build.log

build.log (text/plain), 26.60 KB, created by Agostino Sarubbo on 2020-05-25 10:08:31 UTC

 * Package:    sci-libs/htslib-1.9
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 bzip2 elibc_glibc kernel_linux lzma userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking htslib-1.9.tar.bz2 to /var/tmp/portage/sci-libs/htslib-1.9/work
>>> Source unpacked in /var/tmp/portage/sci-libs/htslib-1.9/work
>>> Preparing source in /var/tmp/portage/sci-libs/htslib-1.9/work/htslib-1.9 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/htslib-1.9/work/htslib-1.9 ...
./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 --docdir=/usr/share/doc/htslib-1.9 --htmldir=/usr/share/doc/htslib-1.9/html --libdir=/usr/lib64 --disable-gcs --disable-plugins --disable-s3 --enable-bz2 --disable-libcurl --enable-lzma
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
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 for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for grep that handles long lines and -e... /bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for x86_64-pc-linux-gnu... plain .so
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-libs/htslib-1.9/work/htslib-1.9 ...
make -j4 
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o kfunc.o kfunc.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o knetfile.o knetfile.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o kstring.o kstring.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o bgzf.o bgzf.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o errmod.o errmod.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o faidx.o faidx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o hfile.o hfile.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9"' > version.h
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o hts_os.o hts_os.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o md5.o md5.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o multipart.o multipart.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o probaln.o probaln.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o realn.o realn.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o regidx.o regidx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o sam.o sam.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o vcf_sweep.o vcf_sweep.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o tbx.o tbx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o textutils.o textutils.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o thread_pool.o thread_pool.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o vcf.o vcf.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o vcfutils.o vcfutils.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_decode.o cram/cram_decode.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_encode.o cram/cram_encode.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_external.o cram/cram_external.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_index.o cram/cram_index.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_io.o cram/cram_io.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/cram_stats.o cram/cram_stats.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/files.o cram/files.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/mFILE.o cram/mFILE.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/rANS_static.o cram/rANS_static.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/sam_header.o cram/sam_header.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o cram/string_alloc.o cram/string_alloc.c
In file included from /usr/include/string.h:495,
                 from cram/string_alloc.c:41:
In function ‘strncpy’,
    inlined from ‘string_ndup’ at cram/string_alloc.c:151:5,
    inlined from ‘string_dup’ at cram/string_alloc.c:143:12:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cram/string_alloc.c: In function ‘string_dup’:
cram/string_alloc.c:143:12: note: length computed here
  143 |     return string_ndup(a_str, instr, strlen(instr));
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o kfunc.pico kfunc.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o knetfile.pico knetfile.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o kstring.pico kstring.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
In file included from /usr/include/string.h:495,
                 from cram/cram_io.c:53:
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3748:13,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3740:9,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘cram_dopen’ at cram/cram_io.c:4126:9:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o bgzf.pico bgzf.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o errmod.pico errmod.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o faidx.pico faidx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o hfile.pico hfile.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o hfile_net.pico hfile_net.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o hts.pico hts.c
hts.c: In function ‘hts_idx_init’:
hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Woverflow-Woverflow]8;;]
 1386 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
      |                                                           ^~~
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o hts_os.pico hts_os.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o md5.pico md5.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o multipart.pico multipart.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o probaln.pico probaln.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o realn.pico realn.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o regidx.pico regidx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o sam.pico sam.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o tbx.pico tbx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o textutils.pico textutils.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o thread_pool.pico thread_pool.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o vcf.pico vcf.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o vcfutils.pico vcfutils.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/files.pico cram/files.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o bgzip.o bgzip.c
In file included from /usr/include/string.h:495,
                 from cram/cram_io.c:53:
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3748:13,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘strncpy’,
    inlined from ‘full_path’ at cram/cram_io.c:3740:9,
    inlined from ‘cram_write_SAM_hdr’ at cram/cram_io.c:3823:17:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o htsfile.o htsfile.c
In function ‘strncpy’,
    inlined from ‘cram_dopen’ at cram/cram_io.c:4126:9:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-truncation-Wstringop-truncation]8;;]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o tabix.o tabix.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/hts_endian.o test/hts_endian.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/fieldarith.o test/fieldarith.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/hfile.o test/hfile.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/sam.o test/sam.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test_bgzf.o test/test_bgzf.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test_realn.o test/test_realn.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test-regidx.o test/test-regidx.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test_view.o test/test_view.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -frecord-gcc-switches -I.  -c -o hts.o hts.c
x86_64-pc-linux-gnu-gcc -shared -Wl,-soname,libhts.so.2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -llzma -lbz2 -lz -lm   -lpthread
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0  -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm  
ln -sf libhts.so libhts.so.2
hts.c: In function ‘hts_idx_init’:
hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Woverflow-Woverflow]8;;]
 1386 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
      |                                                           ^~~
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o 
make: ar: No such file or directory
make: *** [Makefile:246: libhts.a] Error 127
 * ERROR: sci-libs/htslib-1.9::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/htslib-1.9::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/htslib-1.9::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-libs/htslib-1.9:20200525-091012.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/htslib-1.9/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/htslib-1.9/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/htslib-1.9/work/htslib-1.9'
 * S: '/var/tmp/portage/sci-libs/htslib-1.9/work/htslib-1.9'



emerge --info:
Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64)
=================================================================
System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7
KiB Mem:    16011344 total,   1407976 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Mon, 25 May 2020 09:35:30 +0000
sh bash 5.0_p17
ld GNU ld (Gentoo 2.34 p4) 2.34.0
app-shells/bash:          5.0_p17::gentoo
dev-lang/perl:            5.30.2-r2::gentoo
dev-lang/python:          2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/autoconf:       2.69-r5::gentoo
sys-devel/automake:       1.16.2::gentoo
sys-devel/binutils:       2.34-r1::gentoo
sys-devel/gcc:            10.1.0::gentoo
sys-devel/gcc-config:     2.3::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.31-r3::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CC="x86_64-pc-linux-gnu-gcc"
CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXX="x86_64-pc-linux-gnu-g++"
CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="C.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j4"
PKGDIR="/root/.packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS