Question: Issue to install biomaRt, Gviz, rtracklayer, and S4Vectors under BioC 3.0
0
gravatar for Tiphaine Martin
4.5 years ago by
France
Tiphaine Martin40 wrote:

Hi,

I would like to install a list of R packages (rtracklayer, biomaRt, Gviz, S4Vectors) that my new package depends on from the devel (BioC 3.0) repository. But I have error messages that say that they don't exist under BioC 3.0.

Could you help me ?

Regards Tiphaine

### Type of error

biocLite("rtracklayer")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'rtracklayer'
Warning message:
package ‘rtracklayer’ is not available (for R version 3.1.1)

 

biocLite("biomaRt")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'biomaRt'
Warning: dependency ‘S4Vectors’ is not available
also installing the dependencies ‘IRanges’, ‘GenomeInfoDb’, ‘AnnotationDbi’

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/IRanges_1.99.31.tar.gz'
Content type 'application/x-gzip' length 584329 bytes (570 Kb)
opened URL
==================================================
downloaded 570 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/GenomeInfoDb_1.1.26.tar.gz'
Content type 'application/x-gzip' length 262795 bytes (256 Kb)
opened URL
==================================================
downloaded 256 Kb

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/AnnotationDbi_1.27.19.tar.gz'
Content type 'application/x-gzip' length 4255249 bytes (4.1 Mb)
opened URL
==================================================
downloaded 4.1 Mb

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/biomaRt_2.21.5.tar.gz'
Content type 'application/x-gzip' length 276094 bytes (269 Kb)
opened URL
==================================================
downloaded 269 Kb

ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/tiphaine/MynewR/lib64/R/library/IRanges’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/home/tiphaine/MynewR/lib64/R/library/GenomeInfoDb’
ERROR: dependencies ‘GenomeInfoDb’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/tiphaine/MynewR/lib64/R/library/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘biomaRt’
* removing ‘/home/tiphaine/MynewR/lib64/R/library/biomaRt’

The downloaded source packages are in
    ‘/tmp/RtmplVz84K/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘IRanges’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biomaRt’ had non-zero exit status

 

> biocLite("S4Vectors")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'S4Vectors'
Warning message:
package ‘S4Vectors’ is not available (for R version 3.1.1)

 

#### SessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BiocGenerics_0.11.5  BiocInstaller_1.15.5

loaded via a namespace (and not attached):
[1] tools_3.1.1
installation • 3.8k views
ADD COMMENTlink modified 4.4 years ago • written 4.5 years ago by Tiphaine Martin40

These packages are all available again now.

ADD REPLYlink written 4.4 years ago by Dan Tenenbaum8.2k
Answer: Issue to install biomaRt, Gviz, rtracklayer, and S4Vectors under BioC 3.0
1
gravatar for Martin Morgan
4.5 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

When using the 'devel' version of Bioconductor, it usually makes sense to use the most recent appropriate version of R; please update to R-3.1.1 or 3-1-patched.

The problem is that, as part of our standard preparation for the forthcoming release, the 3.0 repository was flushed (all packages removed) and re-populated with the packages from the nightly build. Unfortunately, several packages failed to build correctly (see current build results) and hence were not available in the repository. It seems that two important packages failed to build for a second time, so GenomicRanges is not available for a second day. This will either be remedied in the next build, or manually; the solution is either patience or installation from subversion.

ADD COMMENTlink written 4.5 years ago by Martin Morgan ♦♦ 23k
Answer: Issue to install biomaRt, Gviz, rtracklayer, and S4Vectors under BioC 3.0
0
gravatar for Peter
4.5 years ago by
Peter0
China
Peter0 wrote:

I have the same problem.

ADD COMMENTlink written 4.5 years ago by Peter0
Answer: Issue to install biomaRt, Gviz, rtracklayer, and S4Vectors under BioC 3.0
0
gravatar for Tiphaine Martin
4.4 years ago by
France
Tiphaine Martin40 wrote:

Thanks, I am going to wait that the packages can build.

Thank  Bioconductor team for your work.

Tiph

ADD COMMENTlink written 4.4 years ago by Tiphaine Martin40
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