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Isal decompression

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ISA-L compression support evaluation. #1908

Isal decompression
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Cirrus CI / debian-gcc CFLAGS:-g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow LDFLAGS:-fsanitize=address,undefined UBSAN_OPTIONS:print_stacktrace=1:halt_on_error=1 USE_CONFIG:yes USE_LIBDEFLATE:yes failed Apr 29, 2025 in 31s

Task Summary

Instruction compile failed in 00:13

Details

⚠️ Not enough compute credits to prioritize tasks!

✅ 00:00 clone
✅ 00:07 install
✅ 00:07 libdeflate
❌ 00:13 compile

checking for drand48... yes
checking for srand48_deterministic... no
checking for getauxval... yes
checking for elf_aux_info... no
checking for posix_memalign... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for __attribute__((constructor))... yes
checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes
checking for library containing dlsym... none required
checking whether the compiler accepts -rdynamic... 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 whether htscodecs files are present... yes
checking for libdeflate.h... yes
checking for libdeflate_deflate_compress in -ldeflate... yes
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: WARNING: libcurl not enabled: library not found
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking for library containing regcomp... no
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: linking htscodecs_bundled.mk to htscodecs.mk
make cc-version $MAKE_OPTS
gcc (GCC) 15.1.0
Copyright (C) 2025 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

if test "x$DO_MAINTAINER_CHECKS" = "xyes"; then
  make maintainer-check $MAKE_OPTS
fi
make -j 4 $MAKE_OPTS
gcc -Wall -g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow -fvisibility=hidden -Werror  -I. -I/root/libdeflate -c -o kfunc.o kfunc.c
gcc -Wall -g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow -fvisibility=hidden -Werror  -I. -I/root/libdeflate -c -o kstring.o kstring.c
gcc -Wall -g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow -fvisibility=hidden -Werror  -I. -I/root/libdeflate -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow -fvisibility=hidden -Werror  -I. -I/root/libdeflate -c -o bgzf.o bgzf.c
bgzf.c:47:10: fatal error: isa-l.h: No such file or directory
   47 | #include <isa-l.h>
      |          ^~~~~~~~~
compilation terminated.
make: *** [Makefile:194: bgzf.o] Error 1
make: *** Waiting for unfinished jobs....

Exit status: 2