rwk-unil / sapphire Goto Github PK

[+] Building 344.3s (8/9)                                                                                                docker:default
 => [internal] load build definition from Dockerfile                                                                               0.0s
 => => transferring dockerfile: 1.83kB                                                                                             0.0s
 => WARN: MaintainerDeprecated: Maintainer instruction is deprecated in favor of using label (line 3)                              0.0s
 => [internal] load metadata for docker.io/library/ubuntu:20.04                                                                    1.0s
 => [internal] load .dockerignore                                                                                                  0.0s
 => => transferring context: 2B                                                                                                    0.0s
 => [1/6] FROM docker.io/library/ubuntu:20.04@sha256:0b897358ff6624825fb50d20ffb605ab0eaea77ced0adb8c6a4b756513dec6fc              0.0s
 => CACHED [2/6] RUN apt-get update && apt-get -y upgrade && apt-get install -y  apt-utils curl gnupg gcc g++ make autoconf &&  a  0.0s
 => CACHED [3/6] RUN apt-get update && apt-get -y upgrade && apt-get install -y  git zlib1g-dev libbz2-dev liblzma-dev &&  apt-ge  0.0s
 => CACHED [4/6] RUN apt-get update && apt-get -y upgrade && apt-get install -y  bcftools &&  apt-get clean && apt-get purge &&    0.0s
 => ERROR [5/6] RUN mkdir -p /usr/src/ &&     cd /usr/src/ &&     git clone https://github.com/rwk-unil/pp.git &&     cd /usr/s  343.2s
------                                                                                                                                  
 > [5/6] RUN mkdir -p /usr/src/ &&     cd /usr/src/ &&     git clone https://github.com/rwk-unil/pp.git &&     cd /usr/src/pp &&     git submodule update --init --recursive xSqueezeIt &&     cd xSqueezeIt &&     cd htslib &&     autoheader &&     autoconf &&     automake --add-missing;     ./configure &&     make &&     make install &&     ldconfig &&     cd .. &&     git clone https://github.com/facebook/zstd.git &&     cd zstd &&     make &&     cd .. &&     cd .. &&     cd pp_extractor &&     make &&     chmod +x pp_extract &&     cp pp_extract /usr/local/bin/ &&     chmod +x scripts/run_pp_extract.sh &&     cp scripts/run_pp_extract.sh /usr/local/bin/run_pp_extract &&     cd .. &&     cd phase_caller &&     make &&     chmod +x phase_caller &&     cp phase_caller /usr/local/bin/ &&     cd /usr/src/ &&     rm -rf pp:
1.686 Cloning into 'pp'...
5.654 Submodule 'xSqueezeIt' (https://github.com/rwk-unil/xSqueezeIt.git) registered for path 'xSqueezeIt'
5.751 Cloning into '/usr/src/pp/xSqueezeIt'...
7.740 Submodule path 'xSqueezeIt': checked out 'c3e411c0b4f3e27ec2572232e8a9bbd59f9fb346'
7.832 Submodule 'benchmark' (https://github.com/google/benchmark.git) registered for path 'xSqueezeIt/benchmark'
7.837 Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'xSqueezeIt/htslib'
7.842 Submodule 'test/cukinia' (https://github.com/savoirfairelinux/cukinia) registered for path 'xSqueezeIt/test/cukinia'
7.934 Cloning into '/usr/src/pp/xSqueezeIt/benchmark'...
9.456 Cloning into '/usr/src/pp/xSqueezeIt/htslib'...
12.34 Cloning into '/usr/src/pp/xSqueezeIt/test/cukinia'...
14.77 Submodule path 'xSqueezeIt/benchmark': checked out '8df87f6c879cbcabd17c5cfcec7b89687df36953'
16.52 Submodule path 'xSqueezeIt/htslib': checked out '6143086502567c5c4bb5cacb2951f664ba28ed6e'
16.58 Submodule 'htscodecs' (https://github.com/samtools/htscodecs.git) registered for path 'xSqueezeIt/htslib/htscodecs'
16.65 Cloning into '/usr/src/pp/xSqueezeIt/htslib/htscodecs'...
20.50 Submodule path 'xSqueezeIt/htslib/htscodecs': checked out 'cd0737fff5893b0842b047da5aa3209e5f65442c'
21.02 Submodule path 'xSqueezeIt/test/cukinia': checked out '8dc1f9e7d71172050f4d2ff6deaef22183ab95fe'
25.35 configure.ac: error: no proper invocation of AM_INIT_AUTOMAKE was found.
