[Bioc-devel] is it possible to disable i386 builds on bioconductor
Thomas Girke
thom@@@g|rke @end|ng |rom ucr@edu
Sat Mar 20 00:46:16 CET 2021
Awesome. Thanks for all your help!
Thomas
On Fri, Mar 19, 2021 at 2:42 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:
> 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
>
--
Thomas Girke, Ph.D.
Professor of Bioinformatics
1207F Genomics Building
University of California
Riverside, CA 92521
E-mail: thomas.girke using ucr.edu
URL: https://girke.bioinformatics.ucr.edu
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437
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