"make modbam2bed" fails
ekushele opened this issue · 3 comments
ekushele commented
Hi,
Following the instrctions in the README, I cloned modbam2bed:
git clone --recursive https://github.com/epi2me-labs/modbam2bed.git
I cd into the modbam2bed directory, and ran make modbam2bed, and it failed.
Below is the make modbam2bed output.
What can I do?
Thank you!
make modbam2bed output:
% make modbam2bed
mkdir -p obj && \
cc -c -pthread -Wall -fstack-protector-strong -D_FORTIFY_SOURCE=2 -fpic -msse3 -O3 -std=c99 \
-Isrc -Ihtslib src/modbam2bed.c -o modbam2bed.o
In file included from src/modbam2bed.c:16:
src/counts.h:68:20: warning: inline function ‘is_chg_rev’ declared but never defined
bool extern inline is_chg_rev(size_t rpos, int rlen, char* ref);
^~~~~~~~~~
src/counts.h:67:20: warning: inline function ‘is_chg_fwd’ declared but never defined
bool extern inline is_chg_fwd(size_t rpos, int rlen, char* ref);
^~~~~~~~~~
src/counts.h:65:20: warning: inline function ‘is_chh_rev’ declared but never defined
bool extern inline is_chh_rev(size_t rpos, int rlen, char* ref);
^~~~~~~~~~
src/counts.h:64:20: warning: inline function ‘is_chh_fwd’ declared but never defined
bool extern inline is_chh_fwd(size_t rpos, int rlen, char* ref);
^~~~~~~~~~
src/counts.h:62:20: warning: inline function ‘_is_chn_rev’ declared but never defined
bool extern inline _is_chn_rev(size_t rpos, int rlen, char* ref);
^~~~~~~~~~~
src/counts.h:61:20: warning: inline function ‘_is_chn_fwd’ declared but never defined
bool extern inline _is_chn_fwd(size_t rpos, int rlen, char* ref);
^~~~~~~~~~~
src/counts.h:59:20: warning: inline function ‘is_cpg_rev’ declared but never defined
bool extern inline is_cpg_rev(size_t rpos, int rlen, char* ref);
^~~~~~~~~~
src/counts.h:58:20: warning: inline function ‘is_cpg_fwd’ declared but never defined
bool extern inline is_cpg_fwd(size_t rpos, int rlen, char* ref);
^~~~~~~~~~
mkdir -p obj && \
cc -c -pthread -Wall -fstack-protector-strong -D_FORTIFY_SOURCE=2 -fpic -msse3 -O3 -std=c99 \
-Isrc -Ihtslib src/common.c -o common.o
mkdir -p obj && \
cc -c -pthread -Wall -fstack-protector-strong -D_FORTIFY_SOURCE=2 -fpic -msse3 -O3 -std=c99 \
-Isrc -Ihtslib src/counts.c -o counts.o
mkdir -p obj && \
cc -c -pthread -Wall -fstack-protector-strong -D_FORTIFY_SOURCE=2 -fpic -msse3 -O3 -std=c99 \
-Isrc -Ihtslib src/bamiter.c -o bamiter.o
mkdir -p obj && \
cc -c -pthread -Wall -fstack-protector-strong -D_FORTIFY_SOURCE=2 -fpic -msse3 -O3 -std=c99 \
-Isrc -Ihtslib src/args.c -o args.o
Compiling libhts.a
cd htslib/ \
&& autoreconf -i \
&& autoheader \
&& autoconf \
&& CFLAGS="-fpic -msse3 -O3 -std=c99 " ./configure \
&& make -j 4
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes
checking whether C compiler accepts -mavx2... yes
checking whether C compiler accepts -mavx512f... yes
checking whether C compiler supports ARM Neon... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/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 for srand48_deterministic... no
checking whether fdatasync is declared... no
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... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
checking whether PTHREAD_MUTEX_RECURSIVE is declared... no
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
config.status: linking htscodecs_bundled.mk to htscodecs.mk
make[1]: Entering directory '/home/test_modbam2bed_make/modbam2bed/htslib'
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o kfunc.o kfunc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o kstring.o kstring.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o errmod.o errmod.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o faidx.o faidx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o header.o header.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.16"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS ""' >> config_vars.h
echo '#define HTS_CFLAGS "-Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-fvisibility=hidden "' >> config_vars.h
echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto"' >> config_vars.h
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hts_expr.o hts_expr.c
Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.3.0"
