* Package: sci-biology/SEECER-0.1.3-r2 * Repository: science * Maintainer: mmokrejs@fold.natur.cuni.cz sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking SEECER-0.1.3.tar.gz to /var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work >>> Unpacking SEECER-manual.pdf to /var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work unpack SEECER-manual.pdf: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER ... * Applying remove-hardcoded-paths.patch ... [ ok ] * Applying run_seecer.sh.patch ... [ ok ] * Applying run_jellyfish.sh.patch ... [ ok ] * Applying rename_jellyfish_binary.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER ... * econf: updating SEECER-0.1.3/jellyfish-1.1.11/config.sub with /usr/share/gnuconfig/config.sub * econf: updating SEECER-0.1.3/jellyfish-1.1.11/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --docdir=/usr/share/doc/SEECER-0.1.3-r2 --htmldir=/usr/share/doc/SEECER-0.1.3-r2/html --libdir=/usr/lib64 checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-g++... none checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp checking for GOMP_parallel_start in -lgomp... yes checking for clock_gettime in -lrt... yes checking for cos in -lm... yes checking for main in -lgslcblas... yes checking for main in -lgsl... yes configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER ... make -j1 make all-am make[1]: Entering directory '/var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER' x86_64-pc-linux-gnu-g++ -O3 -g -O2 -pipe -march=native -fno-diagnostics-color -I/opt/local/include -lgomp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L/opt/local/lib -o bin/seecer src/seecer_main.o src/common.o src/hashmap_read_finder.o src/hmm_cluster.o src/smart_hashmap_read_finder.o src/stats_keeper.o -lgsl -lgslcblas -lm -lrt -lgomp /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/seecer_main.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/common.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/hashmap_read_finder.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/hmm_cluster.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/smart_hashmap_read_finder.o: relocation R_X86_64_32S against symbol `_ZN27QGramSmartHashMapReadFinder5codesE' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/stats_keeper.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE collect2: error: ld returned 1 exit status make[1]: *** [Makefile:307: bin/seecer] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER' make: *** [Makefile:191: all] Error 2 * ERROR: sci-biology/SEECER-0.1.3-r2::science failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/SEECER-0.1.3-r2::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/SEECER-0.1.3-r2::science'`. * The complete build log is located at '/var/log/portage/sci-biology:SEECER-0.1.3-r2:20201120-061354.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/SEECER-0.1.3-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/SEECER-0.1.3-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER' * S: '/var/tmp/portage/sci-biology/SEECER-0.1.3-r2/work/SEECER-0.1.3/SEECER'