Awesome, thanks! On Tue, Mar 16, 2021 at 11:40 PM Hervé Pagès <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 > > 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> > >> 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>> 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.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> on behalf of > >> 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> > >> mailing list > >> >>> 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> > >> 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.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