build.log

bowtie-2.2.6:20170907-102138.log (text/x-log), 12.84 KB, created by Kent Fredric (IRC: kent\n) (RETIRED) on 2017-09-07 10:34:45 UTC

[32;01m * [39;49;00mPackage:    sci-biology/bowtie-2.2.6
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 cpu_flags_x86_sse2 elibc_glibc kernel_linux tbb userland_GNU
[32;01m * [39;49;00mFEATURES:   preserve-libs sandbox test userpriv usersandbox
>>> Unpacking source...
>>> Unpacking bowtie2-2.2.6-source.zip to /var/tmp/portage/sci-biology/bowtie-2.2.6/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bowtie-2.2.6/work
>>> Preparing source in /var/tmp/portage/sci-biology/bowtie-2.2.6/work/bowtie2-2.2.6 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bowtie-2.2.6/work/bowtie2-2.2.6 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bowtie-2.2.6/work/bowtie2-2.2.6 ...
make -j3 CC=x86_64-pc-linux-gnu-gcc CPP=x86_64-pc-linux-gnu-g++ CXX=x86_64-pc-linux-gnu-g++ CFLAGS= CXXFLAGS= 'EXTRA_FLAGS=-Wl,-O1 -Wl,--as-needed' 'RELEASE_FLAGS=-march=native -mtune=native -O2 -pipe -msse2' WITH_TBB=1 
x86_64-pc-linux-gnu-g++ -march=native -mtune=native -O2 -pipe -msse2 -DCOMPILER_OPTIONS="\"-march=native -mtune=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
x86_64-pc-linux-gnu-g++ -march=native -mtune=native -O2 -pipe -msse2 -DCOMPILER_OPTIONS="\"-march=native -mtune=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-build-l bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
x86_64-pc-linux-gnu-g++ -march=native -mtune=native -O2 -pipe -msse2 -DCOMPILER_OPTIONS="\"-march=native -mtune=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
In file included from [01m[K/usr/include/tbb/task_group.h:24:0[m[K,
                 from [01m[Kthreading.h:28[m[K,
                 from [01m[Kds.h:30[m[K,
                 from [01m[Ksequence_io.h:28[m[K,
                 from [01m[Kmultikey_qsort.h:24[m[K,
                 from [01m[Kdiff_sample.h:26[m[K,
                 from [01m[Kblockwise_sa.h:29[m[K,
                 from [01m[Kbt2_idx.h:42[m[K,
                 from [01m[Kbt2_search.cpp:33[m[K:
/usr/include/tbb/task.h: In instantiation of ‘[01m[Ktbb::task* tbb::internal::function_task<F>::execute() [with F = multiseedSearchWorker][m[K’:
[01m[Kbt2_search.cpp:4756:1:[m[K   required from here
[01m[K/usr/include/tbb/task.h:926:13:[m[K [01;31m[Kerror: [m[Kno match for call to ‘[01m[K(const multiseedSearchWorker) ()[m[K’
             my_func();
[01;32m[K             ^[m[K
[01m[Kbt2_search.cpp:2795:6:[m[K [01;36m[Knote: [m[Kcandidate: void multiseedSearchWorker::operator()() <near match>
 void multiseedSearchWorker::operator()() {
[01;32m[K      ^[m[K
[01m[Kbt2_search.cpp:2795:6:[m[K [01;36m[Knote: [m[K  passing ‘[01m[Kconst multiseedSearchWorker*[m[K’ as ‘[01m[Kthis[m[K’ argument discards qualifiers
In file included from [01m[K/usr/include/tbb/task_group.h:24:0[m[K,
                 from [01m[Kthreading.h:28[m[K,
                 from [01m[Kds.h:30[m[K,
                 from [01m[Ksequence_io.h:28[m[K,
                 from [01m[Kmultikey_qsort.h:24[m[K,
                 from [01m[Kdiff_sample.h:26[m[K,
                 from [01m[Kblockwise_sa.h:29[m[K,
                 from [01m[Kbt2_idx.h:42[m[K,
                 from [01m[Kbt2_search.cpp:33[m[K:
/usr/include/tbb/task.h: In instantiation of ‘[01m[Ktbb::task* tbb::internal::function_task<F>::execute() [with F = multiseedSearchWorker_2p5][m[K’:
[01m[Kbt2_search.cpp:4756:1:[m[K   required from here
[01m[K/usr/include/tbb/task.h:926:13:[m[K [01;31m[Kerror: [m[Kno match for call to ‘[01m[K(const multiseedSearchWorker_2p5) ()[m[K’
             my_func();
[01;32m[K             ^[m[K
[01m[Kbt2_search.cpp:3899:6:[m[K [01;36m[Knote: [m[Kcandidate: void multiseedSearchWorker_2p5::operator()() <near match>
 void multiseedSearchWorker_2p5::operator()() {
[01;32m[K      ^[m[K
[01m[Kbt2_search.cpp:3899:6:[m[K [01;36m[Knote: [m[K  passing ‘[01m[Kconst multiseedSearchWorker_2p5*[m[K’ as ‘[01m[Kthis[m[K’ argument discards qualifiers