25.35 configure.ac: You should verify that configure.ac invokes AM_INIT_AUTOMAKE,
25.35 configure.ac: that aclocal.m4 is present in the top-level directory,
25.35 configure.ac: and that aclocal.m4 was recently regenerated (using aclocal)
25.35 automake: error: no 'Makefile.am' found for any configure output
26.20 checking for gcc... gcc
26.53 checking whether the C compiler works... yes
33.03 checking for C compiler default output file name... a.out
33.05 checking for suffix of executables... 
37.29 checking whether we are cross compiling... no
41.72 checking for suffix of object files... o
41.99 checking whether we are using the GNU C compiler... yes
42.20 checking whether gcc accepts -g... yes
42.41 checking for gcc option to accept ISO C89... none needed
42.69 checking for ranlib... ranlib
42.69 checking for grep that handles long lines and -e... /usr/bin/grep
42.71 checking for C compiler warning flags... -Wall
42.94 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes
47.44 checking whether C compiler accepts -mavx2... yes
48.13 checking whether C compiler accepts -mavx512f... yes
48.85 checking whether C compiler supports ARM Neon... no
49.15 checking for pkg-config... no
49.15 checking for special C compiler options needed for large files... no
49.15 checking for _FILE_OFFSET_BITS value needed for large files... no
49.50 checking shared library type for unknown-Linux... plain .so
49.50 checking whether the linker supports versioned symbols... yes
49.87 checking whether the compiler accepts -fvisibility=hidden... yes
50.27 checking how to run the C preprocessor... gcc -E
51.05 checking for egrep... /usr/bin/grep -E
51.07 checking for ANSI C header files... yes
52.21 checking for sys/types.h... yes
52.55 checking for sys/stat.h... yes
52.90 checking for stdlib.h... yes
53.23 checking for string.h... yes
53.58 checking for memory.h... yes
53.96 checking for strings.h... yes
54.31 checking for inttypes.h... yes
54.67 checking for stdint.h... yes
55.19 checking for unistd.h... yes
55.75 checking for stdlib.h... (cached) yes
55.83 checking for unistd.h... (cached) yes
55.91 checking for sys/param.h... yes
56.35 checking for getpagesize... yes
56.89 checking for working mmap... yes
57.55 checking for gmtime_r... yes
58.08 checking for fsync... yes
58.62 checking for drand48... yes
59.13 checking for srand48_deterministic... no
59.75 checking whether fdatasync is declared... yes
60.05 checking for fdatasync... yes
60.47 checking for library containing log... -lm
61.36 checking for zlib.h... yes
61.64 checking for inflate in -lz... yes
62.05 checking for library containing recv... none required
62.47 checking for bzlib.h... yes
62.71 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
63.15 checking for lzma.h... yes
63.46 checking for lzma_easy_buffer_encode in -llzma... yes
63.97 checking whether htscodecs files are present... yes
63.97 checking for libdeflate.h... no
64.30 checking for libdeflate_deflate_compress in -ldeflate... no
64.73 checking for curl/curl.h... no
65.01 checking for curl_easy_pause in -lcurl... no
65.57 checking for curl_easy_init in -lcurl... no
66.08 configure: WARNING: libcurl not enabled: library not found
66.08 configure: WARNING: GCS support not enabled: requires libcurl support
66.08 configure: WARNING: S3 support not enabled: requires libcurl support
66.08 checking for library containing regcomp... none required
66.62 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
67.08 configure: creating ./config.status
68.33 config.status: creating config.mk
68.53 config.status: creating htslib.pc.tmp
68.72 config.status: creating config.h
68.82 config.status: linking htscodecs_bundled.mk to htscodecs.mk
69.28 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o kfunc.o kfunc.c
69.60 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o kstring.o kstring.c
70.01 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
71.04 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o bgzf.o bgzf.c
71.97 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o errmod.o errmod.c
72.34 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o faidx.o faidx.c
73.18 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o header.o header.c
74.64 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o hfile.o hfile.c
75.35 echo '#define HTS_VERSION_TEXT "1.17"' > version.h
75.37 printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
75.37 'gcc' \
75.37 '' \
75.37 '-Wall -g -O2 -fvisibility=hidden' \
75.37 '-fvisibility=hidden ' \
75.37 '-llzma -lbz2 -lz -lm  ' > config_vars.h
75.45 Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.4.0"
75.45 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o hts.o hts.c
77.77 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o hts_expr.o hts_expr.c
78.41 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o hts_os.o hts_os.c
78.64 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o md5.o md5.c
78.97 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o multipart.o multipart.c
79.34 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o probaln.o probaln.c
79.75 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o realn.o realn.c
80.38 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o regidx.o regidx.c
80.94 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o region.o region.c
81.46 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o sam.o sam.c
84.67 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
85.80 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o vcf_sweep.o vcf_sweep.c
86.24 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o tbx.o tbx.c
86.70 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o textutils.o textutils.c
87.23 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o thread_pool.o thread_pool.c
87.96 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o vcf.o vcf.c
