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

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.

I have the same problem.

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

Thank  Bioconductor team for your work.

Tiph