Your message dated Sun, 26 Aug 2018 15:34:50 +0000 with message-id <e1ftx3y-000fks...@fasolo.debian.org> and subject line Bug#907007: fixed in kmer 0~20150903+r2013-5 has caused the Debian Bug report #907007, regarding kmer FTBFS on arm64: recompile with -fPIC to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 907007: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=907007 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: kmer Version: 0~20150903+r2013-3 Severity: serious Tags: patch ftbfs buster sid https://tests.reproducible-builds.org/debian/rb-pkg/buster/arm64/kmer.html https://buildd.debian.org/status/fetch.php?pkg=kmer&arch=arm64&ver=0~20150903%2Br2013-4&stamp=1533471604&raw=0 ... rm -f seatac/filter-heavychains.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-heavychains.so seatac/filter-heavychains.o seatac/heavychains.o -pthread -ldl -lm /usr/bin/ld: seatac/heavychains.o: relocation R_AARCH64_ADR_PREL_PG_HI21 against symbol `_Z8x_comparPKvS0_' which may bind externally can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: seatac/heavychains.o: in function `StrandPair::process()': ./seatac/heavychains.H:410:(.text+0x8f0): dangerous relocation: unsupported relocation /usr/bin/ld: seatac/heavychains.o: relocation R_AARCH64_ADR_PREL_PG_HI21 against symbol `_Z8y_comparPKvS0_' which may bind externally can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: ./seatac/heavychains.H:410:(.text+0xd14): dangerous relocation: unsupported relocation /usr/bin/ld: seatac/heavychains.o: relocation R_AARCH64_ADR_PREL_PG_HI21 against symbol `_Z8y_comparPKvS0_' which may bind externally can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: ./seatac/heavychains.H:406:(.text+0x1224): dangerous relocation: unsupported relocation /usr/bin/ld: seatac/heavychains.o: relocation R_AARCH64_ADR_PREL_PG_HI21 against symbol `_Z8y_comparPKvS0_' which may bind externally can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: ./seatac/heavychains.H:410:(.text+0x26c0): dangerous relocation: unsupported relocation /usr/bin/ld: seatac/heavychains.o: relocation R_AARCH64_ADR_PREL_PG_HI21 against symbol `_Z8y_comparPKvS0_' which may bind externally can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: seatac/heavychains.o: in function `DPTree::sort_nodes(DPTree::kd_node)': ./seatac/heavychains.H:410:(.text._ZN6DPTree10sort_nodesENS_7kd_nodeE[_ZN6DPTree10sort_nodesENS_7kd_nodeE]+0x40): dangerous relocation: unsupported relocation /usr/bin/ld: seatac/heavychains.o: relocation R_AARCH64_ADR_PREL_PG_HI21 against symbol `_Z8x_comparPKvS0_' which may bind externally can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: ./seatac/heavychains.H:410:(.text._ZN6DPTree10sort_nodesENS_7kd_nodeE[_ZN6DPTree10sort_nodesENS_7kd_nodeE]+0x44): dangerous relocation: unsupported relocation collect2: error: ld returned 1 exit status make[2]: *** [Make.rules:180: seatac/filter-heavychains.so] Error 1 Fix is attached.Description: Use the same compile flags in all Linux builds, and include -fPIC atac .so were built without -fPIC on !amd64/ia64. Author: Adrian Bunk <b...