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hts_os.o hts_os.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o md5.o md5.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o multipart.o multipart.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o probaln.o probaln.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o realn.o realn.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o regidx.o regidx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o region.o region.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o sam.o sam.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o tbx.o tbx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o textutils.o textutils.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o vcf.o vcf.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -mavx2 -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -mavx512f -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hfile_libcurl.o hfile_libcurl.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hfile_gcs.o hfile_gcs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hfile_s3.o hfile_s3.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hfile_s3_write.o hfile_s3_write.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o kfunc.pico kfunc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o kstring.pico kstring.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o bgzf.pico bgzf.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o errmod.pico errmod.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o faidx.pico faidx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o header.pico header.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hfile.pico hfile.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hts.pico hts.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hts_expr.pico hts_expr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hts_os.pico hts_os.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o md5.pico md5.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o multipart.pico multipart.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o probaln.pico probaln.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o realn.pico realn.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o regidx.pico regidx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o region.pico region.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o sam.pico sam.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o tbx.pico tbx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o textutils.pico textutils.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o thread_pool.pico thread_pool.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o vcf.pico vcf.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -mavx2 -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -mavx512f -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hfile_gcs.pico hfile_gcs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hfile_s3.pico hfile_s3.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -fpic -c -o hfile_s3_write.pico hfile_s3_write.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o bgzip.o bgzip.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o htsfile.o htsfile.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o tabix.o tabix.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/hfile.o test/hfile.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/pileup.o test/pileup.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/pileup_mod.o test/pileup_mod.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/sam.o test/sam.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_expr.o test/test_expr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_kfunc.o test/test_kfunc.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_kstring.o test/test_kstring.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_mod.o test/test_mod.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_realn.o test/test_realn.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_str2int.o test/test_str2int.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_time_funcs.o test/test_time_funcs.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_view.o test/test_view.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_index.o test/test_index.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test_introspection.o test/test_introspection.c
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
gcc -Wall -fpic -msse3 -O3 -std=c99 -fvisibility=hidden -I. -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.3 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.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_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
gcc -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
ln -sf libhts.so libhts.so.3
gcc -fvisibility=hidden -o test/test_time_funcs test/test_time_funcs.o
