installing Demuxlet

[siyao-liu]

Hello,

I am having some trouble installing Demuxlet on my Mac. I followed the instructions step by step by README2.md and everything was ran fine until I was trying to run $make after I downloaded demuxlet. Here is the error message I got:

3 warnings generated. mv -f .deps/filter.Tpo .deps/filter.Po /usr/local/Cellar/llvm/7.0.1/bin/clang++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po /usr/local/Cellar/llvm/7.0.1/bin/clang++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po make[1]: *** No rule to make target../htslib/libhts.a', needed by demuxlet'. Stop. make: *** [all] Error 2

Can someone please help me? Thanks very much!

Siyao

[hyunminkang]

You need to install htslib first in a sibling directory.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Thu, Mar 14, 2019 at 9:48 AM Siyao Liu notifications@github.com wrote:

Hello,

I am having some trouble installing Demuxlet on my Mac. I followed the instructions step by step by README2.md and everything was ran fine until I was trying to run $make after I downloaded demuxlet. Here is the error message I got:

3 warnings generated. mv -f .deps/filter.Tpo .deps/filter.Po /usr/local/Cellar/llvm/7.0.1/bin/clang++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po /usr/local/Cellar/llvm/7.0.1/bin/clang++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po make[1]: No rule to make target ../htslib/libhts.a', needed by demuxlet'. Stop. make: [all] Error 2

Can someone please help me? Thanks very much!

Siyao

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[siyao-liu]

I did install htslib in the silbling folder first.

[hyunminkang]

Does libhts.a exist?

On Fri, Mar 15, 2019, 4:11 PM Hyun Min Kang <hmkang@umich.edu wrote:

You need to install htslib first in a sibling directory.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Thu, Mar 14, 2019 at 9:48 AM Siyao Liu notifications@github.com wrote:

Hello,

I am having some trouble installing Demuxlet on my Mac. I followed the instructions step by step by README2.md and everything was ran fine until I was trying to run $make after I downloaded demuxlet. Here is the error message I got:

3 warnings generated. mv -f .deps/filter.Tpo .deps/filter.Po /usr/local/Cellar/llvm/7.0.1/bin/clang++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po /usr/local/Cellar/llvm/7.0.1/bin/clang++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po make[1]: No rule to make target ../htslib/libhts.a', needed by demuxlet'. Stop. make: [all] Error 2

Can someone please help me? Thanks very much!

Siyao

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[siyao-liu]

Yes. It does exist. Can you please help me fix the error? I really want to try running Demuxlet on my data, but not being able to install the software prevent me from moving further. Thanks!

[ibseq]

is anyone going to pick this up ??...having the same issue :)

[yimmieg]

+Anton who should have some bandwidth to look into these issues.

On Apr 26, 2019, at 7:46 AM, ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

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[hyunminkang]

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ .

[ibseq]

Hi Hyun, This is what I had done from instructions in https://github.com/samtools/htslib https://github.com/samtools/htslib and https://github.com/statgen/demuxlet https://github.com/statgen/demuxlet . In yellow the commands, bottom red, the error. As you can see, demuxlet is in the same directory as htslib

I cloned the htslib-1.9 on my desktop and: (citeseq_tools) wmnd-ibassano:Desktop ibassano$ cd htslib-1.9

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ autoheader

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ autoconf

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ ./configure

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for ranlib... ranlib

checking for grep that handles long lines and -e... /usr/bin/grep

checking for C compiler warning flags... -Wall

checking for special C compiler options needed for large files... no

checking for _FILE_OFFSET_BITS value needed for large files... no

checking for _LARGEFILE_SOURCE value needed for large files... no

checking shared library type for unknown-Darwin... Darwin dylib

checking how to run the C preprocessor... gcc -E

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for stdlib.h... (cached) yes

checking for unistd.h... (cached) yes

checking for sys/param.h... yes

checking for getpagesize... yes

checking for working mmap... yes

checking for gmtime_r... yes

checking for fsync... yes

checking for drand48... yes

checking whether fdatasync is declared... no

checking for library containing log... none required

checking for zlib.h... yes

checking for inflate in -lz... yes

checking for library containing recv... none required

checking for bzlib.h... yes

checking for BZ2_bzBuffToBuffCompress in -lbz2... yes

checking for lzma.h... yes

checking for lzma_easy_buffer_encode in -llzma... yes

checking for libdeflate.h... no

checking for libdeflate_deflate_compress in -ldeflate... no

checking for curl_easy_pause in -lcurl... yes

checking for CCHmac... yes

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

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ make

gcc -Wall -g -O2 -I. -c -o kfunc.o kfunc.c

gcc -Wall -g -O2 -I. -c -o knetfile.o knetfile.c

gcc -Wall -g -O2 -I. -c -o kstring.o kstring.c

gcc -Wall -g -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c

gcc -Wall -g -O2 -I. -c -o bgzf.o bgzf.c

gcc -Wall -g -O2 -I. -c -o errmod.o errmod.c

gcc -Wall -g -O2 -I. -c -o faidx.o faidx.c

gcc -Wall -g -O2 -I. -c -o hfile.o hfile.c

gcc -Wall -g -O2 -I. -c -o hfile_net.o hfile_net.c

echo '#define HTS_VERSION "1.9"' > version.h

gcc -Wall -g -O2 -I. -c -o hts.o hts.c

gcc -Wall -g -O2 -I. -c -o hts_os.o hts_os.c

gcc -Wall -g -O2 -I. -c -o md5.o md5.c

gcc -Wall -g -O2 -I. -c -o multipart.o multipart.c

gcc -Wall -g -O2 -I. -c -o probaln.o probaln.c

gcc -Wall -g -O2 -I. -c -o realn.o realn.c

gcc -Wall -g -O2 -I. -c -o regidx.o regidx.c

gcc -Wall -g -O2 -I. -c -o sam.o sam.c

gcc -Wall -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c

gcc -Wall -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c

gcc -Wall -g -O2 -I. -c -o tbx.o tbx.c

gcc -Wall -g -O2 -I. -c -o textutils.o textutils.c

gcc -Wall -g -O2 -I. -c -o thread_pool.o thread_pool.c

gcc -Wall -g -O2 -I. -c -o vcf.o vcf.c

gcc -Wall -g -O2 -I. -c -o vcfutils.o vcfutils.c

gcc -Wall -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c

gcc -Wall -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c

gcc -Wall -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c

gcc -Wall -g -O2 -I. -c -o cram/cram_external.o cram/cram_external.c

gcc -Wall -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c

gcc -Wall -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c

gcc -Wall -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c

gcc -Wall -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c

gcc -Wall -g -O2 -I. -c -o cram/files.o cram/files.c

gcc -Wall -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c

gcc -Wall -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c

gcc -Wall -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c

gcc -Wall -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c

gcc -Wall -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c

gcc -Wall -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c

gcc -Wall -g -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c

gcc -Wall -g -O2 -I. -c -o hfile_gcs.o hfile_gcs.c

gcc -Wall -g -O2 -I. -c -o hfile_s3.o hfile_s3.c

ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o

ranlib libhts.a

gcc -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.9 -compatibility_version 2 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o -llzma -lbz2 -lz -lcurl

ln -sf libhts.dylib libhts.2.dylib

gcc -Wall -g -O2 -I. -c -o bgzip.o bgzip.c

gcc -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o htsfile.o htsfile.c

gcc -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o tabix.o tabix.c

gcc -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/hts_endian.o test/hts_endian.c

gcc -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lcurl

gcc -Wall -g -O2 -I. -c -o test/fieldarith.o test/fieldarith.c

gcc -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/hfile.o test/hfile.c

gcc -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/sam.o test/sam.c

gcc -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c

gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test_realn.o test/test_realn.c

gcc -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-regidx.o test/test-regidx.c

gcc -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test_view.o test/test_view.c

gcc -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c

gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c

gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c

gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c

gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ 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/lib/pkgconfig

if test -n ""; then mkdir -p -m 755 ; fi

install -p libhts.dylib /usr/local/lib/libhts.1.9.dylib

ln -sf libhts.1.9.dylib /usr/local/lib/libhts.dylib

ln -sf libhts.1.9.dylib /usr/local/lib/libhts.2.dylib

sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9#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

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ git clone https://github.com/statgen/demuxlet.git

Cloning into 'demuxlet'...

remote: Enumerating objects: 4, done.

remote: Counting objects: 100% (4/4), done.

remote: Compressing objects: 100% (4/4), done.

remote: Total 344 (delta 0), reused 0 (delta 0), pack-reused 340

Receiving objects: 100% (344/344), 6.75 MiB | 9.00 MiB/s, done.

Resolving deltas: 100% (174/174), done.