@debian.org> --- kmer-0~20150903+r2013.orig/configure.sh +++ kmer-0~20150903+r2013/configure.sh @@ -57,12 +57,12 @@ if [ "x$target" = "x" ] ; then ;; Linux) target="Linux-i686$opts" - if [ `uname -m` = "x86_64" ] ; then - target="Linux-amd64$opts" - fi - if [ `uname -m` = "ia64" ] ; then - target="Linux-ia64$opts" - fi + #if [ `uname -m` = "x86_64" ] ; then + # target="Linux-amd64$opts" + #fi + #if [ `uname -m` = "ia64" ] ; then + # target="Linux-ia64$opts" + #fi ;; SunOS) target="solaris$opts" @@ -221,11 +221,11 @@ EOF # Linux, optimized CC := $CC SHLIB_FLAGS := -shared -CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +CFLAGS_COMPILE := -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer CLDFLAGS := -L/usr/local/lib CLIBS := -pthread -ldl CXX := $CXX -CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +CXXFLAGS_COMPILE := -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer CXXLDFLAGS := -L/usr/local/lib CXXLIBS := -pthread -ldl ARFLAGS := ruvs @@ -350,7 +350,7 @@ EOF echo " tru64, compaq Tru64, optimized" echo " tru64-debug, compaq-debug Tru64, debug, warnings, trapuv" echo "" - echo " linux Linux, i686, optimized" + echo " linux Linux, optimized" echo " linux64 Linux, Opteron, optimized" echo "" echo " solaris Solaris, gcc, optimized (STALE)"
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--- Begin Message ---Source: kmer Source-Version: 0~20150903+r2013-5 We believe that the bug you reported is fixed in the latest version of kmer, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 907...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated kmer package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 26 Aug 2018 16:58:23 +0200 Source: kmer Binary: kmer libkmer-dev meryl libmeryl-dev leaff sim4db atac Architecture: source Version: 0~20150903+r2013-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: atac - genome assembly-to-assembly comparison kmer - suite of tools for DNA sequence analysis leaff - biological sequence library utilities and applications libkmer-dev - suite of tools for DNA sequence analysis (development lib) libmeryl-dev - in- and out-of-core kmer counting and utilities (development lib) meryl - in- and out-of-core kmer counting and utilities sim4db - batch spliced alignment of cDNA sequences to a target genome Closes: 907007 Changes: kmer (0~20150903+r2013-5) unstable; urgency=medium . * Team upload . [ Adrian Bunk ] * Use the same compile flags in all Linux builds, and include -fPIC atac .so were built without -fPIC on !amd64/ia64. Closes: #907007 . [ Andreas Tille ] * Standards-Version: 4.2.0 Checksums-Sha1: 19d25f7b8d3c28fa50d155393a5f4ba42a87f6e0 2324 kmer_0~20150903+r2013-5.dsc c5df71aeae46275084869a96b6b426f5d6f61c6d 3022024 kmer_0~20150903+r2013-5.debian.tar.xz Checksums-Sha256: 1f1eca7f9302a6bcdbcfabfcc73f6d7d5f922abf7626b117ce744c3567267593 2324 kmer_0~20150903+r2013-5.dsc 981f007b6cdc4faf1a73617c4903697fc79162609c439a0a2e6378d8d1bbb975 3022024 kmer_0~20150903+r2013-5.debian.tar.xz Files: 409e5dced28cb32e399648956d607a23 2324 science optional kmer_0~20150903+r2013-5.dsc a7542c26feed12329aa07b911555317d 3022024 science optional kmer_0~20150903+r2013-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluCw+wRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHEQg/7BcXVMxd9YquHlxuw2PHxn4TVYR3qm2vw RFeguPACVVkp1wIuZmkSZ3CTRuKKSt2ZBTjQG6VzmZqtxORvtEdoma2n8f3dxcSK z8/pERJfKtLJw6A+KIxtdez1oEXb5EFAjWi6MmMubkuWCTmSel/PAZEytoNAFRlH fMt2eCCEbFnsZYz+Y+Fk6nfiQX8ldkblrmKjV0VhIV2yC+/ieiDzDTS89KZv509l 0dIg/aHY1PNjQslyNNjYpLJKK5KzV3t5UFOS5DTLHQ+8E+lMIRDwia3t3umJHSBW YgneUbuXXxGYPfabBDLzPvRWwAEh1fssWBG4l+TJ9CSXHTx8Lj7VVFrTtbkrBKdV y6n/BeAUhjq8qxr77YtzDmqnqjHfgeN4JR7gP3Yx4wih+aSSIqpgI+WpSA/5oxcB 3/WkqQTy0GIpcmTTIiWkMn/tIjS3XexGOhEbrYVZlEvagIZWk/fowQq7D4hGU/80 pFmqmD94Jhxy/2Kc+EwPf75Vil14Dxr3bEmR38qKGTxIXLNed3h19e17RoXQOZyP kK2QhquUIetvPAQfR6/5kM2ljErf8SoH5qOb77DGQY+K9xTm5tZ9co+iIhBWEP2t 0ZSuULMqwNMjB4psiZ+jpGyGIU1xWWgkYl1vJD7/wiNcnTAAqD1JqofxQDXynrkF YxA75cL5OBg= =X6+z -----END PGP SIGNATURE-----
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