91.62 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o vcfutils.o vcfutils.c
92.53 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
94.10 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_decode.o cram/cram_decode.c
95.98 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_encode.o cram/cram_encode.c
98.00 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_external.o cram/cram_external.c
98.58 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_index.o cram/cram_index.c
99.22 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_io.o cram/cram_io.c
101.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/cram_stats.o cram/cram_stats.c
101.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/mFILE.o cram/mFILE.c
102.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
102.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
102.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o cram/string_alloc.o cram/string_alloc.c
102.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
104.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
105.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
105.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
105.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
106.8 gcc -Wall -g -O2 -fvisibility=hidden -mavx2 -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
108.1 gcc -Wall -g -O2 -fvisibility=hidden -mavx512f -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
109.3 gcc -Wall -g -O2 -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
110.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
111.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
112.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
112.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
113.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
113.5 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  
113.8 ranlib libhts.a
113.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o kfunc.pico kfunc.c
114.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o kstring.pico kstring.c
114.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
115.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o bgzf.pico bgzf.c
116.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o errmod.pico errmod.c
117.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o faidx.pico faidx.c
117.8 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o header.pico header.c
119.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o hfile.pico hfile.c
120.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o hts.pico hts.c
122.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o hts_expr.pico hts_expr.c
122.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o hts_os.pico hts_os.c
122.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o md5.pico md5.c
123.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o multipart.pico multipart.c
123.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o probaln.pico probaln.c
124.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o realn.pico realn.c
124.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o regidx.pico regidx.c
125.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o region.pico region.c
125.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o sam.pico sam.c
128.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
130.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
130.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o tbx.pico tbx.c
130.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o textutils.pico textutils.c
131.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o thread_pool.pico thread_pool.c
131.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o vcf.pico vcf.c
135.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o vcfutils.pico vcfutils.c
136.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
137.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
139.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
142.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
142.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
143.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
145.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
146.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
146.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
147.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
147.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
147.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c
148.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c
149.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c
149.8 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c
150.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c
151.7 gcc -Wall -g -O2 -fvisibility=hidden -mavx2 -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c
153.1 gcc -Wall -g -O2 -fvisibility=hidden -mavx512f -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c
154.4 gcc -Wall -g -O2 -fvisibility=hidden -mssse3 -mpopcnt -msse4.1 -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c
155.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c
156.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c
157.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c
157.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c
158.3 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -fpic -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c
158.7 gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -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 -llzma -lbz2 -lz -lm   -lpthread
159.4 ln -sf libhts.so libhts.so.3
159.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o bgzip.o bgzip.c
159.8 gcc -fvisibility=hidden  -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
