Issue using ballgown
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Entering edit mode
dualeahmed • 0
@dualeahmed-17404
Last seen 3.0 years ago

I’ve used ballgown in the past with no issues but currently when I try to load the program on R, it is unable to but it is missing the dependency “GenomeInfoDbData”. I’ve tried to install it separately but that also failed. I've attached the output and hopefully would be able to help me out.

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help

> biocLite("ballgown")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 Patched (2018-09-11
  r75286).
Installing package(s) ‘ballgown’
also installing the dependencies ‘GenomeInfoDbData’, ‘GenomeInfoDb’

trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/GenomeInfoDb_1.16.0.zip'
Content type 'application/zip' length 3830739 bytes (3.7 MB)
downloaded 3.7 MB

trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/ballgown_2.12.0.zip'
Content type 'application/zip' length 3360539 bytes (3.2 MB)
downloaded 3.2 MB

package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked
package ‘ballgown’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Duale A\AppData\Local\Temp\Rtmp8UPLBX\downloaded_packages
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz'
Content type 'application/x-gzip' length 8204728 bytes (7.8 MB)
downloaded 7.8 MB

Warning: invalid package 'C:\Users\Duale'
Warning: invalid package 'A\AppData\Local\Temp\Rtmp8UPLBX/downloaded_packages/GenomeInfoDbData_1.1.0.tar.gz'
Error: ERROR: no packages specified
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\Duale A\AppData\Local\Temp\Rtmp8UPLBX\downloaded_packages’
Old packages: 'stringi'
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is later:
        binary source needs_compilation
stringi  1.1.7  1.2.4              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/stringi_1.1.7.zip'
Content type 'application/zip' length 14368013 bytes (13.7 MB)
downloaded 13.7 MB

package ‘stringi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Duale A\AppData\Local\Temp\Rtmp8UPLBX\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

> biocLite("GenomeInfoDbData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 Patched (2018-09-11
  r75286).
Installing package(s) ‘GenomeInfoDbData’
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz'
Content type 'application/x-gzip' length 8204728 bytes (7.8 MB)
downloaded 7.8 MB

Warning: invalid package 'C:\Users\Duale'
Warning: invalid package 'A\AppData\Local\Temp\Rtmp8UPLBX/downloaded_packages/GenomeInfoDbData_1.1.0.tar.gz'
Error: ERROR: no packages specified
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\Duale A\AppData\Local\Temp\Rtmp8UPLBX\downloaded_packages’
Old packages: 'stringi'
Update all/some/none? [a/s/n]: a

  There is a binary version available but the source version is later:
        binary source needs_compilation
stringi  1.1.7  1.2.4              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/stringi_1.1.7.zip'
Content type 'application/zip' length 14368013 bytes (13.7 MB)
downloaded 13.7 MB

package ‘stringi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Duale A\AppData\Local\Temp\Rtmp8UPLBX\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

 

software error ballgown genomeinfodbdata genomeinfodb • 708 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 48 minutes ago
United States

R doesn't like the space in your tempdir. You can pass an argument for the 'destDir' to some directory that doesn't have a space, although your user dir is the problem, so you may need to find a dir for which you have write permissions that doesn't have a space.

OR you could try

setwd("C:\Users\Duale A\AppData\Local\Temp\Rtmp8UPLBX\downloaded_packages")
install.packages("GenomeInfoDbData_1.1.0.tar.gz", repos = NULL, type = "source")

which should work as well.

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