daviesrob
commented
3 years ago It looks like you were trying to build HTSlib in a conda environment. This rarely goes well. You need to install the HTSlib conda package, or build it outside of conda.
Something like this should work for conda HTSlib:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install 'htslib>=1.13'You may also be able to get the installation you already made to work using:
CPPFLAGS='-I/usr/local/include' LDFLAGS='-L/usr/local/lib -Wl,-R/usr/local/lib'but I wouldn't like to guarantee it.
You may also have similar conda compatibility problems with methpipe, if you didn't install it using a conda package.
Hannah1746
I am trying to install a program called methpipe witch uses HTSLib. I have installed HTSLib on my computer: (base) lab@lab:~/Documents/apps/htslib$ ./configure checking for gcc... lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc 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 lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc accepts -g... yes checking for lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed checking for ranlib... lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ranlib checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall 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... lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cpp 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 for srand48_deterministic... no 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 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... yes 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 (base) lab@lab:~/Documents/apps/htslib$ make lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o kfunc.o kfunc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o kstring.o kstring.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o bcf_sr_sort.o bcf_sr_sort.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o bgzf.o bgzf.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o errmod.o errmod.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o faidx.o faidx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o header.o header.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.13-23-g3eada2f"' > version.h echo '#define HTS_CC "lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc"' > config_vars.h echo '#define HTS_CPPFLAGS "-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include"' >> config_vars.h echo '#define HTS_CFLAGS "-Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden "' >> config_vars.h echo '#define HTS_LIBS "-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto"' >> config_vars.h Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.1.1-1-ged325d7" lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hts.o hts.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hts_expr.o hts_expr.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hts_os.o hts_os.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o md5.o md5.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o multipart.o multipart.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o probaln.o probaln.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o realn.o realn.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o regidx.o regidx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o region.o region.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o sam.o sam.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o synced_bcf_reader.o synced_bcf_reader.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o vcf_sweep.o vcf_sweep.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o tbx.o tbx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o textutils.o textutils.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o thread_pool.o thread_pool.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o vcf.o vcf.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o vcfutils.o vcfutils.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_codecs.o cram/cram_codecs.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_decode.o cram/cram_decode.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_encode.o cram/cram_encode.c cram/cram_encode.c: In function 'process_one_read': cram/cram_encode.c:3059:24: warning: unused variable 'brg' [-Wunused-variable] sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN"); ^~~ lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_external.o cram/cram_external.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_index.o cram/cram_index.c cram/cram_index.c: In function 'cram_index_build': cram/cram_index.c:738:17: warning: variable 'hpos' set but not used [-Wunused-but-set-variable] off_t cpos, hpos; ^~~~ lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_io.o cram/cram_io.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/cram_stats.o cram/cram_stats.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/mFILE.o cram/mFILE.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/open_trace_file.o cram/open_trace_file.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o cram/string_alloc.o cram/string_alloc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hfile_libcurl.o hfile_libcurl.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hfile_gcs.o hfile_gcs.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hfile_s3.o hfile_s3.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o hfile_s3_write.o hfile_s3_write.c 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_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-ranlib libhts.a lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o kfunc.pico kfunc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o kstring.pico kstring.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o bgzf.pico bgzf.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o errmod.pico errmod.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o faidx.pico faidx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o header.pico header.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hfile.pico hfile.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hts.pico hts.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hts_expr.pico hts_expr.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hts_os.pico hts_os.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o md5.pico md5.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o multipart.pico multipart.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o probaln.pico probaln.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o realn.pico realn.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o regidx.pico regidx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o region.pico region.