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)"