Awesome. Thanks for all your help! Thomas
On Fri, Mar 19, 2021 at 2:42 PM Hervé Pagès <hpages.on.git...@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.git...@gmail.com > > <mailto:hpages.on.git...@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 g...@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 <kho...@cs.ucr.edu > > <mailto:kho...@cs.ucr.edu> > > >> <mailto:kho...@cs.ucr.edu <mailto:kho...@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.b...@gmail.com <mailto:mtmorgan.b...@gmail.com> > > <mailto:mtmorgan.b...@gmail.com <mailto:mtmorgan.b...@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-boun...@r-project.org > > <mailto:bioc-devel-boun...@r-project.org> > > >> <mailto:bioc-devel-boun...@r-project.org > > <mailto:bioc-devel-boun...@r-project.org>> on behalf of > > >> kho...@cs.ucr.edu <mailto:kho...@cs.ucr.edu> > > <mailto:kho...@cs.ucr.edu <mailto:kho...@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@r-project.org > > <mailto:Bioc-devel@r-project.org> <mailto:Bioc-devel@r-project.org > > <mailto:Bioc-devel@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@r-project.org > > <mailto:Bioc-devel@r-project.org> <mailto:Bioc-devel@r-project.org > > <mailto:Bioc-devel@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.gi...@ucr.edu <mailto:thomas.gi...@ucr.edu> > > <mailto:thomas.gi...@ucr.edu <mailto:thomas.gi...@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.git...@gmail.com <mailto:hpages.on.git...@gmail.com> > > > > > > > > -- > > Thomas Girke, Ph.D. > > Professor of Bioinformatics > > 1207F Genomics Building > > University of California > > Riverside, CA 92521 > > > > E-mail: thomas.gi...@ucr.edu <mailto:thomas.gi...@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.git...@gmail.com > -- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521 E-mail: thomas.gi...@ucr.edu URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