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ cd demuxlet/

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ autoreconf -vfi

autoreconf: Entering directory `.'

autoreconf: configure.ac: not using Gettext

autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS}

aclocal: warning: couldn't open directory 'm4': No such file or directory

autoreconf: configure.ac: tracing

autoreconf: configure.ac: creating directory aux-dist

autoreconf: running: glibtoolize --copy --force

glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'aux-dist'.

glibtoolize: copying file 'aux-dist/ltmain.sh'

glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.

glibtoolize: copying file 'm4/libtool.m4'

glibtoolize: copying file 'm4/ltoptions.m4'

glibtoolize: copying file 'm4/ltsugar.m4'

glibtoolize: copying file 'm4/ltversion.m4'

glibtoolize: copying file 'm4/lt~obsolete.m4'

autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force

autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force

autoreconf: running: automake --add-missing --copy --force-missing

configure.ac:45: installing 'aux-dist/compile'

configure.ac:45: installing 'aux-dist/config.guess'

configure.ac:45: installing 'aux-dist/config.sub'

configure.ac:7: installing 'aux-dist/install-sh'

configure.ac:7: installing 'aux-dist/missing'

Makefile.am: installing 'aux-dist/depcomp'

autoreconf: Leaving directory `.'

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure --prefix/usr/local/

configure: error: unrecognized option: `--prefix/usr/local/'

Try `./configure --help' for more information

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure --prefix=/usr/local/

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... aux-dist/install-sh -c -d

checking for gawk... no

checking for mawk... no

checking for nawk... no

checking for awk... awk

checking whether make sets $(MAKE)... yes

checking whether make supports nested variables... yes

checking whether make sets $(MAKE)... (cached) yes

checking for g++... g++

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 g++ accepts -g... yes

checking whether make supports the include directive... yes (GNU style)

checking dependency style of g++... gcc3

checking whether we are using the GNU C++ compiler... (cached) yes

checking whether g++ accepts -g... (cached) yes

checking dependency style of g++... (cached) gcc3

checking how to run the C++ preprocessor... g++ -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking limits.h usability... yes

checking limits.h presence... yes

checking for limits.h... yes

checking stddef.h usability... yes

checking stddef.h presence... yes

checking for stddef.h... yes

checking for stdint.h... (cached) yes

checking for stdlib.h... (cached) yes

checking for string.h... (cached) yes

checking for unistd.h... (cached) yes

checking for stdbool.h that conforms to C99... no

checking for _Bool... no

checking for inline... inline

checking for int32_t... yes

checking for int64_t... yes

checking for C/C++ restrict keyword... __restrict

checking for size_t... yes

checking for uint16_t... yes

checking for uint32_t... yes

checking for uint64_t... yes

checking for uint8_t... yes

checking for ptrdiff_t... yes

checking for error_at_line... no

checking for stdlib.h... (cached) yes

checking for GNU libc compatible malloc... yes

checking whether sys/types.h defines makedev... yes

checking for stdlib.h... (cached) yes

checking for GNU libc compatible realloc... yes

checking for working strtod... yes

checking for floor... yes

checking for gethostname... yes

checking for memset... yes

checking for pow... yes

checking for select... yes

checking for sqrt... yes

checking for strchr... yes

checking for strstr... yes

checking for strtol... yes

checking for gzopen in -lz... yes

checking for erf in -lm... yes

checking for erfc in -lm... yes

checking build system type... x86_64-apple-darwin18.5.0

checking host system type... x86_64-apple-darwin18.5.0

checking how to print strings... printf

checking for gcc... gcc

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking whether gcc understands -c and -o together... yes

checking dependency style of gcc... gcc3

checking for a sed that does not truncate output... /usr/bin/sed

checking for fgrep... /usr/bin/grep -F

checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld

checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 196608

checking how to convert x86_64-apple-darwin18.5.0 file names to x86_64-apple-darwin18.5.0 format... func_convert_file_noop

checking how to convert x86_64-apple-darwin18.5.0 file names to toolchain format... func_convert_file_noop

checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r

checking for objdump... objdump

checking how to recognize dependent libraries... pass_all

checking for dlltool... no

checking how to associate runtime and link libraries... printf %s\n

checking for ar... ar

checking for archiver @FILE support... no

checking for strip... strip

checking for ranlib... ranlib

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /bin/dd

checking how to truncate binary pipes... /bin/dd bs=4096 count=1

checking for mt... no

checking if : is a manifest tool... no

checking for dsymutil... dsymutil

checking for nmedit... nmedit

checking for lipo... lipo

checking for otool... otool

checking for otool64... no

checking for -single_module linker flag... yes

checking for -exported_symbols_list linker flag... yes

checking for -force_load linker flag... yes

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... yes

checking for gcc option to produce PIC... -fno-common -DPIC

checking if gcc PIC flag -fno-common -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

checking dynamic linker characteristics... darwin18.5.0 dyld

checking how to hardcode library paths into programs... immediate

checking for dlopen in -ldl... yes

checking whether a program can dlopen itself... yes

checking whether a statically linked program can dlopen itself... yes

checking whether stripping libraries is possible... yes

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... yes

checking how to run the C++ preprocessor... g++ -E

checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld

checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no

checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

checking for g++ option to produce PIC... -fno-common -DPIC

checking if g++ PIC flag -fno-common -DPIC works... yes

checking if g++ static flag -static works... no

checking if g++ supports -c -o file.o... yes

checking if g++ supports -c -o file.o... (cached) yes

checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

checking dynamic linker characteristics... darwin18.5.0 dyld

checking how to hardcode library paths into programs... immediate

checking that generated files are newer than configure... done

configure: creating ./config.status

config.status: creating Makefile

config.status: creating config.h

config.status: executing depfiles commands

config.status: executing libtool commands

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ make

/Library/Developer/CommandLineTools/usr/bin/make all-am

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT Error.o -MD -MP -MF .deps/Error.Tpo -c -o Error.o Error.cpp

mv -f .deps/Error.Tpo .deps/Error.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT PhredHelper.o -MD -MP -MF .deps/PhredHelper.Tpo -c -o PhredHelper.o PhredHelper.cpp

mv -f .deps/PhredHelper.Tpo .deps/PhredHelper.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT params.o -MD -MP -MF .deps/params.Tpo -c -o params.o params.cpp

params.cpp:77:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]

::printf(buf);

         ^~~

params.cpp:77:14: note: treat the string as an argument to avoid this

::printf(buf);

         ^

         "%s", 

1 warning generated.

mv -f .deps/params.Tpo .deps/params.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT hts_utils.o -MD -MP -MF .deps/hts_utils.Tpo -c -o hts_utils.o hts_utils.cpp

mv -f .deps/hts_utils.Tpo .deps/hts_utils.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_ordered_reader.o -MD -MP -MF .deps/bcf_ordered_reader.Tpo -c -o bcf_ordered_reader.o bcf_ordered_reader.cpp

mv -f .deps/bcf_ordered_reader.Tpo .deps/bcf_ordered_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval.o -MD -MP -MF .deps/interval.Tpo -c -o interval.o interval.cpp

mv -f .deps/interval.Tpo .deps/interval.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval_tree.o -MD -MP -MF .deps/interval_tree.Tpo -c -o interval_tree.o interval_tree.cpp

mv -f .deps/interval_tree.Tpo .deps/interval_tree.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.cpp

mv -f .deps/utils.Tpo .deps/utils.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genome_interval.o -MD -MP -MF .deps/genome_interval.Tpo -c -o genome_interval.o genome_interval.cpp

mv -f .deps/genome_interval.Tpo .deps/genome_interval.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT reference_sequence.o -MD -MP -MF .deps/reference_sequence.Tpo -c -o reference_sequence.o reference_sequence.cpp

mv -f .deps/reference_sequence.Tpo .deps/reference_sequence.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_chunked_reader.o -MD -MP -MF .deps/bcf_chunked_reader.Tpo -c -o bcf_chunked_reader.o bcf_chunked_reader.cpp

mv -f .deps/bcf_chunked_reader.Tpo .deps/bcf_chunked_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genomeChunk.o -MD -MP -MF .deps/genomeChunk.Tpo -c -o genomeChunk.o genomeChunk.cpp

mv -f .deps/genomeChunk.Tpo .deps/genomeChunk.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sam_filtered_reader.o -MD -MP -MF .deps/sam_filtered_reader.Tpo -c -o sam_filtered_reader.o sam_filtered_reader.cpp

mv -f .deps/sam_filtered_reader.Tpo .deps/sam_filtered_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sc_drop_seq.o -MD -MP -MF .deps/sc_drop_seq.Tpo -c -o sc_drop_seq.o sc_drop_seq.cpp

mv -f .deps/sc_drop_seq.Tpo .deps/sc_drop_seq.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_filtered_reader.o -MD -MP -MF .deps/bcf_filtered_reader.Tpo -c -o bcf_filtered_reader.o bcf_filtered_reader.cpp

mv -f .deps/bcf_filtered_reader.Tpo .deps/bcf_filtered_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.cpp

filter.cpp:1637:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]

        else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i;

                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

filter.cpp:1639:22: note: uninitialized use occurs here

        if ( out[ival].tok_type!=TOK_VAL || !out[ival].key )

                 ^~~~

filter.cpp:1637:18: note: remove the 'if' if its condition is always true

        else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i;

             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                      ~

filter.cpp:1631:31: note: initialize the variable 'ival' to silence this warning

        int itok = i, ival;

                          ^

                           = 0

filter.cpp:1615:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]

        else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

filter.cpp:1617:34: note: uninitialized use occurs here

        if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival]...