160.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o htsfile.o htsfile.c
160.4 gcc -fvisibility=hidden  -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
160.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o tabix.o tabix.c
161.6 gcc -fvisibility=hidden  -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
161.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/hts_endian.o test/hts_endian.c
162.3 gcc -fvisibility=hidden  -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm  
162.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/fieldarith.o test/fieldarith.c
162.9 gcc -fvisibility=hidden  -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
163.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/hfile.o test/hfile.c
163.5 gcc -fvisibility=hidden  -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
163.8 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/pileup.o test/pileup.c
164.2 gcc -fvisibility=hidden  -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
164.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/pileup_mod.o test/pileup_mod.c
164.8 gcc -fvisibility=hidden  -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
165.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/plugins-dlhts.o test/plugins-dlhts.c
165.3 gcc -fvisibility=hidden  -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm  
165.5 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/sam.o test/sam.c
166.5 gcc -fvisibility=hidden  -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
166.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_bgzf.o test/test_bgzf.c
167.5 gcc -fvisibility=hidden  -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
167.8 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_expr.o test/test_expr.c
168.1 gcc -fvisibility=hidden  -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
168.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_faidx.o test/test_faidx.c
168.8 gcc -fvisibility=hidden  -o test/test_faidx test/test_faidx.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
169.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_kfunc.o test/test_kfunc.c
169.5 gcc -fvisibility=hidden  -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
169.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_kstring.o test/test_kstring.c
170.2 gcc -fvisibility=hidden  -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
170.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_mod.o test/test_mod.c
170.7 gcc -fvisibility=hidden  -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
171.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_realn.o test/test_realn.c
171.3 gcc -fvisibility=hidden  -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
171.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-regidx.o test/test-regidx.c
172.1 gcc -fvisibility=hidden  -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
172.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_str2int.o test/test_str2int.c
172.8 gcc -fvisibility=hidden  -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
173.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_time_funcs.o test/test_time_funcs.c
173.5 gcc -fvisibility=hidden  -o test/test_time_funcs test/test_time_funcs.o
173.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_view.o test/test_view.c
174.2 gcc -fvisibility=hidden  -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
174.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_index.o test/test_index.c
174.7 gcc -fvisibility=hidden  -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
175.1 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
175.7 gcc -fvisibility=hidden  -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
175.9 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
176.3 gcc -fvisibility=hidden  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
176.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
176.9 gcc -fvisibility=hidden  -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
177.2 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
177.7 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
178.1 gcc -fvisibility=hidden  -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm   -lpthread
178.4 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-parse-reg.o test/test-parse-reg.c
178.7 gcc -fvisibility=hidden  -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
179.0 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test_introspection.o test/test_introspection.c
179.3 gcc -fvisibility=hidden  -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
179.6 gcc -Wall -g -O2 -fvisibility=hidden  -I.  -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c
183.3 gcc -fvisibility=hidden  -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm   -lpthread
183.7 sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
183.7 sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
184.1 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
184.1 if test -n ""; then mkdir -p -m 755 ; fi
184.1 install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.17
184.2 ln -sf libhts.so.1.17 /usr/local/lib/libhts.so
184.2 ln -sf libhts.so.1.17 /usr/local/lib/libhts.so.3
184.2 sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.17#g' htslib.pc.tmp > /usr/local/lib/pkgconfig/htslib.pc
184.2 chmod 644 /usr/local/lib/pkgconfig/htslib.pc
184.2 install -p bgzip htsfile tabix /usr/local/bin
184.3 if test -n ""; then install -p  ; fi
184.3 install -p -m 644 htslib/*.h /usr/local/include/htslib
184.4 install -p -m 644 libhts.a /usr/local/lib/libhts.a
184.5 install -p -m 644 bgzip.1 htsfile.1 tabix.1 /usr/local/share/man/man1
184.5 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5
184.5 install -p -m 644 htslib-s3-plugin.7 /usr/local/share/man/man7
185.3 Cloning into 'zstd'...
Updating files: 100% (638/638), done.
