[Bioc-devel] is it possible to disable i386 builds on bioconductor

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Mon Mar 15 18:10:01 CET 2021

Hi Thomas, Kevin,

We still need to install the system deps on the devel Windows builders 
(riesling1 and tokay2). We'll do it this week. Thanks for the reminder 
and for making the OpenBabel-3.0.0 Windows Binaries available on your 
GitHub repo.

Note that OpenBabel 3 is installed on machv2 (devel macOS builders):

   machv2:~ biocbuild$ which obabel

   machv2:~ biocbuild$ obabel -V
   Open Babel 3.1.0 -- Oct 21 2020 -- 21:57:42

   machv2:~ biocbuild$ pkg-config --cflags openbabel-3

   machv2:~ biocbuild$ pkg-config --libs openbabel-3
   -L/usr/local/Cellar/open-babel/3.1.1_1/lib -lopenbabel

In release: The reason ChemmineOB does not compile on malbec1 is because 
it requires OpenBabel 3 but malbec1 only has OpenBabel 2 which is what 
Ubuntu 18.04 comes with. OpenBabel 3 only became available starting with 
Ubuntu 20.04.

To workaround this we could propagate the ChemmineOB_1.28.2.tar.gz 
source tarball produced on nebbiolo1 (Ubuntu 20.04), or, if you know an 
easy way to get OpenBabel 3 installed on an Ubuntu 18.04 system, let us 
know and we will do that. The best thing would be to be able to use a 
.deb package for this. The easiest the procedure, the more likely people 
that are still using Ubuntu 18.04 will be able to install ChemmineOB.


On 3/12/21 11:10 AM, Thomas Girke wrote:
> Dear Hervé and Martin,
> It seems the above problem on the Windows builds has been resolved for some
> time now. However, any updates on Linux in the release branch are not
> taking effect since some/all of the Openbabel dependencies are not
> available on the corresponding Linux build system (here Ubuntu 18.04).
> However, Ubuntu 20.04 seems to be fine but may not be used to create the
> source download instance at the moment? As a result, the package is only
> up-to-date for Windows and OSX (ChemmineOB_1.28.2.) but not Linux (still at
> ChemmineOB_1.28.0.tar.gz):
> http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html. To fix
> this, one suggestion would be whether the functional build from the 20.04
> system could be pushed instead of 18.04? Not sure whether this is less
> effort than installing the dependencies on 18.04 that may be discontinued
> soon - just a suggestion/question?
> On the development branch the situation is opposite where the
> dependencies are missing on Windows and OSX but Linux is fine:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/.
> We realize that the dependencies of the ChemmineOB package creates extra
> workload for the Bioc team, and we are extremely grateful for the support
> by the Bioc core team. Please let us know if there is anything on our end
> that could be done to resolve this and/or to minimize your workload as much
> as possible.
> Thanks,
> Thomas
> On Mon, Feb 8, 2021 at 10:02 AM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>> It's likely failing because your package has C source code that accesses
>> memory in an invalid way. Likely the bug is present on all platforms, but
>> only apparent, for the tests you have written, on Windows. The right thing
>> to do is to fix the bug, rather than avoid by not running on the
>> troublesome platform.
>> Under Linux you'd likely have success with valgrind or UBSAN; if you were
>> reasonably confident that the package occurred in unit tests, and you have
>> a script to run the unit tests run_tests.R then something like
>>    R -d valgrind -f run_tests.R
>> may be productive. valgrind is slow so it pays to narrow the problem down
>> as much as possible.
>> Maartin
>> On 2/8/21, 12:43 PM, "Bioc-devel on behalf of Kevin Horan" <
>> bioc-devel-bounces using r-project.org on behalf of khoran using cs.ucr.edu> wrote:
>>           I have a package which randomly segfaults when running my unit
>>      tests only on windows i386, but never on x64, or any other OS. I can't
>>      imagine there are many out there still running i386 systems are there?
>>      Is it possible to just disable the i386 build on bioconductor so that
>>      the tests are not run on that architecture?
>>           I have of course done my best to debug the issue, but all I get
>> is
>>      an error in some nt dll file, with no useful message or location. I'm
>> I
>>      Linux guy, I don't know how to do the in-depth debugging that would be
>>      required to track this bug down on windows. I tried disabling each
>> test
>>      one by one to see which one caused the crash, but as is typical with
>>      segfaults, changing the setup can mask the bug even when the bad code
>> is
>>      still be executed. Each test runs fine in isolation.
>>      Thanks
>>      Kevin
>>      _______________________________________________
>>      Bioc-devel using r-project.org mailing list
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Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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