
Last seen 4.1 years ago

Hi there

I am trying to install DESeq but the package GenomeInfoDb will not load:

> library(DESeq2)
Error: package or namespace load failed for �GenomeInfoDb� in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called �GenomeInfoDbData�
Error: package ‘GenomeInfoDb’ could not be loaded

Even when trying to load the package seperately:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help

> biocLite("GenomeInfoDb")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).

Installing package(s) �GenomeInfoDb�

also installing the dependency �GenomeInfoDbData�

Content type 'application/zip' length 7073643 bytes (6.7 MB)

package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked

installing the source package �GenomeInfoDbData�

Content type 'application/x-gzip' length 16238792 bytes (15.5 MB)

'\\csce.datastore.ed.ac.uk\csce\biology\users\s14747**\Data\RNA expression\Analysis'

CMD.EXE was started with the above path as the current directory.

UNC paths are not supported.  Defaulting to Windows directory.

'C:\Program' is not recognized as an internal or external command,

operable program or batch file.

Any help appreciated.

N

deseq2 genomeinfodb • 4.5k views
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@james-w-macdonald-5106
Last seen 32 minutes ago
United States

The main problem here is that you appear to be trying to install packages on a server rather than your local machine, but you have R running on the local machine. This is a suboptimal approach. If you are going to run R on your local machine you should put the library directory on that machine's own hard drive, not on a server share.

The error

CMD.EXE was started with the above path as the current directory.

UNC paths are not supported.  Defaulting to Windows directory.

Is coming directly from Windows, not R. There is a tech note from Microsoft that seems to indicate that you need an updated version of CMD.exe, but the tech note seems to indicate that this is a problem with Windows NT. And since it's not, like, 1999, I sort of doubt you are running that OS. So it's probably a big mystery that you can easily fix by not using a server share for your library dir.

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I think also you can map the network drive to a letter, so that \\csce.datastore.ed.ac.uk\csce can be referred to as z:\csce\...

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Hi, I have a similar error when trying to install Ballgown package from Bioconductor.

Following is the error message:

> install.packages("C:/Users/a1207602/RStudio-1.1.383/R/downloaded_packages/GenomeInfoDbData_0.99.1.tar.gz", repos = NULL, type = "source")
Installing package into ‘\\UOFA/USERS$/users2/a1207602/R/win-library/3.4’ (as ‘lib’ is unspecified) '\\UOFA\USERS$\users2\a1207602'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
Warning in install.packages :
installation of package ‘C:/Users/a1207602/RStudio-1.1.383/R/downloaded_packages/GenomeInfoDbData_0.99.1.tar.gz’ had non-zero exit status

Any help appreciated.