192.9 make[1]: Entering directory '/usr/src/pp/xSqueezeIt/zstd/lib'
194.7 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/debug.o
195.2 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/entropy_common.o
195.6 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/error_private.o
195.9 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/fse_decompress.o
196.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/pool.o
196.7 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/threading.o
196.9 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/xxhash.o
197.2 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_common.o
197.7 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_v05.o
199.1 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_v06.o
200.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_v07.o
202.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/fse_compress.o
202.9 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/hist.o
203.5 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/huf_compress.o
204.6 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_compress.o
206.9 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_compress_literals.o
207.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_compress_sequences.o
207.9 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_compress_superblock.o
208.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_double_fast.o
210.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_fast.o
212.6 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_lazy.o
218.7 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_ldm.o
219.3 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_opt.o
221.6 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstdmt_compress.o
222.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/huf_decompress.o
224.5 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_ddict.o
225.2 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_decompress.o
226.4 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zstd_decompress_block.o
228.1 AS obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/huf_decompress_amd64.o
228.3 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/cover.o
228.8 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/divsufsort.o
230.1 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/fastcover.o
230.8 CC obj/conf_d76dfb92bd6d89e2677c5ccc8ddcf17e/static/zdict.o
231.4 compiling single-threaded static library 1.5.6
232.3 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/debug.o
232.5 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/entropy_common.o
233.0 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/error_private.o
233.2 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/fse_decompress.o
233.8 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/pool.o
234.1 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/threading.o
234.4 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/xxhash.o
234.8 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_common.o
235.1 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_v05.o
236.5 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_v06.o
237.9 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_v07.o
239.9 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/fse_compress.o
240.4 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/hist.o
240.7 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/huf_compress.o
241.9 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_compress.o
244.2 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_compress_literals.o
244.7 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_compress_sequences.o
245.3 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_compress_superblock.o
245.8 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_double_fast.o
247.6 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_fast.o
249.4 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_lazy.o
256.1 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_ldm.o
256.6 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_opt.o
