[Bioc-devel] is it possible to disable i386 builds on bioconductor
Hervé Pagès
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Mar 19 22:41:53 CET 2021
Hi Thomas, Kevin,
Looks like ChemmineOB 1.28.2 is finally green on malbec1 and is now
available in BioC 3.12 via BiocManager::install():
https://bioconductor.org/checkResults/3.12/bioc-LATEST/ChemmineOB/
Cheers,
H.
On 3/17/21 10:23 AM, Thomas Girke wrote:
> Awesome, thanks!
>
> On Tue, Mar 16, 2021 at 11:40 PM Hervé Pagès <hpages.on.github using gmail.com
> <mailto:hpages.on.github using gmail.com>> wrote:
>
> Hi Thomas, Kevin,
>
> openbabel3 is now on malbec1 (Ubuntu 18.04). Kevin's
> ubuntu_18.04_openbabel3_debs.tar.gz worked like a charm. Thanks for
> making it so easy.
>
> Note that this addition will affect ChemmineOB build/check results on
> malbec1 on Thursday only:
>
>
> https://bioconductor.org/checkResults/3.12/bioc-LATEST/ChemmineOB/malbec1-install.html
> <https://bioconductor.org/checkResults/3.12/bioc-LATEST/ChemmineOB/malbec1-install.html>
>
> Cheers,
> H.
>
>
> On 3/16/21 10:24 AM, Hervé Pagès wrote:
> > @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>
> >> <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>
> >> <mailto: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>
> >>
> >>
> <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>
> >>
> <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/>
> >>
> <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>
> <mailto: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>
> >> <mailto: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>
> <mailto: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> <mailto: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>
> >> <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> <mailto: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>
> >> <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>
> <mailto:thomas.girke using ucr.edu <mailto:thomas.girke using ucr.edu>>
> >> URL: https://girke.bioinformatics.ucr.edu
> <https://girke.bioinformatics.ucr.edu>
> >> <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 <mailto:hpages.on.github using gmail.com>
>
>
>
> --
> 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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