                             ^~~~

filter.cpp:1615:18: note: remove the 'if' if its condition is always true

        else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                          ~

filter.cpp:1611:27: note: initialize the variable 'ival' to silence this warning

        int itok, ival;

                      ^

                       = 0

filter.cpp:1615:23: warning: variable 'itok' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]

        else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

filter.cpp:1623:22: note: uninitialized use occurs here

        if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and;

                 ^~~~

filter.cpp:1615:18: note: remove the 'if' if its condition is always true

        else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                          ~

filter.cpp:1611:21: note: initialize the variable 'itok' to silence this warning

        int itok, ival;

                ^

                 = 0

3 warnings generated.

mv -f .deps/filter.Tpo .deps/filter.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp

mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp

mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po

make[1]: *** No rule to make target ../htslib/libhts.a', needed bydemuxlet'. Stop.

make: *** [all] Error 2

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487091420, or mute the thread https://github.com/notifications/unsubscribe-auth/AH76DQ6LO75W2LAENK6ZBEDPSMLEFANCNFSM4G6QX6UQ.

[hyunminkang]

The compiler says libhts.a does not exist, but do you see them exist? That was my question. If so, what is the directory structure?

On Fri, Apr 26, 2019, 12:12 PM ibseq notifications@github.com wrote:

Hi Hyun, This is what I had done from instructions in https://github.com/samtools/htslib https://github.com/samtools/htslib and https://github.com/statgen/demuxlet < https://github.com/statgen/demuxlet> . In yellow the commands, bottom red, the error. As you can see, demuxlet is in the same directory as htslib

I cloned the htslib-1.9 on my desktop and: (citeseq_tools) wmnd-ibassano:Desktop ibassano$ cd htslib-1.9

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ autoheader

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ autoconf

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ ./configure

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for ranlib... ranlib

checking for grep that handles long lines and -e... /usr/bin/grep

checking for C compiler warning flags... -Wall

checking for special C compiler options needed for large files... no

checking for _FILE_OFFSET_BITS value needed for large files... no

checking for _LARGEFILE_SOURCE value needed for large files... no

checking shared library type for unknown-Darwin... Darwin dylib

checking how to run the C preprocessor... gcc -E

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for stdlib.h... (cached) yes

checking for unistd.h... (cached) yes

checking for sys/param.h... yes

checking for getpagesize... yes

checking for working mmap... yes

checking for gmtime_r... yes

checking for fsync... yes

checking for drand48... yes

checking whether fdatasync is declared... no

checking for library containing log... none required

checking for zlib.h... yes

checking for inflate in -lz... yes

checking for library containing recv... none required

checking for bzlib.h... yes

checking for BZ2_bzBuffToBuffCompress in -lbz2... yes

checking for lzma.h... yes

checking for lzma_easy_buffer_encode in -llzma... yes

checking for libdeflate.h... no

checking for libdeflate_deflate_compress in -ldeflate... no

checking for curl_easy_pause in -lcurl... yes

checking for CCHmac... yes

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

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ make

gcc -Wall -g -O2 -I. -c -o kfunc.o kfunc.c

gcc -Wall -g -O2 -I. -c -o knetfile.o knetfile.c

gcc -Wall -g -O2 -I. -c -o kstring.o kstring.c

gcc -Wall -g -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c

gcc -Wall -g -O2 -I. -c -o bgzf.o bgzf.c

gcc -Wall -g -O2 -I. -c -o errmod.o errmod.c

gcc -Wall -g -O2 -I. -c -o faidx.o faidx.c

gcc -Wall -g -O2 -I. -c -o hfile.o hfile.c

gcc -Wall -g -O2 -I. -c -o hfile_net.o hfile_net.c

echo '#define HTS_VERSION "1.9"' > version.h

gcc -Wall -g -O2 -I. -c -o hts.o hts.c

gcc -Wall -g -O2 -I. -c -o hts_os.o hts_os.c

gcc -Wall -g -O2 -I. -c -o md5.o md5.c

gcc -Wall -g -O2 -I. -c -o multipart.o multipart.c

gcc -Wall -g -O2 -I. -c -o probaln.o probaln.c

gcc -Wall -g -O2 -I. -c -o realn.o realn.c

gcc -Wall -g -O2 -I. -c -o regidx.o regidx.c

gcc -Wall -g -O2 -I. -c -o sam.o sam.c

gcc -Wall -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c

gcc -Wall -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c

gcc -Wall -g -O2 -I. -c -o tbx.o tbx.c

gcc -Wall -g -O2 -I. -c -o textutils.o textutils.c

gcc -Wall -g -O2 -I. -c -o thread_pool.o thread_pool.c

gcc -Wall -g -O2 -I. -c -o vcf.o vcf.c

gcc -Wall -g -O2 -I. -c -o vcfutils.o vcfutils.c

gcc -Wall -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c

gcc -Wall -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c

gcc -Wall -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c

gcc -Wall -g -O2 -I. -c -o cram/cram_external.o cram/cram_external.c

gcc -Wall -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c

gcc -Wall -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c

gcc -Wall -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c

gcc -Wall -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c

gcc -Wall -g -O2 -I. -c -o cram/files.o cram/files.c

gcc -Wall -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c

gcc -Wall -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c

gcc -Wall -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c

gcc -Wall -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c

gcc -Wall -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c

gcc -Wall -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c

gcc -Wall -g -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c

gcc -Wall -g -O2 -I. -c -o hfile_gcs.o hfile_gcs.c

gcc -Wall -g -O2 -I. -c -o hfile_s3.o hfile_s3.c

ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o

ranlib libhts.a

gcc -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.9 -compatibility_version 2 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o -llzma -lbz2 -lz -lcurl

ln -sf libhts.dylib libhts.2.dylib

gcc -Wall -g -O2 -I. -c -o bgzip.o bgzip.c

gcc -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o htsfile.o htsfile.c

gcc -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o tabix.o tabix.c

gcc -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/hts_endian.o test/hts_endian.c

gcc -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lcurl

gcc -Wall -g -O2 -I. -c -o test/fieldarith.o test/fieldarith.c

gcc -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/hfile.o test/hfile.c

gcc -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/sam.o test/sam.c

gcc -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c

gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test_realn.o test/test_realn.c

gcc -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-regidx.o test/test-regidx.c

gcc -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test_view.o test/test_view.c

gcc -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c

gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c

gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c

gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread

gcc -Wall -g -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c

gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ 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/lib/pkgconfig

if test -n ""; then mkdir -p -m 755 ; fi

install -p libhts.dylib /usr/local/lib/libhts.1.9.dylib

ln -sf libhts.1.9.dylib /usr/local/lib/libhts.dylib

ln -sf libhts.1.9.dylib /usr/local/lib/libhts.2.dylib

sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@

/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9#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

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ git clone https://github.com/statgen/demuxlet.git

Cloning into 'demuxlet'...

remote: Enumerating objects: 4, done.

remote: Counting objects: 100% (4/4), done.

remote: Compressing objects: 100% (4/4), done.

remote: Total 344 (delta 0), reused 0 (delta 0), pack-reused 340

Receiving objects: 100% (344/344), 6.75 MiB | 9.00 MiB/s, done.

Resolving deltas: 100% (174/174), done.

(citeseq_tools) wmnd-ibassano:htslib-1.9 ibassano$ cd demuxlet/

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ autoreconf -vfi

autoreconf: Entering directory `.'

autoreconf: configure.ac: not using Gettext

autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS}

aclocal: warning: couldn't open directory 'm4': No such file or directory

autoreconf: configure.ac: tracing

autoreconf: configure.ac: creating directory aux-dist

autoreconf: running: glibtoolize --copy --force

glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'aux-dist'.

glibtoolize: copying file 'aux-dist/ltmain.sh'

glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.

glibtoolize: copying file 'm4/libtool.m4'

glibtoolize: copying file 'm4/ltoptions.m4'

glibtoolize: copying file 'm4/ltsugar.m4'

glibtoolize: copying file 'm4/ltversion.m4'

glibtoolize: copying file 'm4/lt~obsolete.m4'

autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force

autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force

autoreconf: running: automake --add-missing --copy --force-missing

configure.ac:45: installing 'aux-dist/compile'

configure.ac:45: installing 'aux-dist/config.guess'

configure.ac:45: installing 'aux-dist/config.sub'

configure.ac:7: installing 'aux-dist/install-sh'

configure.ac:7: installing 'aux-dist/missing'

Makefile.am: installing 'aux-dist/depcomp'

autoreconf: Leaving directory `.'