258.6 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstdmt_compress.o
259.3 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/huf_decompress.o
261.3 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_ddict.o
261.6 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_decompress.o
262.4 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zstd_decompress_block.o
264.6 AS obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/huf_decompress_amd64.o
264.9 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/cover.o
265.7 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/divsufsort.o
267.0 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/fastcover.o
267.5 CC obj/conf_29e47afa01b5ea3b9c205d2d4bbad92c/dynamic/zdict.o
268.2 compiling multi-threaded dynamic library 1.5.6
268.8 creating versioned links
268.9 creating pkgconfig
268.9 release build completed
268.9 make[1]: Leaving directory '/usr/src/pp/xSqueezeIt/zstd/lib'
268.9 make[1]: Entering directory '/usr/src/pp/xSqueezeIt/zstd/programs'
273.5 CC obj/conf_20daa47e8058f816896e54abab38685b/debug.o
273.7 CC obj/conf_20daa47e8058f816896e54abab38685b/entropy_common.o
274.0 CC obj/conf_20daa47e8058f816896e54abab38685b/error_private.o
274.3 CC obj/conf_20daa47e8058f816896e54abab38685b/fse_decompress.o
274.8 CC obj/conf_20daa47e8058f816896e54abab38685b/pool.o
275.1 CC obj/conf_20daa47e8058f816896e54abab38685b/threading.o
275.3 CC obj/conf_20daa47e8058f816896e54abab38685b/xxhash.o
275.7 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_common.o
276.0 CC obj/conf_20daa47e8058f816896e54abab38685b/fse_compress.o
276.5 CC obj/conf_20daa47e8058f816896e54abab38685b/hist.o
276.8 CC obj/conf_20daa47e8058f816896e54abab38685b/huf_compress.o
277.9 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_compress.o
280.2 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_compress_literals.o
280.6 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_compress_sequences.o
281.0 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_compress_superblock.o
281.4 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_double_fast.o
283.4 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_fast.o
285.4 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_lazy.o
291.8 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_ldm.o
292.3 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_opt.o
294.6 CC obj/conf_20daa47e8058f816896e54abab38685b/zstdmt_compress.o
295.3 CC obj/conf_20daa47e8058f816896e54abab38685b/huf_decompress.o
297.4 AS obj/conf_20daa47e8058f816896e54abab38685b/huf_decompress_amd64.o
297.5 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_ddict.o
298.1 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_decompress.o
299.1 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_decompress_block.o
300.8 CC obj/conf_20daa47e8058f816896e54abab38685b/cover.o
301.4 CC obj/conf_20daa47e8058f816896e54abab38685b/divsufsort.o
302.5 CC obj/conf_20daa47e8058f816896e54abab38685b/fastcover.o
303.2 CC obj/conf_20daa47e8058f816896e54abab38685b/zdict.o
304.0 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_v05.o
305.4 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_v06.o
307.0 CC obj/conf_20daa47e8058f816896e54abab38685b/zstd_v07.o
309.2 CC obj/conf_20daa47e8058f816896e54abab38685b/benchfn.o
309.4 CC obj/conf_20daa47e8058f816896e54abab38685b/benchzstd.o
310.0 CC obj/conf_20daa47e8058f816896e54abab38685b/datagen.o
310.3 CC obj/conf_20daa47e8058f816896e54abab38685b/dibio.o
310.7 CC obj/conf_20daa47e8058f816896e54abab38685b/fileio.o
312.2 CC obj/conf_20daa47e8058f816896e54abab38685b/fileio_asyncio.o
312.8 CC obj/conf_20daa47e8058f816896e54abab38685b/lorem.o
313.0 CC obj/conf_20daa47e8058f816896e54abab38685b/timefn.o
313.3 CC obj/conf_20daa47e8058f816896e54abab38685b/util.o
313.9 CC obj/conf_20daa47e8058f816896e54abab38685b/zstdcli.o
314.8 CC obj/conf_20daa47e8058f816896e54abab38685b/zstdcli_trace.o
315.1 ==> building with threading support
315.2 ==> building zstd with .gz compression support
315.2 ==> building zstd with .xz/.lzma compression support
315.2 ==> no liblz4, building zstd without .lz4 support