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o
ranlib libhts.a
gcc -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
gcc -fvisibility=hidden -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread
make[1]: Leaving directory '/home/test_modbam2bed_make/modbam2bed/htslib'
cc -pthread -Wall -fstack-protector-strong -D_FORTIFY_SOURCE=2 -fpic -msse3 -O3 -std=c99 \
-Isrc -Ihtslib \
modbam2bed.o common.o counts.o bamiter.o args.o htslib/libhts.a \
-lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto \
-o modbam2bed
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `uint7_decode_crc64':
cram_io.c:(.text+0x7a1): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `sint7_decode_crc32':
cram_io.c:(.text+0x999): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `uint7_decode_crc32':
cram_io.c:(.text+0xb99): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `cram_compress_by_method':
cram_io.c:(.text+0xe9c): undefined reference to `libdeflate_alloc_compressor'
/usr/bin/ld: cram_io.c:(.text+0xf09): undefined reference to `libdeflate_gzip_compress'
/usr/bin/ld: cram_io.c:(.text+0xf14): undefined reference to `libdeflate_free_compressor'
/usr/bin/ld: cram_io.c:(.text+0x13c7): undefined reference to `libdeflate_free_compressor'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `itf8_decode_crc':
cram_io.c:(.text+0x4104): undefined reference to `libdeflate_crc32'
/usr/bin/ld: cram_io.c:(.text+0x4163): undefined reference to `libdeflate_crc32'
/usr/bin/ld: cram_io.c:(.text+0x4192): undefined reference to `libdeflate_crc32'
/usr/bin/ld: cram_io.c:(.text+0x41ce): undefined reference to `libdeflate_crc32'
/usr/bin/ld: cram_io.c:(.text+0x4216): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o):cram_io.c:(.text+0x6723): more undefined references to `libdeflate_crc32' follow
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `zlib_mem_inflate':
cram_io.c:(.text+0x7d98): undefined reference to `libdeflate_alloc_decompressor'
/usr/bin/ld: cram_io.c:(.text+0x7de5): undefined reference to `libdeflate_gzip_decompress'
/usr/bin/ld: cram_io.c:(.text+0x7dfa): undefined reference to `libdeflate_free_decompressor'
/usr/bin/ld: cram_io.c:(.text+0x7e98): undefined reference to `libdeflate_free_decompressor'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `cram_read_block':
cram_io.c:(.text+0x7fe2): undefined reference to `libdeflate_crc32'
/usr/bin/ld: cram_io.c:(.text+0x801b): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `cram_write_block':
cram_io.c:(.text+0x8603): undefined reference to `libdeflate_crc32'
/usr/bin/ld: cram_io.c:(.text+0x862a): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o): in function `cram_uncompress_block':
cram_io.c:(.text+0x88de): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(cram_io.o):cram_io.c:(.text+0xb91e): more undefined references to `libdeflate_crc32' follow
/usr/bin/ld: htslib/libhts.a(bgzf.o): in function `bgzf_decode_func':
bgzf.c:(.text+0x343): undefined reference to `libdeflate_alloc_decompressor'
/usr/bin/ld: bgzf.c:(.text+0x36c): undefined reference to `libdeflate_deflate_decompress'
/usr/bin/ld: bgzf.c:(.text+0x376): undefined reference to `libdeflate_free_decompressor'
/usr/bin/ld: bgzf.c:(.text+0x38b): undefined reference to `libdeflate_crc32'
/usr/bin/ld: htslib/libhts.a(bgzf.o): in function `bgzf_compress':
bgzf.c:(.text+0x1a8b): undefined reference to `libdeflate_crc32'
/usr/bin/ld: bgzf.c:(.text+0x1af2): undefined reference to `libdeflate_alloc_compressor'
/usr/bin/ld: bgzf.c:(.text+0x1b14): undefined reference to `libdeflate_deflate_compress'
/usr/bin/ld: bgzf.c:(.text+0x1b29): undefined reference to `libdeflate_free_compressor'
/usr/bin/ld: bgzf.c:(.text+0x1b5a): undefined reference to `libdeflate_free_compressor'
/usr/bin/ld: htslib/libhts.a(bgzf.o): in function `bgzf_read_block':
bgzf.c:(.text+0x2e1e): undefined reference to `libdeflate_alloc_decompressor'
/usr/bin/ld: bgzf.c:(.text+0x2e45): undefined reference to `libdeflate_deflate_decompress'
/usr/bin/ld: bgzf.c:(.text+0x2e4f): undefined reference to `libdeflate_free_decompressor'
/usr/bin/ld: bgzf.c:(.text+0x2e66): undefined reference to `libdeflate_crc32'
collect2: error: ld returned 1 exit status
make: *** [Makefile:79: modbam2bed] Error 1
cjw85 commented
The error suggests that you do not have libz on your system. You need the following libraries available to link:
-lm -lz -llzma -lbz2 -lpthread -lcurl -lcrypto
ekushele commented
This was fast! Thank you!
jguhlin commented
Exact same issue, all libraries installed, tried with ubuntu zlib and zlib-dev.