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure --prefix/usr/local/

configure: error: unrecognized option: `--prefix/usr/local/'

Try `./configure --help' for more information

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure --prefix=/usr/local/

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... aux-dist/install-sh -c -d

checking for gawk... no

checking for mawk... no

checking for nawk... no

checking for awk... awk

checking whether make sets $(MAKE)... yes

checking whether make supports nested variables... yes

checking whether make sets $(MAKE)... (cached) yes

checking for g++... g++

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 g++ accepts -g... yes

checking whether make supports the include directive... yes (GNU style)

checking dependency style of g++... gcc3

checking whether we are using the GNU C++ compiler... (cached) yes

checking whether g++ accepts -g... (cached) yes

checking dependency style of g++... (cached) gcc3

checking how to run the C++ preprocessor... g++ -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking limits.h usability... yes

checking limits.h presence... yes

checking for limits.h... yes

checking stddef.h usability... yes

checking stddef.h presence... yes

checking for stddef.h... yes

checking for stdint.h... (cached) yes

checking for stdlib.h... (cached) yes

checking for string.h... (cached) yes

checking for unistd.h... (cached) yes

checking for stdbool.h that conforms to C99... no

checking for _Bool... no

checking for inline... inline

checking for int32_t... yes

checking for int64_t... yes

checking for C/C++ restrict keyword... __restrict

checking for size_t... yes

checking for uint16_t... yes

checking for uint32_t... yes

checking for uint64_t... yes

checking for uint8_t... yes

checking for ptrdiff_t... yes

checking for error_at_line... no

checking for stdlib.h... (cached) yes

checking for GNU libc compatible malloc... yes

checking whether sys/types.h defines makedev... yes

checking for stdlib.h... (cached) yes

checking for GNU libc compatible realloc... yes

checking for working strtod... yes

checking for floor... yes

checking for gethostname... yes

checking for memset... yes

checking for pow... yes

checking for select... yes

checking for sqrt... yes

checking for strchr... yes

checking for strstr... yes

checking for strtol... yes

checking for gzopen in -lz... yes

checking for erf in -lm... yes

checking for erfc in -lm... yes

checking build system type... x86_64-apple-darwin18.5.0

checking host system type... x86_64-apple-darwin18.5.0

checking how to print strings... printf

checking for gcc... gcc

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking whether gcc understands -c and -o together... yes

checking dependency style of gcc... gcc3

checking for a sed that does not truncate output... /usr/bin/sed

checking for fgrep... /usr/bin/grep -F

checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld

checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 196608

checking how to convert x86_64-apple-darwin18.5.0 file names to x86_64-apple-darwin18.5.0 format... func_convert_file_noop

checking how to convert x86_64-apple-darwin18.5.0 file names to toolchain format... func_convert_file_noop

checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r

checking for objdump... objdump

checking how to recognize dependent libraries... pass_all

checking for dlltool... no

checking how to associate runtime and link libraries... printf %s\n

checking for ar... ar

checking for archiver @FILE support... no

checking for strip... strip

checking for ranlib... ranlib

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /bin/dd

checking how to truncate binary pipes... /bin/dd bs=4096 count=1

checking for mt... no

checking if : is a manifest tool... no

checking for dsymutil... dsymutil

checking for nmedit... nmedit

checking for lipo... lipo

checking for otool... otool

checking for otool64... no

checking for -single_module linker flag... yes

checking for -exported_symbols_list linker flag... yes

checking for -force_load linker flag... yes

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... yes

checking for gcc option to produce PIC... -fno-common -DPIC

checking if gcc PIC flag -fno-common -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

checking dynamic linker characteristics... darwin18.5.0 dyld

checking how to hardcode library paths into programs... immediate

checking for dlopen in -ldl... yes

checking whether a program can dlopen itself... yes

checking whether a statically linked program can dlopen itself... yes

checking whether stripping libraries is possible... yes

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... yes

checking how to run the C++ preprocessor... g++ -E

checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld

checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no

checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

checking for g++ option to produce PIC... -fno-common -DPIC

checking if g++ PIC flag -fno-common -DPIC works... yes

checking if g++ static flag -static works... no

checking if g++ supports -c -o file.o... yes

checking if g++ supports -c -o file.o... (cached) yes

checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

checking dynamic linker characteristics... darwin18.5.0 dyld

checking how to hardcode library paths into programs... immediate

checking that generated files are newer than configure... done

configure: creating ./config.status

config.status: creating Makefile

config.status: creating config.h

config.status: executing depfiles commands

config.status: executing libtool commands

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$ make

/Library/Developer/CommandLineTools/usr/bin/make all-am

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT Error.o -MD -MP -MF .deps/Error.Tpo -c -o Error.o Error.cpp

mv -f .deps/Error.Tpo .deps/Error.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT PhredHelper.o -MD -MP -MF .deps/PhredHelper.Tpo -c -o PhredHelper.o PhredHelper.cpp

mv -f .deps/PhredHelper.Tpo .deps/PhredHelper.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT params.o -MD -MP -MF .deps/params.Tpo -c -o params.o params.cpp

params.cpp:77:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]

::printf(buf);

^~~

params.cpp:77:14: note: treat the string as an argument to avoid this

::printf(buf);

^

"%s",

1 warning generated.

mv -f .deps/params.Tpo .deps/params.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT hts_utils.o -MD -MP -MF .deps/hts_utils.Tpo -c -o hts_utils.o hts_utils.cpp

mv -f .deps/hts_utils.Tpo .deps/hts_utils.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_ordered_reader.o -MD -MP -MF .deps/bcf_ordered_reader.Tpo -c -o bcf_ordered_reader.o bcf_ordered_reader.cpp

mv -f .deps/bcf_ordered_reader.Tpo .deps/bcf_ordered_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval.o -MD -MP -MF .deps/interval.Tpo -c -o interval.o interval.cpp

mv -f .deps/interval.Tpo .deps/interval.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval_tree.o -MD -MP -MF .deps/interval_tree.Tpo -c -o interval_tree.o interval_tree.cpp

mv -f .deps/interval_tree.Tpo .deps/interval_tree.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.cpp

mv -f .deps/utils.Tpo .deps/utils.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genome_interval.o -MD -MP -MF .deps/genome_interval.Tpo -c -o genome_interval.o genome_interval.cpp

mv -f .deps/genome_interval.Tpo .deps/genome_interval.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT reference_sequence.o -MD -MP -MF .deps/reference_sequence.Tpo -c -o reference_sequence.o reference_sequence.cpp

mv -f .deps/reference_sequence.Tpo .deps/reference_sequence.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_chunked_reader.o -MD -MP -MF .deps/bcf_chunked_reader.Tpo -c -o bcf_chunked_reader.o bcf_chunked_reader.cpp

mv -f .deps/bcf_chunked_reader.Tpo .deps/bcf_chunked_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genomeChunk.o -MD -MP -MF .deps/genomeChunk.Tpo -c -o genomeChunk.o genomeChunk.cpp

mv -f .deps/genomeChunk.Tpo .deps/genomeChunk.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sam_filtered_reader.o -MD -MP -MF .deps/sam_filtered_reader.Tpo -c -o sam_filtered_reader.o sam_filtered_reader.cpp

mv -f .deps/sam_filtered_reader.Tpo .deps/sam_filtered_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sc_drop_seq.o -MD -MP -MF .deps/sc_drop_seq.Tpo -c -o sc_drop_seq.o sc_drop_seq.cpp

mv -f .deps/sc_drop_seq.Tpo .deps/sc_drop_seq.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_filtered_reader.o -MD -MP -MF .deps/bcf_filtered_reader.Tpo -c -o bcf_filtered_reader.o bcf_filtered_reader.cpp

mv -f .deps/bcf_filtered_reader.Tpo .deps/bcf_filtered_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.cpp

filter.cpp:1637:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]

else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i;

^~~~~~~~

filter.cpp:1639:22: note: uninitialized use occurs here

if ( out[ival].tok_type!=TOK_VAL || !out[ival].key )

^~~~

filter.cpp:1637:18: note: remove the 'if' if its condition is always true

else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i;

^~~~~~~~ ~

filter.cpp:1631:31: note: initialize the variable 'ival' to silence this warning

int itok = i, ival;

^

= 0

filter.cpp:1615:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]

else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

^~~~~~~~~~~~~~~

filter.cpp:1617:34: note: uninitialized use occurs here

if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival]...

^~~~

filter.cpp:1615:18: note: remove the 'if' if its condition is always true

else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

^~~~~~~~~~~~~~~ ~

filter.cpp:1611:27: note: initialize the variable 'ival' to silence this warning

int itok, ival;

^

= 0

filter.cpp:1615:23: warning: variable 'itok' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]

else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

^~~~~~~~~~~~~~~

filter.cpp:1623:22: note: uninitialized use occurs here

if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and;

^~~~

filter.cpp:1615:18: note: remove the 'if' if its condition is always true

else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;

^~~~~~~~~~~~~~~ ~

filter.cpp:1611:21: note: initialize the variable 'itok' to silence this warning

int itok, ival;

^

= 0

3 warnings generated.

mv -f .deps/filter.Tpo .deps/filter.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp

mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po

g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp

mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po

make[1]: *** No rule to make target ../htslib/libhts.a', needed by demuxlet'. Stop.

make: *** [all] Error 2

(citeseq_tools) wmnd-ibassano:demuxlet ibassano$

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ

.

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— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487113683, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPY5OOCAGMDKCNW35XRPFLPSMSWRANCNFSM4G6QX6UQ .

[ibseq]

Hi Hyun, The first two work, the last doesn’t

Just to make sure I understood: I cloned htslib first and follow instruction to install it. In the same folder I cloned demuxlet, cd to demuxlet and installed it.

Correct?

About : “The compiler says libhts.a does not exist, but do you see them exist? That was my question. If so, what is the directory structure?”

I opend the htslib folder and a file named “/libhts.a” is found in Desktop/htslib-1.9/libhts.a

Demuxlet is found in Desktop/htslib-1.9/demuxlet

Bw Irene

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487091420, or mute the thread https://github.com/notifications/unsubscribe-auth/AH76DQ6LO75W2LAENK6ZBEDPSMLEFANCNFSM4G6QX6UQ.

