Thank you both for your responses and help! Kurt-- your message makes a lot of sense. I'll try to debug soon and will reach out if I have more questions.
Thanks, Michelle ________________________________ From: Kurt Hornik <kurt.hor...@wu.ac.at> Sent: Wednesday, May 22, 2024 3:57 AM To: Dirk Eddelbuettel <e...@debian.org> Cc: Nixon, Michelle Pistner <map5...@psu.edu>; r-package-devel@r-project.org <r-package-devel@r-project.org>; Kurt Hornik <kurt.hor...@wu.ac.at> Subject: Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP [You don't often get email from kurt.hor...@wu.ac.at. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] >>>>> Dirk Eddelbuettel writes: Friends, the Debian pretest check system uses LLVM 18 and has the corresponding OpenMP headers and libraries installed, but R is configured not to use these. However, the configure test in fido does cat <<EOF > test-omp.cpp #include <omp.h> int main() { return omp_get_num_threads(); } EOF ## Execute R CMD SHLIB. "${R_HOME}/bin/R" CMD SHLIB test-omp.cpp >/dev/null 2>&1 if test x"$?" = x"0"; then AC_MSG_RESULT([yes]) openmp_already_works="yes" else AC_MSG_RESULT([no]) fi which does not work as intended: R CMD SHLIB will happily link but the .so will end up with an unresolved symbol: $ nm test-omp.so | grep omp_ U omp_get_num_threads Hth -k > Hi Michelle, > On 21 May 2024 at 13:46, Nixon, Michelle Pistner wrote: > | Hi all, > | > | I'm running into build issues for my package (fido: > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjsilve24%2Ffido&data=05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500263726%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=C4BI6%2FUgTjd%2FCRPzBF8NuUkPvlQkIxb2r1%2BzIqKNPpE%3D&reserved=0)<https://github.com/jsilve24/fido> > on the r-devel-linux-x86_64-debian-clang system on CRAN (full check log > here: > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwin-builder.r-project.org%2Fincoming_pretest%2Ffido_1.1.0_20240515_211644%2FDebian%2F00install.out&data=05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500272862%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=TKpQrkImemwz%2FuK7yYqCLEECU6WCCvgYwcrAId%2Bpmb0%3D&reserved=0)<https://win-builder.r-project.org/incoming_pretest/fido_1.1.0_20240515_211644/Debian/00install.out>. > fido relies on several of the Rcpp packages, and I think the error is due to > how OpenMP is set up in our package. The error in question states: > | > | "Error: package or namespace load failed for �fido� in dyn.load(file, > DLLpath = DLLpath, ...): > | unable to load shared object > '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-fido/00new/fido/libs/fido.so': > | > /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-fido/00new/fido/libs/fido.so: > undefined symbol: omp_get_thread_num" > | > | I've had a hard time recreating the error, as I can successfully get the > package to build on other systems (GitHub action results here: > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjsilve24%2Ffido%2Factions&data=05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500275695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=zXCul23gWAevfEhCsfyJg8KewU8fjSuy1qZgZemNy7M%3D&reserved=0)<https://github.com/jsilve24/fido/actions> > including a system using the same version of R/clang as the failing CRAN > check. Looking at the logs between the two, the major difference is the lack > of -fopenmp in the compiling function on the CRAN version (which is there on > the r-hub check version with the same specifications): > | > | (From the CRAN version) clang++-18 -std=gnu++17 -shared > -L/home/hornik/tmp/R-d-clang-18/lib -Wl,-O1 -o fido.so ConjugateLinearModel.o > MaltipooCollapsed_LGH.o MaltipooCollapsed_Optim.o MatrixAlgebra.o > PibbleCollapsed_LGH.o PibbleCollapsed_Optim.o PibbleCollapsed_Uncollapse.o > PibbleCollapsed_Uncollapse_sigmaKnown.o RcppExports.o SpecialFunctions.o > test_LaplaceApproximation.o test_MultDirichletBoot.o test_utils.o > -L/home/hornik/tmp/R-d-clang-18/lib -lR > | > | My initial thought was an issue in the configure scripts (which we borrowed > heavily from RcppArmadillo but made slight changes to (which is the most > likely cause if there is issue here)) or that there is some mismatch > somewhere as to whether or not OpenMP is available, but there isn't an > obvious bug to me. > | > | Any guidance on how to debug would be greatly appreciated! > I seem to recall that that machine is 'known-bad' for OpenMP due to the > reliance on clang-18 which cannot (?) build with it. Might be best to > contact Kurt Hornik (CC'ed) and/or CRAN. > Best, Dirk > | Thanks, > | Michelle > | > | Michelle Nixon, PhD > | > | Assistant Research Professor > | College of Information Sciences and Technology > | The Pennsylvania State University > | > | [[alternative HTML version deleted]] > | > | ______________________________________________ > | R-package-devel@r-project.org mailing list > | > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-package-devel&data=05%7C02%7Cmap5672%40psu.edu%7C7993944f52ae4a017d3d08dc7a34d1d6%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638519614500278321%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=LdxZWjZQvd1slPS4Tc8GkeKeV5OyoU5YL2NraN6chuY%3D&reserved=0<https://stat.ethz.ch/mailman/listinfo/r-package-devel> > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
