Flush-Packages-HOWTO.Rmd
To remove stale software packages, we flush the software repository. This might be necessary when a build machine has transition from devel to release to try to remove odd version-numbered packages.
It’s important to reserve enough time and carefully check the results of the report so that it doesn’t negatively impact users.
The following are instructions to flush the software repository for the 3.14 builds as an example.
Verify that the software report for the day looks good and that you
have at least an hour before the next build. Look for packages, such as
GenomicFeatures
, that are dependencies for many packages
and ensure that they are not failing. If they are failing, you should
wait until they are passing before attempting to flush the software
repository.
As biocpush
, comment out the crontab entry for bioc.
This will prevent master from resyncing with staging on the build
machine you’re working on.
Create a backup of the software packages in case a package that is a
dependency for several packages, such as GenomicFeatures
,
that was passing later fails in the new build report after removing all
packages.
As biocpush
Remove all packages from ~biocpush/PACKAGES/3.14/bioc
for source, windows, and mac binaries. Everything except for the
Archives
directories should be gone and the
PACKAGES
files should be replaced with blank files.
As biocpush
postrun.sh
As biocbuild
rerun postrun.sh
so that we
get a new report. Check that the new report has green leds and that
important packages, such as GenomicFeatures
, pass so that
we don’t have a lot of failures.
If the report is not good, replace bioc
with
bioc.backup
and rerun the postrun.sh
.