Install bioconductor packages from SVN

Author

António Domingues

Published

February 25, 2015

Due to some issues with the way DEXseq calculates the log2foldchanges I decided to re-run an analysis with the issue fixed. Since it is not yet in the development branch, an install from svn was needed - my first!

Firstly the source code was downloaded with:

svn co --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DEXSeq DEXSeq

This followed a build to generated a package:

R CMD build --no-build-vignettes DEXSeq

I had issues with the build process, which failed during the vignette build. As I don’t care about it, using --no-build-vignettes bypassed the problem. Then it was a simply matter of starting R and installing the package:

install.packages("DEXSeq_1.12.2.tar.gz", repos=NULL)

Simple.

Reuse

Citation

BibTeX citation:
@online{domingues2015,
  author = {Domingues, António},
  title = {Install Bioconductor Packages from {SVN}},
  date = {2015-02-25},
  url = {https://amjdomingues.com/posts/2015-02-25-install-bioconductor-packages-from-svn/},
  langid = {en}
}
For attribution, please cite this work as:
Domingues, António. 2015. “Install Bioconductor Packages from SVN.” February 25, 2015. https://amjdomingues.com/posts/2015-02-25-install-bioconductor-packages-from-svn/.