Jennifer,
Any progress on this? I see ChemmineOB is not building on either mac right now. Kevin On 10/1/24 8:37 AM, Kevin Horan wrote: > > Jennifer, > > Great, thanks. > > > Regarding mac arm64, I'm not familiar with that platform, and I don't > have access to it to test on. However, there is an open issue on > github with several folks working with OpenBabel on arm64, they might > be able to help. Perhaps you could post your question here: > https://github.com/girke-lab/ChemmineOB/issues/35 > > > The issue is regarding getting ChemmineOB working on arm64, but since > that requires OpenBabel as well, the issues are related. > > > Kevin > > > On 10/1/24 8:00 AM, Jennifer Wokaty wrote: >> Hi Kevin, >> >> I've reinstalled OpenBabel on the Windows release builder, palomino7. >> However, I need additional guidance to set up on Mac ARM64 as it must >> be compiled. On the Intel macs, we brew install OpenBabel, so I tried >> the same with the Mac ARM64 machines; however, running R CMD build >> with the brewed version gives the missing header error. If you could >> provide more guidance, I can try compiling it. >> >> Jennifer Wokaty (they/them) >> >> Waldron Lab at CUNY SPH >> Bioconductor Core Team >> ------------------------------------------------------------------------ >> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of >> Kevin Horan <kho...@cs.ucr.edu> >> *Sent:* Thursday, September 26, 2024 11:21 AM >> *To:* bioc-devel@r-project.org <bioc-devel@r-project.org> >> *Subject:* [Bioc-devel] ChemmineOB build failures >> * This email originates from a sender outside of CUNY. Verify the >> sender before replying or clicking on links and attachments. * >> >> My package ChemmineOB is failing to build on Windows and mac arm64 >> (kjohnson1). They both show the same error, that a header file is >> missing from the OpenBabel installation. >> >> clang++ -arch arm64 -std=gnu++17 >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST >> -DHAVE_EIGEN -I/usr/local/include/eigen3 >> -I/usr/local/include/openbabel3 >> -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' >> >> -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' >> >> -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' >> >> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 >> -c ChemmineOB.cpp -o ChemmineOB.o >> ChemmineOB.cpp:1569:10: fatal error: 'openbabel/obutil.h' file not found >> #include <openbabel/obutil.h> >> ^~~~~~~~~~~~~~~~~~~~ >> 1 error generated. >> >> >> >> Here is the build report: >> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FChemmineOB%2Fpalomino7-install.html__%3B!!PxiZbSOawA!IoRSgkcxOph1i6RrC5vHOKp5RSfWoFdI30XdtBA0JO6BtHFTCriOSf7f4fF5tJrD0fs6t9kEYFHG4-9KYTrk6wH_gLta%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C1c238f6a100543fa6bb708dcde3ef985%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638629609273870937%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=3WWApsB2%2F6QehII6qR0RYgFObft3KZq1yTH1yGFVzeY%3D&reserved=0 >> >> <https://urldefense.com/v3/__https://www.bioconductor.org/checkResults/3.19/bioc-LATEST/ChemmineOB/palomino7-install.html__;!!PxiZbSOawA!IoRSgkcxOph1i6RrC5vHOKp5RSfWoFdI30XdtBA0JO6BtHFTCriOSf7f4fF5tJrD0fs6t9kEYFHG4-9KYTrk6wH_gLta$> >> >> It is saying that the file openbabel/obutil.h is missing. That file >> appears normally when I install OpenBabel myself, so could you check >> that OpenBabel is installed on those machines and confirm whether or not >> that file is present? Could you also let me know what directory >> openbabel is installed in? Thank you. >> >> Kevin >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel__%3B!!PxiZbSOawA!IoRSgkcxOph1i6RrC5vHOKp5RSfWoFdI30XdtBA0JO6BtHFTCriOSf7f4fF5tJrD0fs6t9kEYFHG4-9KYTrk6ztNkzbY%24&data=05%7C02%7Cjennifer.wokaty%40sph.cuny.edu%7C1c238f6a100543fa6bb708dcde3ef985%7C6f60f0b35f064e099715989dba8cc7d8%7C0%7C0%7C638629609273894284%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=gwUPBCd3eS2ZMo%2BHvbv7Ljxi02uHfi89008F5X0mY58%3D&reserved=0 >> >> <https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!PxiZbSOawA!IoRSgkcxOph1i6RrC5vHOKp5RSfWoFdI30XdtBA0JO6BtHFTCriOSf7f4fF5tJrD0fs6t9kEYFHG4-9KYTrk6ztNkzbY$> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
