Remove Lock Files

[jwokaty]

Occasionally, installation will be blocked by locked files. We need a mechanism to remove the locked files before or at the start of the run.

[hpages]

We already remove LOCK files at the start of the run on Linux and Mac:

BBS/utils/clean-before-run.sh

Line 4 in 41e656b

rm -rf "$BBS_R_HOME/library/00LOCK"

Looks like we don't do it on Windows (https://github.com/Bioconductor/BBS/blob/devel/utils/clean-before-run.bat), not sure why.

Note that clean-before-run.sh and clean-before-run.bat are called by run.sh and run.bat, respectively

I suspect that the LOCK files that we see occasionally on the Mac builders that get in the way get created during the INSTALL stage itself (STAGE2).

LOCK files are expected: R CMD INSTALL automatically creates them at the beginning of a package installation and removes them at the end, whether the installation was succesful or not. In other words, R CMD INSTALL should remove them no matter what. So we need to understand why sometimes a LOCK file gets in the way. One possible cause could be that 2 build runs are overlapping and are both trying to install the same package at the same time. Another reason could be that for some reason R CMD INSTALL dies before it has a chance to remove the LOCK file (e.g. BBS kills it after a TIMEOUT?). Another reason could be an issue with R CMD INSTALL itself where, under some circumstances, it does not or cannot remove the LOCK file. This will require some non-trivial detective work.

BTW, now that we install in <R_HOME>/site-library/ on Linux, clean-before-run.sh should remove LOCK files from that folder too.

Thanks

[jwokaty]

There were locks recently on a mac arm64 builder (https://support.bioconductor.org/p/9152542/#9152543), so in that case it wasn't an overlap of builds. It might be related to a timeout; however, it should still remove the locks on the next run.

Maybe rm -rf "$BBS_R_HOME/library/00LOCK" should be changed to rm -rf "$BBS_R_HOME/library/00LOCK*" with an asterisk since lock files are named 00LOCK-packageName as in /usr/local/lib/R/site-library/00LOCK-fgsea?

[hpages]

Good catch! The rm -rf "$BBS_R_HOME/library/00LOCK" command is from the ancient times when R CMD INSTALL only supported a per-library lock file. Per-package lock files are more recent and I think they are used by default (contrary to R CMD INSTALL --help claim).

There's also the option to disable locking completely by using R CMD INSTALL --no-lock but I'm not too confortable with that.

Since you are on this, make sure to clean <R_HOME>/site-library/ in addition to <R_HOME>/library/.

Thanks