FWIW BiocManager::install() really delegates to install.packages(). The
packages are downloaded to 'destdir=' as documented on ?install.packages --
typically file.path(tempdir(), "downloaded_packages") -- and one path to
troubleshooting installs is to tackle the problematic installation(s)
I certainly have run into this situation with R generally. It seems like a
patch to
install.packages would be the best approach to introduce this
functionality. I wonder
if Henrik Bengtsson or Dirk Eddelbuettel have pondered this.
In any case, I am sympathetic with the suggestion but I believe
Sometimes I will go to update a machine / do a clean Bioconductor install
and a large number of packages will need to be downloaded.
If something goes wrong during the installation, which is not uncommon in
cases where the number of packages being installed is large, then the
process has to be
I made sure I was using Bioc-3.13 and that my packages were valid
> BiocManager::version()
[1] '3.13'
> BiocManager::valid()
[1] TRUE
I then ran purl() and source(), eventually arriving at the error on the build
system
> knitr::purl("multiGSEA.rmd")
[1] "multiGSEA.R"
> source("multiGSEA.R",
Here's what happened when I tried to build your package as instructed in
the report page:
stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES$ R_ENVIRON_USER=~/.Renviron.bioc
Rdev CMD build multiGSEA
1/9 packages newly attached/loaded, see sessionInfo() for details.
* checking for file ‘multiGSEA/DESCRIPTION’
Dear BioC-Developers,
after the Release of Bioconductor 3.12 I encountered a building error of
the multiGSEA package in the devel branch (building the vignette causes
the error, see:
http://bioconductor.org/checkResults/devel/bioc-LATEST/multiGSEA/machv2-buildsrc.html
).
Until now, I am not
