Notes for r-bioc-summarizedexperiment - reproducible builds result

Version annotated: 1.2.0-1
Identified issues:
Identifier: randomness_in_r_rdb_rds_databases
Description R creates .rdb files and .rds with some randomness. They are a serialisation of some
sorts, related to lazy loading of modules?
Randomness seems to come from using absolute paths in .rd[bs] files.
.
Is not related to https://bugs.debian.org/774031 / r_base_appends_built_header_to_description_files
.
We have a pending patch to fix most of these (463/478) packages at the time
of writing) upstream in R:
.
https://stat.ethz.ch/pipermail/r-devel/2017-April/074138.html
.
When this is accepted into R upstream, commit 28d4af25 may be
(un-)reverted to remove these packages. In the meantime, please do not
remove this issue, nor mark it as deterministic, nor untag these packages.
.
The remaining ~15 packages are not completely fixed by this patch, so this
issue should remain, even when our upstream patch is accepted. These
packages will need to be investigated and fixed individually, see our blog
post on how to do that:
.
https://reproducible-builds.org/news/2017/05/03/reproduciing-r-packages/
Identifier: gcc_captures_build_path
Description Captures build path, e.g., /build/1st/foo-42.0 v. /build/foo-42.0/2nd
Currently we vary the build path only when testing packages from unstable
and experimental, for stretch we recommend that rebuilds are done in the same
path as the original build.
.
These packages should all be reproducible, because Jenkins is running a custom
toolchain which contains a patch to fix this specific issue:
.
https://gcc.gnu.org/ml/gcc-patches/2017-04/msg00513.html
.
When this is accepted into GCC upstream, we could remove this note.
In the meantime, please do not remove this issue, nor mark it as deterministic,
nor untag these packages.
 

Our notes about issues affecting packages are stored in notes.git and are targeted at packages in Debian in 'unstable/amd64' (unless they say otherwise).