[hyunminkang]

You need to have demuxlet as a sibling directory to htslib, for example Desktop/demuxlet.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 4:58 AM ibseq notifications@github.com wrote:

Hi Hyun, The first two work, the last doesn’t

Just to make sure I understood: I cloned htslib first and follow instruction to install it. In the same folder I cloned demuxlet, cd to demuxlet and installed it.

Correct?

About : “The compiler says libhts.a does not exist, but do you see them exist? That was my question. If so, what is the directory structure?”

I opend the htslib folder and a file named “/libhts.a” is found in Desktop/htslib-1.9/libhts.a

Demuxlet is found in Desktop/htslib-1.9/demuxlet

Bw Irene

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/statgen/demuxlet/issues/40#issuecomment-487091420>, or mute the thread < https://github.com/notifications/unsubscribe-auth/AH76DQ6LO75W2LAENK6ZBEDPSMLEFANCNFSM4G6QX6UQ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487505608, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPY5OML3LGT6CEUJP5MJHTPS22DDANCNFSM4G6QX6UQ .

[hyunminkang]

Also, rename htslib as Desktop/htslib, for example.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 8:04 AM Hyun Min Kang hmkang@umich.edu wrote:

You need to have demuxlet as a sibling directory to htslib, for example Desktop/demuxlet.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 4:58 AM ibseq notifications@github.com wrote:

Hi Hyun, The first two work, the last doesn’t

Just to make sure I understood: I cloned htslib first and follow instruction to install it. In the same folder I cloned demuxlet, cd to demuxlet and installed it.

Correct?

About : “The compiler says libhts.a does not exist, but do you see them exist? That was my question. If so, what is the directory structure?”

I opend the htslib folder and a file named “/libhts.a” is found in Desktop/htslib-1.9/libhts.a

Demuxlet is found in Desktop/htslib-1.9/demuxlet

Bw Irene

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/statgen/demuxlet/issues/40#issuecomment-487091420>, or mute the thread < https://github.com/notifications/unsubscribe-auth/AH76DQ6LO75W2LAENK6ZBEDPSMLEFANCNFSM4G6QX6UQ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/statgen/demuxlet/issues/40#issuecomment-487505608, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPY5OML3LGT6CEUJP5MJHTPS22DDANCNFSM4G6QX6UQ .

[ibseq]

Hi Hyun, I did all the below. See attached. I also upgraded gcc at is seemed the prob but still nothing

BW Irene

On 29 Apr 2019, at 13:37, Hyun Min Kang notifications@github.com wrote:

Also, rename htslib as Desktop/htslib, for example.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 8:04 AM Hyun Min Kang hmkang@umich.edu wrote:

You need to have demuxlet as a sibling directory to htslib, for example Desktop/demuxlet.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 4:58 AM ibseq notifications@github.com wrote:

Hi Hyun, The first two work, the last doesn’t

Just to make sure I understood: I cloned htslib first and follow instruction to install it. In the same folder I cloned demuxlet, cd to demuxlet and installed it.

Correct?

About : “The compiler says libhts.a does not exist, but do you see them exist? That was my question. If so, what is the directory structure?”

I opend the htslib folder and a file named “/libhts.a” is found in Desktop/htslib-1.9/libhts.a

Demuxlet is found in Desktop/htslib-1.9/demuxlet

Bw Irene

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/statgen/demuxlet/issues/40#issuecomment-487083885 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ABPY5OIS25GXQ5FBRYUAQQ3PSMIUVANCNFSM4G6QX6UQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/statgen/demuxlet/issues/40#issuecomment-487091420>, or mute the thread < https://github.com/notifications/unsubscribe-auth/AH76DQ6LO75W2LAENK6ZBEDPSMLEFANCNFSM4G6QX6UQ .

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Last login: Mon Apr 29 13:14:52 on ttys004 (base) wmnd-ibassano:~ ibassano$ cd Desktop/ (base) wmnd-ibassano:Desktop ibassano$ brew install gcc Updating Homebrew... ==> Auto-updated Homebrew! Updated 2 taps (homebrew/core and homebrew/cask). ==> Updated Formulae r ✔ golang-migrate neovim readline ✔ gradle netdata argyll-cms grpc opencoarrays badtouch iamy pcapplusplus ballerina imagemagick@6 pdnsrec binaryen ipython quazip buildkit istioctl shfmt ccache kubeprod silk cmocka libcoap skaffold erlang libfixbuf swiftlint exploitdb libiconv traefik faas-cli libjson-rpc-cpp typescript flatbuffers liblinear volt flow libxo webdis fn lmod wtf gel mysql yaf ghq nats-streaming-server you-get

Error: gcc 8.2.0 is already installed To upgrade to 8.3.0_2, run brew upgrade gcc. (base) wmnd-ibassano:Desktop ibassano$ brew upgrade gcc ==> Upgrading 1 outdated package: gcc 8.2.0 -> 8.3.0_2 ==> Upgrading gcc ==> Installing dependencies for gcc: isl and mpfr ==> Installing gcc dependency: isl ==> Downloading https://homebrew.bintray.com/bottles/isl-0.21.mojave.bottle.tar. ==> Downloading from https://akamai.bintray.com/f9/f9188b5d486b2a835cd865f219be1 ######################################################################## 100.0% ==> Pouring isl-0.21.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/isl/0.21: 72 files, 4.3MB ==> Installing gcc dependency: mpfr ==> Downloading https://homebrew.bintray.com/bottles/mpfr-4.0.2.mojave.bottle.ta ==> Downloading from https://akamai.bintray.com/cf/cfce7ab866e98360c9364cd924da6 ######################################################################## 100.0% ==> Pouring mpfr-4.0.2.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/mpfr/4.0.2: 28 files, 4.7MB ==> Installing gcc ==> Downloading https://homebrew.bintray.com/bottles/gcc-8.3.0_2.mojave.bottle.t ==> Downloading from https://akamai.bintray.com/78/78b5b3a98b82f7c89263c5d972a11 ######################################################################## 100.0% ==> Pouring gcc-8.3.0_2.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/gcc/8.3.0_2: 1,414 files, 288.5MB Removing: /usr/local/Cellar/gcc/8.2.0... (1,413 files, 295.9MB) ==> Upgrading 3 dependents: hdf5 1.10.4 -> 1.10.5, kallisto 0.45.0 -> 0.45.1, r 3.5.2_2 -> 3.6.0 ==> Upgrading hdf5 ==> Downloading https://homebrew.bintray.com/bottles/hdf5-1.10.5.mojave.bottle.t ==> Downloading from https://akamai.bintray.com/6d/6dc444fd95265b221047a69348d7a ######################################################################## 100.0% ==> Pouring hdf5-1.10.5.mojave.bottle.tar.gz Warning: hdf5 dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. 🍺 /usr/local/Cellar/hdf5/1.10.5: 256 files, 14.7MB Removing: /usr/local/Cellar/hdf5/1.10.4... (262 files, 14.8MB) ==> Upgrading kallisto ==> Downloading https://homebrew.bintray.com/bottles/kallisto-0.45.1.mojave.bott ==> Downloading from https://akamai.bintray.com/60/60b4b2ac31be396caaf7a07d403be ######################################################################## 100.0% ==> Pouring kallisto-0.45.1.mojave.bottle.tar.gz Warning: kallisto dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. 🍺 /usr/local/Cellar/kallisto/0.45.1: 5 files, 917.3KB Removing: /usr/local/Cellar/kallisto/0.45.0... (5 files, 1014.7KB) ==> Upgrading r ==> Installing dependencies for r: libpng, pcre and readline ==> Installing r dependency: libpng ==> Downloading https://homebrew.bintray.com/bottles/libpng-1.6.37.mojave.bottle ==> Downloading from https://akamai.bintray.com/53/53bbd14cc27c86c16605e256e7646 ######################################################################## 100.0% ==> Pouring libpng-1.6.37.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/libpng/1.6.37: 27 files, 1.2MB ==> Installing r dependency: pcre ==> Downloading https://homebrew.bintray.com/bottles/pcre-8.43.mojave.bottle.tar ==> Downloading from https://akamai.bintray.com/08/08e7414a7641d1e184c936537ff67 ######################################################################## 100.0% ==> Pouring pcre-8.43.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/pcre/8.43: 204 files, 5.5MB ==> Installing r dependency: readline ==> Downloading https://homebrew.bintray.com/bottles/readline-8.0.0_1.mojave.bot ==> Downloading from https://akamai.bintray.com/fa/faab004773e6449dd97971311cb62 ######################################################################## 100.0% ==> Pouring readline-8.0.0_1.mojave.bottle.tar.gz ==> Caveats readline is keg-only, which means it was not symlinked into /usr/local, because macOS provides the BSD libedit library, which shadows libreadline. In order to prevent conflicts when programs look for libreadline we are defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set: export LDFLAGS="-L/usr/local/opt/readline/lib" export CPPFLAGS="-I/usr/local/opt/readline/include"

For pkg-config to find readline you may need to set: export PKG_CONFIG_PATH="/usr/local/opt/readline/lib/pkgconfig"

