Question: Trouble installing DESeq / GenomeInfoDb
0
gravatar for nathan.medd
2.3 years ago by
nathan.medd0 wrote:

Hi there 

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

> library(DESeq2)
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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�

 

cannot open URL 'https://bioconductor.org/packages/3.5/data/annotation/bin/windows/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.5/data/experiment/bin/windows/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/GenomeInfoDb_1.12.2.zip'

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

downloaded 6.7 MB

 

package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in

C:\Users\s14747**\AppData\Local\Temp\RtmpgFRc4Z\downloaded_packages

installing the source package �GenomeInfoDbData�

 

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz'

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

downloaded 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.

running command '"C:/Program Files/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "\\csce.datastore.ed.ac.uk\csce\biology\users\s14747**\R\win-library\3.4" C:\Users\s14747**\AppData\Local\Temp\RtmpgFRc4Z/downloaded_packages/GenomeInfoDbData_0.99.0.tar.gz' had status 1installation of package �GenomeInfoDbData� had non-zero exit status

The downloaded source packages are in

‘C:\Users\s14747**\AppData\Local\Temp\RtmpgFRc4Z\downloaded_packages’

Any help appreciated.

N

deseq2 genomeinfodb • 2.8k views
ADD COMMENTlink modified 2.3 years ago by James W. MacDonald51k • written 2.3 years ago by nathan.medd0
Answer: Trouble installing DESeq / GenomeInfoDb
0
gravatar for James W. MacDonald
2.3 years ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 2.3 years ago by James W. MacDonald51k

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\...

ADD REPLYlink written 2.3 years ago by Martin Morgan ♦♦ 24k

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 :
  running command '"C:/Program Files/R/R-34~1.2/bin/x64/R" CMD INSTALL -l "\\UOFA\USERS$\users2\a1207602\R\win-library\3.4" "C:/Users/a1207602/RStudio-1.1.383/R/downloaded_packages/GenomeInfoDbData_0.99.1.tar.gz"' had status 1
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.

Thanks in advance.

ADD REPLYlink written 23 months ago by amy160
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