x86_64-pc-linux-gnu-g++ -march=native -mtune=native -O2 -pipe -msse2 -DCOMPILER_OPTIONS="\"-march=native -mtune=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-align-l bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
x86_64-pc-linux-gnu-g++ -march=native -mtune=native -O2 -pipe -msse2 \
	-DCOMPILER_OPTIONS="\"-march=native -mtune=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
	 -I third_party -I . \
	-o bowtie2-inspect-s bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
In file included from [01m[K/usr/include/tbb/task_group.h:24:0[m[K,
                 from [01m[Kthreading.h:28[m[K,
                 from [01m[Kds.h:30[m[K,
                 from [01m[Ksequence_io.h:28[m[K,
                 from [01m[Kmultikey_qsort.h:24[m[K,
                 from [01m[Kdiff_sample.h:26[m[K,
                 from [01m[Kblockwise_sa.h:29[m[K,
                 from [01m[Kbt2_idx.h:42[m[K,
                 from [01m[Kbt2_search.cpp:33[m[K:
/usr/include/tbb/task.h: In instantiation of ‘[01m[Ktbb::task* tbb::internal::function_task<F>::execute() [with F = multiseedSearchWorker][m[K’:
[01m[Kbt2_search.cpp:4756:1:[m[K   required from here
[01m[K/usr/include/tbb/task.h:926:13:[m[K [01;31m[Kerror: [m[Kno match for call to ‘[01m[K(const multiseedSearchWorker) ()[m[K’
             my_func();
[01;32m[K             ^[m[K
[01m[Kbt2_search.cpp:2795:6:[m[K [01;36m[Knote: [m[Kcandidate: void multiseedSearchWorker::operator()() <near match>
 void multiseedSearchWorker::operator()() {
[01;32m[K      ^[m[K
[01m[Kbt2_search.cpp:2795:6:[m[K [01;36m[Knote: [m[K  passing ‘[01m[Kconst multiseedSearchWorker*[m[K’ as ‘[01m[Kthis[m[K’ argument discards qualifiers
In file included from [01m[K/usr/include/tbb/task_group.h:24:0[m[K,
                 from [01m[Kthreading.h:28[m[K,
                 from [01m[Kds.h:30[m[K,
                 from [01m[Ksequence_io.h:28[m[K,
                 from [01m[Kmultikey_qsort.h:24[m[K,
                 from [01m[Kdiff_sample.h:26[m[K,
                 from [01m[Kblockwise_sa.h:29[m[K,
                 from [01m[Kbt2_idx.h:42[m[K,
                 from [01m[Kbt2_search.cpp:33[m[K:
/usr/include/tbb/task.h: In instantiation of ‘[01m[Ktbb::task* tbb::internal::function_task<F>::execute() [with F = multiseedSearchWorker_2p5][m[K’:
[01m[Kbt2_search.cpp:4756:1:[m[K   required from here
[01m[K/usr/include/tbb/task.h:926:13:[m[K [01;31m[Kerror: [m[Kno match for call to ‘[01m[K(const multiseedSearchWorker_2p5) ()[m[K’
             my_func();
[01;32m[K             ^[m[K
[01m[Kbt2_search.cpp:3899:6:[m[K [01;36m[Knote: [m[Kcandidate: void multiseedSearchWorker_2p5::operator()() <near match>
 void multiseedSearchWorker_2p5::operator()() {
[01;32m[K      ^[m[K
[01m[Kbt2_search.cpp:3899:6:[m[K [01;36m[Knote: [m[K  passing ‘[01m[Kconst multiseedSearchWorker_2p5*[m[K’ as ‘[01m[Kthis[m[K’ argument discards qualifiers
x86_64-pc-linux-gnu-g++ -march=native -mtune=native -O2 -pipe -msse2 \
	-DCOMPILER_OPTIONS="\"-march=native -mtune=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \
	 -I third_party -I . \
	-o bowtie2-inspect-l bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
make: *** [Makefile:292: bowtie2-align-s] Error 1
make: *** Waiting for unfinished jobs....
make: *** [Makefile:300: bowtie2-align-l] Error 1
 [31;01m*[0m ERROR: sci-biology/bowtie-2.2.6::gentoo failed (compile phase):
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/bowtie-2.2.6::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/bowtie-2.2.6::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/log/portage-build/build/sci-biology/bowtie-2.2.6:20170907-102138.log'.
 [31;01m*[0m For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/bowtie-2.2.6/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/bowtie-2.2.6/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-biology/bowtie-2.2.6/work/bowtie2-2.2.6'
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/bowtie-2.2.6/work/bowtie2-2.2.6'