==> Summary 🍺 /usr/local/Cellar/readline/8.0.0_1: 48 files, 1.5MB ==> Installing r ==> Downloading https://homebrew.bintray.com/bottles/r-3.6.0.mojave.bottle.tar.g ==> Downloading from https://akamai.bintray.com/99/99d04c26f4c4a94b6158e106fd7e6 ######################################################################## 100.0% ==> Pouring r-3.6.0.mojave.bottle.tar.gz Error: The brew link step did not complete successfully The formula built, but is not symlinked into /usr/local Could not symlink bin/R Target /usr/local/bin/R already exists. You may want to remove it: rm '/usr/local/bin/R'

To force the link and overwrite all conflicting files: brew link --overwrite r

To list all files that would be deleted: brew link --overwrite --dry-run r

Possible conflicting files are: /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/Rscript -> /Library/Frameworks/R.framework/Resources/bin/Rscript ==> Summary 🍺 /usr/local/Cellar/r/3.6.0: 2,121 files, 56.5MB Removing: /usr/local/Cellar/r/3.5.2_2... (2,117 files, 55.7MB) ==> Caveats ==> readline readline is keg-only, which means it was not symlinked into /usr/local, because macOS provides the BSD libedit library, which shadows libreadline. In order to prevent conflicts when programs look for libreadline we are defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set: export LDFLAGS="-L/usr/local/opt/readline/lib" export CPPFLAGS="-I/usr/local/opt/readline/include"

For pkg-config to find readline you may need to set: export PKG_CONFIG_PATH="/usr/local/opt/readline/lib/pkgconfig"

(base) wmnd-ibassano:Desktop ibassano$ git clone https://github.com/statgen/demuxlet.git Cloning into 'demuxlet'... remote: Enumerating objects: 4, done. remote: Counting objects: 100% (4/4), done. remote: Compressing objects: 100% (4/4), done. remote: Total 344 (delta 0), reused 0 (delta 0), pack-reused 340 Receiving objects: 100% (344/344), 6.75 MiB | 8.85 MiB/s, done. Resolving deltas: 100% (174/174), done. (base) wmnd-ibassano:Desktop ibassano$ git clone https://github.com/samtools/htslib.git Cloning into 'htslib'... remote: Enumerating objects: 4, done. remote: Counting objects: 100% (4/4), done. remote: Compressing objects: 100% (4/4), done. remote: Total 10770 (delta 0), reused 1 (delta 0), pack-reused 10766 Receiving objects: 100% (10770/10770), 7.99 MiB | 9.89 MiB/s, done. Resolving deltas: 100% (7539/7539), done. (base) wmnd-ibassano:Desktop ibassano$ conda info --envs

conda environments:

# base * /anaconda3 BCR_analysis /anaconda3/envs/BCR_analysis citeseq_tools /anaconda3/envs/citeseq_tools igdiscover /anaconda3/envs/igdiscover

(base) wmnd-ibassano:Desktop ibassano$ source activate citeseq_tools (citeseq_tools) wmnd-ibassano:Desktop ibassano$ cd htslib/ (citeseq_tools) wmnd-ibassano:htslib ibassano$ autoheader (citeseq_tools) wmnd-ibassano:htslib ibassano$ autoconf (citeseq_tools) wmnd-ibassano:htslib ibassano$ ./configure checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... /usr/local/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 for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Darwin... Darwin dylib checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking whether fdatasync is declared... no checking for library containing log... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl_easy_pause in -lcurl... yes checking for CCHmac... yes 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 (citeseq_tools) wmnd-ibassano:htslib ibassano$ make gcc -Wall -g -O2 -I. -c -o kfunc.o kfunc.c gcc -Wall -g -O2 -I. -c -o knetfile.o knetfile.c gcc -Wall -g -O2 -I. -c -o kstring.o kstring.c gcc -Wall -g -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -Wall -g -O2 -I. -c -o bgzf.o bgzf.c gcc -Wall -g -O2 -I. -c -o errmod.o errmod.c gcc -Wall -g -O2 -I. -c -o faidx.o faidx.c gcc -Wall -g -O2 -I. -c -o hfile.o hfile.c gcc -Wall -g -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9-149-gf5b75ff"' > version.h gcc -Wall -g -O2 -I. -c -o hts.o hts.c gcc -Wall -g -O2 -I. -c -o hts_os.o hts_os.c gcc -Wall -g -O2 -I. -c -o md5.o md5.c gcc -Wall -g -O2 -I. -c -o multipart.o multipart.c gcc -Wall -g -O2 -I. -c -o probaln.o probaln.c gcc -Wall -g -O2 -I. -c -o realn.o realn.c gcc -Wall -g -O2 -I. -c -o regidx.o regidx.c gcc -Wall -g -O2 -I. -c -o region.o region.c gcc -Wall -g -O2 -I. -c -o sam.o sam.c gcc -Wall -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -Wall -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -Wall -g -O2 -I. -c -o tbx.o tbx.c gcc -Wall -g -O2 -I. -c -o textutils.o textutils.c gcc -Wall -g -O2 -I. -c -o thread_pool.o thread_pool.c gcc -Wall -g -O2 -I. -c -o vcf.o vcf.c gcc -Wall -g -O2 -I. -c -o vcfutils.o vcfutils.c gcc -Wall -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -Wall -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -Wall -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -Wall -g -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -Wall -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -Wall -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -Wall -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -Wall -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -Wall -g -O2 -I. -c -o cram/files.o cram/files.c gcc -Wall -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -Wall -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -Wall -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -Wall -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -Wall -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -Wall -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -Wall -g -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c gcc -Wall -g -O2 -I. -c -o hfile_gcs.o hfile_gcs.c gcc -Wall -g -O2 -I. -c -o hfile_s3.o hfile_s3.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o 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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o ranlib libhts.a gcc -dynamiclib -install_name /usr/local/lib/libhts.2to3part5.dylib -current_version 1.9.255 -compatibility_version 2.5 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o 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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o -llzma -lbz2 -lz -lcurl ln -sf libhts.dylib libhts.2to3part5.dylib gcc -Wall -g -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/hts_endian.o test/hts_endian.c gcc -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lcurl gcc -Wall -g -O2 -I. -c -o test/fieldarith.o test/fieldarith.c gcc -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/hfile.o test/hfile.c gcc -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/pileup.o test/pileup.c gcc -pthread -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/sam.o test/sam.c gcc -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_kstring.o test/test_kstring.c gcc -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_realn.o test/test_realn.c gcc -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-regidx.o test/test-regidx.c gcc -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_view.o test/test_view.c gcc -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_index.o test/test_index.c gcc -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -Wall -g -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread (citeseq_tools) wmnd-ibassano:htslib ibassano$ sudo make install Password: Sorry, try again. Password: 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/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p libhts.dylib /usr/local/lib/libhts.1.9-149-gf5b75ff.dylib ln -sf libhts.1.9-149-gf5b75ff.dylib /usr/local/lib/libhts.dylib ln -sf libhts.1.9-149-gf5b75ff.dylib /usr/local/lib/libhts.2to3part5.dylib sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9-149-gf5b75ff#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 (citeseq_tools) wmnd-ibassano:htslib ibassano$ cd ../demuxlet/ (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ autoreconf -vfi autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS} aclocal: warning: couldn't open directory 'm4': No such file or directory autoreconf: configure.ac: tracing autoreconf: configure.ac: creating directory aux-dist autoreconf: running: glibtoolize --copy --force glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'aux-dist'. glibtoolize: copying file 'aux-dist/ltmain.sh' glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. glibtoolize: copying file 'm4/libtool.m4' glibtoolize: copying file 'm4/ltoptions.m4' glibtoolize: copying file 'm4/ltsugar.m4' glibtoolize: copying file 'm4/ltversion.m4' glibtoolize: copying file 'm4/lt~obsolete.m4' autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:45: installing 'aux-dist/compile' configure.ac:45: installing 'aux-dist/config.guess' configure.ac:45: installing 'aux-dist/config.sub' configure.ac:7: installing 'aux-dist/install-sh' configure.ac:7: installing 'aux-dist/missing' Makefile.am: installing 'aux-dist/depcomp' autoreconf: Leaving directory.' (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... aux-dist/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for g++... g++ 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 g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for int32_t... yes checking for int64_t... yes checking for C/C++ restrict keyword... restrict checking for size_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for ptrdiff_t... yes checking for error_at_line... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking whether sys/types.h defines makedev... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for gethostname... yes checking for memset... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for strtol... yes checking for gzopen in -lz... yes checking for erf in -lm... yes checking for erfc in -lm... yes checking build system type... x86_64-apple-darwin18.5.0 checking host system type... x86_64-apple-darwin18.5.0 checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert x86_64-apple-darwin18.5.0 file names to x86_64-apple-darwin18.5.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin18.5.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ autoreconf -vfi autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS} autoreconf: configure.ac: tracing autoreconf: running: glibtoolize --copy --force glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'aux-dist'. glibtoolize: copying file 'aux-dist/ltmain.sh' glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. glibtoolize: copying file 'm4/libtool.m4' glibtoolize: copying file 'm4/ltoptions.m4' glibtoolize: copying file 'm4/ltsugar.m4' glibtoolize: copying file 'm4/ltversion.m4' glibtoolize: copying file 'm4/lt~obsolete.m4' autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:45: installing 'aux-dist/compile' configure.ac:7: installing 'aux-dist/missing' Makefile.am: installing 'aux-dist/depcomp' autoreconf: Leaving directory.' (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... aux-dist/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for g++... g++ 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 g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for int32_t... yes checking for int64_t... yes checking for C/C++ restrict keyword... restrict checking for size_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for ptrdiff_t... yes checking for error_at_line... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking whether sys/types.h defines makedev... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for gethostname... yes checking for memset... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for strtol... yes checking for gzopen in -lz... yes checking for erf in -lm... yes checking for erfc in -lm... yes checking build system type... x86_64-apple-darwin18.5.0 checking host system type... x86_64-apple-darwin18.5.0 checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert x86_64-apple-darwin18.5.0 file names to x86_64-apple-darwin18.5.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin18.5.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ make /Library/Developer/CommandLineTools/usr/bin/make all-am g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT Error.o -MD -MP -MF .deps/Error.Tpo -c -o Error.o Error.cpp mv -f .deps/Error.Tpo .deps/Error.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT PhredHelper.o -MD -MP -MF .deps/PhredHelper.Tpo -c -o PhredHelper.o PhredHelper.cpp mv -f .deps/PhredHelper.Tpo .deps/PhredHelper.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT params.o -MD -MP -MF .deps/params.Tpo -c -o params.o params.cpp params.cpp:77:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security] ::printf(buf); ^~~ params.cpp:77:14: note: treat the string as an argument to avoid this ::printf(buf); ^ "%s", 1 warning generated. mv -f .deps/params.Tpo .deps/params.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT hts_utils.o -MD -MP -MF .deps/hts_utils.Tpo -c -o hts_utils.o hts_utils.cpp mv -f .deps/hts_utils.Tpo .deps/hts_utils.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_ordered_reader.o -MD -MP -MF .deps/bcf_ordered_reader.Tpo -c -o bcf_ordered_reader.o bcf_ordered_reader.cpp mv -f .deps/bcf_ordered_reader.Tpo .deps/bcf_ordered_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval.o -MD -MP -MF .deps/interval.Tpo -c -o interval.o interval.cpp mv -f .deps/interval.Tpo .deps/interval.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval_tree.o -MD -MP -MF .deps/interval_tree.Tpo -c -o interval_tree.o interval_tree.cpp mv -f .deps/interval_tree.Tpo .deps/interval_tree.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.cpp mv -f .deps/utils.Tpo .deps/utils.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genome_interval.o -MD -MP -MF .deps/genome_interval.Tpo -c -o genome_interval.o genome_interval.cpp mv -f .deps/genome_interval.Tpo .deps/genome_interval.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT reference_sequence.o -MD -MP -MF .deps/reference_sequence.Tpo -c -o reference_sequence.o reference_sequence.cpp mv -f .deps/reference_sequence.Tpo .deps/reference_sequence.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_chunked_reader.o -MD -MP -MF .deps/bcf_chunked_reader.Tpo -c -o bcf_chunked_reader.o bcf_chunked_reader.cpp mv -f .deps/bcf_chunked_reader.Tpo .deps/bcf_chunked_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genomeChunk.o -MD -MP -MF .deps/genomeChunk.Tpo -c -o genomeChunk.o genomeChunk.cpp mv -f .deps/genomeChunk.Tpo .deps/genomeChunk.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sam_filtered_reader.o -MD -MP -MF .deps/sam_filtered_reader.Tpo -c -o sam_filtered_reader.o sam_filtered_reader.cpp mv -f .deps/sam_filtered_reader.Tpo .deps/sam_filtered_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sc_drop_seq.o -MD -MP -MF .deps/sc_drop_seq.Tpo -c -o sc_drop_seq.o sc_drop_seq.cpp mv -f .deps/sc_drop_seq.Tpo .deps/sc_drop_seq.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_filtered_reader.o -MD -MP -MF .deps/bcf_filtered_reader.Tpo -c -o bcf_filtered_reader.o bcf_filtered_reader.cpp mv -f .deps/bcf_filtered_reader.Tpo .deps/bcf_filtered_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.cpp filter.cpp:1637:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i; ^~~~~~~~ filter.cpp:1639:22: note: uninitialized use occurs here if ( out[ival].tok_type!=TOK_VAL || !out[ival].key ) ^~~~ filter.cpp:1637:18: note: remove the 'if' if its condition is always true else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i; ^~~~~~~~ ~ filter.cpp:1631:31: note: initialize the variable 'ival' to silence this warning int itok = i, ival; ^ = 0 filter.cpp:1615:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = ... ^~~~~~~~~~~~~~~ filter.cpp:1617:34: note: uninitialized use occurs here if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { ... ^~~~ filter.cpp:1615:18: note: remove the 'if' if its condition is always true ...if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1; ^~~~~~~~~~~~~~~ ~ filter.cpp:1611:27: note: initialize the variable 'ival' to silence this warning int itok, ival; ^ = 0 filter.cpp:1615:23: warning: variable 'itok' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = ... ^~~~~~~~~~~~~~~ filter.cpp:1623:22: note: uninitialized use occurs here if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].... ^~~~ filter.cpp:1615:18: note: remove the 'if' if its condition is always true ...if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1; ^~~~~~~~~~~~~~~ ~ filter.cpp:1611:21: note: initialize the variable 'itok' to silence this warning int itok, ival; ^ = 0 3 warnings generated. mv -f .deps/filter.Tpo .deps/filter.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po /bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -o demuxlet Error.o PhredHelper.o params.o hts_utils.o bcf_ordered_reader.o interval.o interval_tree.o utils.o genome_interval.o reference_sequence.o bcf_chunked_reader.o genomeChunk.o sam_filtered_reader.o sc_drop_seq.o bcf_filtered_reader.o filter.o tsv_reader.o cmd_cram_demuxlet.o ../htslib/libhts.a -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto -lz libtool: link: g++ -g -O2 -o demuxlet Error.o PhredHelper.o params.o hts_utils.o bcf_ordered_reader.o interval.o interval_tree.o utils.o genome_interval.o reference_sequence.o bcf_chunked_reader.o genomeChunk.o sam_filtered_reader.o sc_drop_seq.o bcf_filtered_reader.o filter.o tsv_reader.o cmd_cram_demuxlet.o -Wl,-bind_at_load ../htslib/libhts.a -lpthread -llzma -lbz2 -lgomp -lcurl -lcrypto -lz ld: library not found for -lgomp clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: [demuxlet] Error 1 make: [all] Error 2 (citeseq_tools) wmnd-ibassano:demuxlet ibassano$

