A colleague of mine (RS) is trying to install the
clusterProfiler package that depends on
GO.db on his Windows laptop using R 3.5 and Bioconductor 3.8. We haven't been able to install it via
BiocManager::install() due to an error with
untar2(). If we download the source
.tar.gz file on my macOS laptop, uncompress it, copy the contents to the Windows laptop and try installing with
R CMD INSTALL GO.db we then get a second type of error.
A second colleague (EB) installed R 3.5 (a fresh install) on her Windows laptop and was able to install
I have no idea what difference between the 2 Windows computers is affecting the installation and would appreciate any leads on where to look next. My colleague RS has:
- Disabled his antivirus
- Checked the permissions of his R installation directory
- Has WinRAR associated with .gz files.
- If he searches for
tar.exehe has 2 versions. One under
Rtoolsand another one in elsewhere.
The issue with
untar2() also affects RS's ability to install the latest version of
rcmdcheck. I'm hoping that if we are able to resolve the
untar2() problem, then everything will work. That is, I hope we don't run into the second problem
Error: object 'ÿ_' not found.
In this gist https://gist.github.com/lcolladotor/fb4de1d002e0b200302a51c9c10f0e3d you can find all the code and R session information for both RS and EB. Note that both are using BiocManager version 1.30.4. In general RS has no problems installing Windows binary versions of packages, but GO.db is only available via source at https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz.
Let us know if there's any other piece of information we could give you that would be helpful.