sci-biology:SEECER-0.1.3-r2:20201120-061354.log

sci-biology:SEECER-0.1.3-r2:20201120-061354.log (text/plain), 5.88 KB, created by Toralf Förster on 2020-11-20 15:55:27 UTC

 * Package:    sci-biology/SEECER-0.1.3-r2
 * Repository: science
 * Maintainer: [e-mail] [e-mail]
 * 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'