[Bioc-devel] is it possible to disable i386 builds on bioconductor
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 Herv? Pag?s <hpages.on.github at gmail.com
<mailto:hpages.on.github at 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, Herv? Pag?s 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 Herv? 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
>> git clone git at 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 at cs.ucr.edu
<mailto:khoran at cs.ucr.edu>
>> <mailto:khoran at cs.ucr.edu <mailto:khoran at 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, Herv? Pag?s 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 Herv? 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 at gmail.com <mailto:mtmorgan.bioc at gmail.com>
<mailto:mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at 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 at r-project.org
<mailto:bioc-devel-bounces at r-project.org>
>> ??? <mailto:bioc-devel-bounces at r-project.org
<mailto:bioc-devel-bounces at r-project.org>> on behalf of
>> khoran at cs.ucr.edu <mailto:khoran at cs.ucr.edu>
<mailto:khoran at cs.ucr.edu <mailto:khoran at 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 at r-project.org
<mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
<mailto:Bioc-devel at r-project.org>>
>> ??? mailing list
>> ???? >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> ???? >>> _______________________________________________
>> ???? >>> Bioc-devel at r-project.org
<mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
<mailto:Bioc-devel at r-project.org>>
>> ??? mailing list
>> ???? >>> 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 at ucr.edu <mailto:thomas.girke at ucr.edu>
<mailto:thomas.girke at ucr.edu <mailto:thomas.girke at ucr.edu>>
>> Phone/Cell/Text: 951-732-7072
>> Fax: 951-827-4437
>
--
Herv? Pag?s
Bioconductor Core Team
hpages.on.github at gmail.com <mailto:hpages.on.github at gmail.com>
--
Thomas Girke, Ph.D.
Professor of Bioinformatics
1207F Genomics Building
University of California
Riverside, CA 92521
E-mail: thomas.girke at ucr.edu <mailto:thomas.girke at ucr.edu>
URL: https://girke.bioinformatics.ucr.edu
<https://girke.bioinformatics.ucr.edu>
Phone/Cell/Text: 951-732-7072
Fax: 951-827-4437
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com