* Tom Callaway: > One of my packages failed the mass rebuild, but only on ppc64le and > aarch64. The error they both hit is this: > > Error: package or namespace load failed for 'BiocParallel' in > dyn.load(file, DLLpath = DLLpath, ...): > unable to load shared object > '/builddir/build/BUILDROOT/R-BiocParallel-1.16.5-1.fc30.ppc64le/usr/lib64/R/library/BiocParallel/libs/BiocParallel.so': > > /builddir/build/BUILDROOT/R-BiocParallel-1.16.5-1.fc30.ppc64le/usr/lib64/R/library/BiocParallel/libs/BiocParallel.so: > undefined symbol: shm_open > Error: loading failed
Is this an error message from the R interpreter? On x86-64, the R interpreter already loads librt: 7f0f2635a000-7f0f2635c000 r--p 00000000 fd:01 402963247 /usr/lib64/librt-2.29.so 7f0f2635c000-7f0f26360000 r-xp 00002000 fd:01 402963247 /usr/lib64/librt-2.29.so 7f0f26360000-7f0f26362000 r--p 00006000 fd:01 402963247 /usr/lib64/librt-2.29.so 7f0f26362000-7f0f26363000 r--p 00007000 fd:01 402963247 /usr/lib64/librt-2.29.so 7f0f26363000-7f0f26364000 rw-p 00008000 fd:01 402963247 /usr/lib64/librt-2.29.so That's because libR loads it: $ readelf -d /usr/lib64/R/lib/libR.so … 0x0000000000000001 (NEEDED) Shared library: [librt.so.1] … The way dynamic linking works is that it searches for symbols in the caller's namespace, and not just what's referenced by DT_NEEDED. > Here's the linker invocation: > > g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro > -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld > -o BiocParallel.so ipcmutex.o -L/usr/lib64/R/lib -lR > > Now, google says this might be due to a lack of -lrt, but what's not > clear to me is why it only fails on these two architectures (I've > confirmed that none of the others have -lrt either). In general, underlinking can be very problematic because it causes the base symbol version to be used at run time, even if your program actually requires a newer symbol version (for example, due to the headers used at build time). Here it does not matter (today) because we only have one symbol version for shm_open. But you do get interesting effects with timer_create. Thanks, Florian _______________________________________________ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://getfedora.org/code-of-conduct.html List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org