315.2 LINK obj/conf_20daa47e8058f816896e54abab38685b/zstd
315.5 zstd build completed
315.5 make[1]: Leaving directory '/usr/src/pp/xSqueezeIt/zstd/programs'
315.7 g++ -I include -I ..//include -I ..//xSqueezeIt//htslib -I ..//xSqueezeIt//htslib/htslib -I ..//xSqueezeIt//zstd/lib -I ..//xSqueezeIt//include -MG -MP -MM -MT 'pp_show.o' pp_show.cpp -MF pp_show.d
316.8 g++ -I include -I ..//include -I ..//xSqueezeIt//htslib -I ..//xSqueezeIt//htslib/htslib -I ..//xSqueezeIt//zstd/lib -I ..//xSqueezeIt//include -MG -MP -MM -MT 'pp_extract.o' pp_extract.cpp -MF pp_extract.d
317.7 echo "#define GIT_REVISION 0x73d90d3" > include/git_rev.h
317.8 g++ -O3 -g -Wall -std=c++17 -I include -I ..//include -I ..//xSqueezeIt//htslib -I ..//xSqueezeIt//htslib/htslib -I ..//xSqueezeIt//zstd/lib -I ..//xSqueezeIt//include     -c -o pp_extract.o pp_extract.cpp
319.8 In file included from pp_extract.cpp:4:
319.8 include/extractors.hpp: In member function 'virtual void PPExtractTraversal::handle_bcf_line()':
319.8 include/extractors.hpp:133:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
319.8   133 |             if (line_counter == -1) {
319.8       |                 ~~~~~~~~~~~~~^~~~~
333.0 g++ -O3 -g -Wall -std=c++17 -I include -I ..//include -I ..//xSqueezeIt//htslib -I ..//xSqueezeIt//htslib/htslib -I ..//xSqueezeIt//zstd/lib -I ..//xSqueezeIt//include     -c -o ..//xSqueezeIt//xcf.o ..//xSqueezeIt//xcf.cpp
341.0 g++ -O3 -g -Wall -std=c++17 -I include -I ..//include -I ..//xSqueezeIt//htslib -I ..//xSqueezeIt//htslib/htslib -I ..//xSqueezeIt//zstd/lib -I ..//xSqueezeIt//include     -c -o ..//xSqueezeIt//bcf_traversal.o ..//xSqueezeIt//bcf_traversal.cpp
342.8 g++ -O3   pp_extract.o ..//xSqueezeIt//xcf.o ..//xSqueezeIt//bcf_traversal.o  -lhts -lzstd -pthread -o pp_extract
343.0 /usr/bin/ld: cannot find -lzstd
343.0 collect2: error: ld returned 1 exit status
343.0 make: *** [<builtin>: pp_extract] Error 1
------
Dockerfile:24
--------------------
  23 |     # Clone Source Code Repository
  24 | >>> RUN mkdir -p /usr/src/ && \
  25 | >>>     cd /usr/src/ && \
  26 | >>>     git clone https://github.com/rwk-unil/pp.git && \
  27 | >>>     cd /usr/src/pp && \
  28 | >>>     git submodule update --init --recursive xSqueezeIt && \
  29 | >>>     cd xSqueezeIt && \
  30 | >>>     cd htslib && \
  31 | >>>     autoheader && \
  32 | >>>     autoconf && \
  33 | >>>     automake --add-missing; \
  34 | >>>     ./configure && \
  35 | >>>     make && \
  36 | >>>     make install && \
  37 | >>>     ldconfig && \
  38 | >>>     cd .. && \
  39 | >>>     git clone https://github.com/facebook/zstd.git && \
  40 | >>>     cd zstd && \
  41 | >>>     make && \
  42 | >>>     cd .. && \
  43 | >>>     cd .. && \
  44 | >>>     cd pp_extractor && \
  45 | >>>     make && \
  46 | >>>     chmod +x pp_extract && \
  47 | >>>     cp pp_extract /usr/local/bin/ && \
  48 | >>>     chmod +x scripts/run_pp_extract.sh && \
  49 | >>>     cp scripts/run_pp_extract.sh /usr/local/bin/run_pp_extract && \
  50 | >>>     cd .. && \
  51 | >>>     cd phase_caller && \
  52 | >>>     make && \
  53 | >>>     chmod +x phase_caller && \
  54 | >>>     cp phase_caller /usr/local/bin/ && \
  55 | >>>     cd /usr/src/ && \
  56 | >>>     rm -rf pp
  57 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c mkdir -p /usr/src/ &&     cd /usr/src/ &&     git clone https://github.com/rwk-unil/pp.git &&     cd /usr/src/pp &&     git submodule update --init --recursive xSqueezeIt &&     cd xSqueezeIt &&     cd htslib &&     autoheader &&     autoconf &&     automake --add-missing;     ./configure &&     make &&     make install &&     ldconfig &&     cd .. &&     git clone https://github.com/facebook/zstd.git &&     cd zstd &&     make &&     cd .. &&     cd .. &&     cd pp_extractor &&     make &&     chmod +x pp_extract &&     cp pp_extract /usr/local/bin/ &&     chmod +x scripts/run_pp_extract.sh &&     cp scripts/run_pp_extract.sh /usr/local/bin/run_pp_extract &&     cd .. &&     cd phase_caller &&     make &&     chmod +x phase_caller &&     cp phase_caller /usr/local/bin/ &&     cd /usr/src/ &&     rm -rf pp" did not complete successfully: exit code: 2