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o sam.pico sam.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o vcf_sweep.pico vcf_sweep.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o tbx.pico tbx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o textutils.pico textutils.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o thread_pool.pico thread_pool.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o vcf.pico vcf.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o vcfutils.pico vcfutils.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_decode.pico cram/cram_decode.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_encode.pico cram/cram_encode.c cram/cram_encode.c: In function 'process_one_read': cram/cram_encode.c:3059:24: warning: unused variable 'brg' [-Wunused-variable] sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN"); ^~~ lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_external.pico cram/cram_external.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_index.pico cram/cram_index.c cram/cram_index.c: In function 'cram_index_build': cram/cram_index.c:738:17: warning: variable 'hpos' set but not used [-Wunused-but-set-variable] off_t cpos, hpos; ^~~~ lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_io.pico cram/cram_io.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/mFILE.pico cram/mFILE.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hfile_libcurl.pico hfile_libcurl.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hfile_gcs.pico hfile_gcs.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hfile_s3.pico hfile_s3.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -fpic -c -o hfile_s3_write.pico hfile_s3_write.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -shared -Wl,-soname,libhts.so.3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -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_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico hfile_gcs.pico hfile_s3.pico hfile_s3_write.pico -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread ln -sf libhts.so libhts.so.3 lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o bgzip.o bgzip.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o bgzip bgzip.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o htsfile.o htsfile.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o htsfile htsfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o tabix.o tabix.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o tabix tabix.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/hts_endian.o test/hts_endian.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/hts_endian test/hts_endian.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/fieldarith.o test/fieldarith.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/hfile.o test/hfile.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/pileup.o test/pileup.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/pileup_mod.o test/pileup_mod.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/plugins-dlhts.o test/plugins-dlhts.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/sam.o test/sam.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/sam test/sam.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_bgzf.o test/test_bgzf.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_expr.o test/test_expr.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_kfunc.o test/test_kfunc.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_kstring.o test/test_kstring.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_mod.o test/test_mod.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_realn.o test/test_realn.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test-regidx.o test/test-regidx.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_str2int.o test/test_str2int.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_view.o test/test_view.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_index.o test/test_index.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test-vcf-api.o test/test-vcf-api.c test/test-vcf-api.c: In function 'bcf_to_vcf': test/test-vcf-api.c:361:9: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result] fwrite(line.s,1,line.l,stdout); ^
~~~~~~~~~ lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test-bcf-sr.o test/test-bcf-sr.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test-bcf-translate.o test/test-bcf-translate.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test-parse-reg.o test/test-parse-reg.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem lab/Documents/apps/anaconda3/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem lab/Documents/apps/anaconda3/include -c -o test/test_introspection.o test/test_introspection.c lab/Documents/apps/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,lab/Documents/apps/anaconda3/lib -Wl,-rpath-link,lab/Documents/apps/anaconda3/lib -Llab/Documents/apps/anaconda3/lib -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpthread 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 (base) lab@lab:~/Documents/apps/htslib$ make install mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/share/man/man7 /usr/local/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.13-23-g3eada2f install: cannot create regular file '/usr/local/lib/libhts.so.1.13-23-g3eada2f': Permission denied make: ** [Makefile:729: install-so] Error 1 (base) lab@lab:~/Documents/apps/htslib$ sudo make install [sudo] password for krablab: mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/share/man/man7 /usr/local/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.13-23-g3eada2f ln -sf libhts.so.1.13-23-g3eada2f /usr/local/lib/libhts.so ln -sf libhts.so.1.13-23-g3eada2f /usr/local/lib/libhts.so.3 sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.13-23-g3eada2f#g' htslib.pc.tmp > /usr/local/lib/pkgconfig/htslib.pc chmod 644 /usr/local/lib/pkgconfig/htslib.pc install -p bgzip htsfile tabix /usr/local/bin if test -n ""; then install -p ; fi install -p -m 644 htslib/.h /usr/local/include/htslib install -p -m 644 libhts.a /usr/local/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /usr/local/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /usr/local/share/man/man7When I try to install methpipe I get this message: configure: error: in `lab/Documents/apps/methpipe-5.0.0/build': configure: error: Failed to locate HTSLib on your system. Please use the LDFLAGS and CPPFLAGS variables to specify the directories where the HTSLib library and headers can be found.
Where are the location of the files I need to flag?
Thank you so much, Hannah