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

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Tue Mar 16 18:24:36 CET 2021


@Kevin: Thanks for providing openbabel3 for Ubuntu 18.04. Will take a 
look ASAP.

@Thomas: Yes, the Ubuntu 18.04 builds are only used for the BioC 3.12 
builds (release). BioC 3.13 and further BioC releases are/will be using 
Ubuntu >= 20.04.

Best,
H.


On 3/15/21 1:59 PM, Thomas Girke wrote:
> Thanks Hervé for your help with this.
> 
> Kevin has provided the *.deb package for installing OpenBabel 3.x on 
> Ubuntu 18.04. Just in case, below is how we usually install OpenBabel 
> 3.x.x across different Ubuntu/Debian systems.
> 
> BTW: is it correct to assume that the Ubuntu 18.04 builds will be 
> discontinued in the next release in April?
> 
> Thanks,
> 
> Thomas
> 
> 
> ## Install ChemmineOB with OpenBabel 3.x from source
> 
> ## First uninstall libopenbabel-dev (which is version 2.x.x) if already 
> installed via
> sudo apt-get remove libopenbabel-dev; sudo apt-get purge 
> libopenbabel-dev; sudo apt-get --purge autoremove libopenbabel-dev
> ## Some dependencies to install
> sudo apt install cmake libeigen3-dev libboost-all-dev
> ## Clone OpenBabel 3.x.x from GitHub here: 
> https://github.com/openbabel/openbabel 
> <https://github.com/openbabel/openbabel>
> git clone git using github.com:openbabel/openbabel.git
> mkdir build; cd build
> cmake ../openbabel
> make
> sudo make install
> ## Install ChemmineOB where you provide environment variables including 
> header files and ChemmineOB package iprovided as *.tar.gz (adjust paths 
> if not correct)
> R CMD INSTALL 
> --configure-args='--with-openbabel-include=/usr/local/include/openbabel3/ --with-openbabel-lib=/usr/local/lib/openbabel/3.1.1' 
> ChemmineOB_1.28.0.tar.gz
> 
> On Mon, Mar 15, 2021 at 1:12 PM Kevin Horan <khoran using cs.ucr.edu 
> <mailto:khoran using cs.ucr.edu>> wrote:
> 
>     Herve,
> 
>           I've backported openbabel3 from 20.04 to 18.04. You can
>     download a
>     tarball with all the deb files in here:
> 
>     http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz
>     <http://cluster.hpcc.ucr.edu/~khoran/ubuntu_18.04_openbabel3_debs.tar.gz>
> 
>     Kevin
> 
>     On 3/15/21 10:10 AM, Hervé Pagès wrote:
>      > 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
>      >   /usr/local/bin/obabel
>      >
>      >   machv2:~ biocbuild$ obabel -V
>      >   Open Babel 3.1.0 -- Oct 21 2020 -- 21:57:42
>      >
>      >   machv2:~ biocbuild$ pkg-config --cflags openbabel-3
>      >   -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3
>      >
>      >   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.
>      >
>      > Best,
>      > H.
>      >
>      >
>      >
>      > 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
>     <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/
>     <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 <mailto: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
>     <mailto:bioc-devel-bounces using r-project.org> on behalf of
>     khoran using cs.ucr.edu <mailto: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 <mailto:Bioc-devel using r-project.org>
>     mailing list
>      >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>      >>> _______________________________________________
>      >>> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
>     mailing list
>      >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>      >>>
>      >>
>      >>
>      >
> 
> 
> 
> -- 
> Thomas Girke, Ph.D.
> Professor of Bioinformatics
> 1207F Genomics Building
> University of California
> Riverside, CA 92521
> 
> E-mail: thomas.girke using ucr.edu <mailto:thomas.girke using ucr.edu>
> URL: https://girke.bioinformatics.ucr.edu 
> <https://girke.bioinformatics.ucr.edu>
> Phone/Cell/Text: 951-732-7072
> Fax: 951-827-4437

-- 
Hervé Pagès

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



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