[hyunminkang]

You need to install openmp library or remove -lgomp from the Makefile.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 8:53 AM ibseq notifications@github.com wrote:

Hi Hyun, I did all the below. See attached. I also upgraded gcc at is seemed the prob but still nothing

BW Irene

On 29 Apr 2019, at 13:37, Hyun Min Kang notifications@github.com wrote:

Also, rename htslib as Desktop/htslib, for example.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 8:04 AM Hyun Min Kang hmkang@umich.edu wrote:

You need to have demuxlet as a sibling directory to htslib, for example Desktop/demuxlet.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Mon, Apr 29, 2019 at 4:58 AM ibseq notifications@github.com wrote:

Hi Hyun, The first two work, the last doesn’t

Just to make sure I understood: I cloned htslib first and follow instruction to install it. In the same folder I cloned demuxlet, cd to demuxlet and installed it.

Correct?

About : “The compiler says libhts.a does not exist, but do you see them exist? That was my question. If so, what is the directory structure?”

I opend the htslib folder and a file named “/libhts.a” is found in Desktop/htslib-1.9/libhts.a

Demuxlet is found in Desktop/htslib-1.9/demuxlet

Bw Irene

On 26 Apr 2019, at 16:07, Hyun Min Kang notifications@github.com wrote:

I believe that this is because htslib.a does not exist in the proper place, as the error message shows.

Go to the parent folder of demuxlet and try if all three commands works $ ls demuxlet/ $ ls htslib/ $ ls htslib/libhts.a

If all three commands works without errors, please let me know what the output is.

Hyun.

Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu

On Fri, Apr 26, 2019 at 10:46 AM ibseq notifications@github.com wrote:

is anyone going to pick this up ??...having the same issue :)

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Last login: Mon Apr 29 13:14:52 on ttys004 (base) wmnd-ibassano:~ ibassano$ cd Desktop/ (base) wmnd-ibassano:Desktop ibassano$ brew install gcc Updating Homebrew... ==> Auto-updated Homebrew! Updated 2 taps (homebrew/core and homebrew/cask). ==> Updated Formulae r ✔ golang-migrate neovim readline ✔ gradle netdata argyll-cms grpc opencoarrays badtouch iamy pcapplusplus ballerina imagemagick@6 pdnsrec binaryen ipython quazip buildkit istioctl shfmt ccache kubeprod silk cmocka libcoap skaffold erlang libfixbuf swiftlint exploitdb libiconv traefik faas-cli libjson-rpc-cpp typescript flatbuffers liblinear volt flow libxo webdis fn lmod wtf gel mysql yaf ghq nats-streaming-server you-get

Error: gcc 8.2.0 is already installed To upgrade to 8.3.0_2, run brew upgrade gcc. (base) wmnd-ibassano:Desktop ibassano$ brew upgrade gcc ==> Upgrading 1 outdated package: gcc 8.2.0 -> 8.3.0_2 ==> Upgrading gcc ==> Installing dependencies for gcc: isl and mpfr ==> Installing gcc dependency: isl ==> Downloading https://homebrew.bintray.com/bottles/isl-0.21.mojave.bottle.tar. ==> Downloading from https://akamai.bintray.com/f9/f9188b5d486b2a835cd865f219be1 ######################################################################## 100.0% ==> Pouring isl-0.21.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/isl/0.21: 72 files, 4.3MB ==> Installing gcc dependency: mpfr ==> Downloading https://homebrew.bintray.com/bottles/mpfr-4.0.2.mojave.bottle.ta ==> Downloading from https://akamai.bintray.com/cf/cfce7ab866e98360c9364cd924da6 ######################################################################## 100.0% ==> Pouring mpfr-4.0.2.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/mpfr/4.0.2: 28 files, 4.7MB ==> Installing gcc ==> Downloading https://homebrew.bintray.com/bottles/gcc-8.3.0_2.mojave.bottle.t ==> Downloading from https://akamai.bintray.com/78/78b5b3a98b82f7c89263c5d972a11 ######################################################################## 100.0% ==> Pouring gcc-8.3.0_2.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/gcc/8.3.0_2: 1,414 files, 288.5MB Removing: /usr/local/Cellar/gcc/8.2.0... (1,413 files, 295.9MB) ==> Upgrading 3 dependents: hdf5 1.10.4 -> 1.10.5, kallisto 0.45.0 -> 0.45.1, r 3.5.2_2 -> 3.6.0 ==> Upgrading hdf5 ==> Downloading https://homebrew.bintray.com/bottles/hdf5-1.10.5.mojave.bottle.t ==> Downloading from https://akamai.bintray.com/6d/6dc444fd95265b221047a69348d7a ######################################################################## 100.0% ==> Pouring hdf5-1.10.5.mojave.bottle.tar.gz Warning: hdf5 dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. 🍺 /usr/local/Cellar/hdf5/1.10.5: 256 files, 14.7MB Removing: /usr/local/Cellar/hdf5/1.10.4... (262 files, 14.8MB) ==> Upgrading kallisto ==> Downloading https://homebrew.bintray.com/bottles/kallisto-0.45.1.mojave.bott ==> Downloading from https://akamai.bintray.com/60/60b4b2ac31be396caaf7a07d403be ######################################################################## 100.0% ==> Pouring kallisto-0.45.1.mojave.bottle.tar.gz Warning: kallisto dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. 🍺 /usr/local/Cellar/kallisto/0.45.1: 5 files, 917.3KB Removing: /usr/local/Cellar/kallisto/0.45.0... (5 files, 1014.7KB) ==> Upgrading r ==> Installing dependencies for r: libpng, pcre and readline ==> Installing r dependency: libpng ==> Downloading https://homebrew.bintray.com/bottles/libpng-1.6.37.mojave.bottle ==> Downloading from https://akamai.bintray.com/53/53bbd14cc27c86c16605e256e7646 ######################################################################## 100.0% ==> Pouring libpng-1.6.37.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/libpng/1.6.37: 27 files, 1.2MB ==> Installing r dependency: pcre ==> Downloading https://homebrew.bintray.com/bottles/pcre-8.43.mojave.bottle.tar ==> Downloading from https://akamai.bintray.com/08/08e7414a7641d1e184c936537ff67 ######################################################################## 100.0% ==> Pouring pcre-8.43.mojave.bottle.tar.gz 🍺 /usr/local/Cellar/pcre/8.43: 204 files, 5.5MB ==> Installing r dependency: readline ==> Downloading https://homebrew.bintray.com/bottles/readline-8.0.0_1.mojave.bot ==> Downloading from https://akamai.bintray.com/fa/faab004773e6449dd97971311cb62 ######################################################################## 100.0% ==> Pouring readline-8.0.0_1.mojave.bottle.tar.gz ==> Caveats readline is keg-only, which means it was not symlinked into /usr/local, because macOS provides the BSD libedit library, which shadows libreadline. In order to prevent conflicts when programs look for libreadline we are defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set: export LDFLAGS="-L/usr/local/opt/readline/lib" export CPPFLAGS="-I/usr/local/opt/readline/include"

For pkg-config to find readline you may need to set: export PKG_CONFIG_PATH="/usr/local/opt/readline/lib/pkgconfig"

==> Summary 🍺 /usr/local/Cellar/readline/8.0.0_1: 48 files, 1.5MB ==> Installing r ==> Downloading https://homebrew.bintray.com/bottles/r-3.6.0.mojave.bottle.tar.g ==> Downloading from https://akamai.bintray.com/99/99d04c26f4c4a94b6158e106fd7e6 ######################################################################## 100.0% ==> Pouring r-3.6.0.mojave.bottle.tar.gz Error: The brew link step did not complete successfully The formula built, but is not symlinked into /usr/local Could not symlink bin/R Target /usr/local/bin/R already exists. You may want to remove it: rm '/usr/local/bin/R'

To force the link and overwrite all conflicting files: brew link --overwrite r

To list all files that would be deleted: brew link --overwrite --dry-run r

Possible conflicting files are: /usr/local/bin/R -> /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/Rscript -> /Library/Frameworks/R.framework/Resources/bin/Rscript ==> Summary 🍺 /usr/local/Cellar/r/3.6.0: 2,121 files, 56.5MB Removing: /usr/local/Cellar/r/3.5.2_2... (2,117 files, 55.7MB) ==> Caveats ==> readline readline is keg-only, which means it was not symlinked into /usr/local, because macOS provides the BSD libedit library, which shadows libreadline. In order to prevent conflicts when programs look for libreadline we are defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set: export LDFLAGS="-L/usr/local/opt/readline/lib" export CPPFLAGS="-I/usr/local/opt/readline/include"

For pkg-config to find readline you may need to set: export PKG_CONFIG_PATH="/usr/local/opt/readline/lib/pkgconfig"

(base) wmnd-ibassano:Desktop ibassano$ git clone https://github.com/statgen/demuxlet.git Cloning into 'demuxlet'... remote: Enumerating objects: 4, done. remote: Counting objects: 100% (4/4), done. remote: Compressing objects: 100% (4/4), done. remote: Total 344 (delta 0), reused 0 (delta 0), pack-reused 340 Receiving objects: 100% (344/344), 6.75 MiB | 8.85 MiB/s, done. Resolving deltas: 100% (174/174), done. (base) wmnd-ibassano:Desktop ibassano$ git clone https://github.com/samtools/htslib.git Cloning into 'htslib'... remote: Enumerating objects: 4, done. remote: Counting objects: 100% (4/4), done. remote: Compressing objects: 100% (4/4), done. remote: Total 10770 (delta 0), reused 1 (delta 0), pack-reused 10766 Receiving objects: 100% (10770/10770), 7.99 MiB | 9.89 MiB/s, done. Resolving deltas: 100% (7539/7539), done. (base) wmnd-ibassano:Desktop ibassano$ conda info --envs

conda environments:

# base * /anaconda3 BCR_analysis /anaconda3/envs/BCR_analysis citeseq_tools /anaconda3/envs/citeseq_tools igdiscover /anaconda3/envs/igdiscover

(base) wmnd-ibassano:Desktop ibassano$ source activate citeseq_tools (citeseq_tools) wmnd-ibassano:Desktop ibassano$ cd htslib/ (citeseq_tools) wmnd-ibassano:htslib ibassano$ autoheader (citeseq_tools) wmnd-ibassano:htslib ibassano$ autoconf (citeseq_tools) wmnd-ibassano:htslib ibassano$ ./configure checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... /usr/local/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 for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Darwin... Darwin dylib checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking whether fdatasync is declared... no checking for library containing log... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl_easy_pause in -lcurl... yes checking for CCHmac... yes 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 (citeseq_tools) wmnd-ibassano:htslib ibassano$ make gcc -Wall -g -O2 -I. -c -o kfunc.o kfunc.c gcc -Wall -g -O2 -I. -c -o knetfile.o knetfile.c gcc -Wall -g -O2 -I. -c -o kstring.o kstring.c gcc -Wall -g -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -Wall -g -O2 -I. -c -o bgzf.o bgzf.c gcc -Wall -g -O2 -I. -c -o errmod.o errmod.c gcc -Wall -g -O2 -I. -c -o faidx.o faidx.c gcc -Wall -g -O2 -I. -c -o hfile.o hfile.c gcc -Wall -g -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9-149-gf5b75ff"' > version.h gcc -Wall -g -O2 -I. -c -o hts.o hts.c gcc -Wall -g -O2 -I. -c -o hts_os.o hts_os.c gcc -Wall -g -O2 -I. -c -o md5.o md5.c gcc -Wall -g -O2 -I. -c -o multipart.o multipart.c gcc -Wall -g -O2 -I. -c -o probaln.o probaln.c gcc -Wall -g -O2 -I. -c -o realn.o realn.c gcc -Wall -g -O2 -I. -c -o regidx.o regidx.c gcc -Wall -g -O2 -I. -c -o region.o region.c gcc -Wall -g -O2 -I. -c -o sam.o sam.c gcc -Wall -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -Wall -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -Wall -g -O2 -I. -c -o tbx.o tbx.c gcc -Wall -g -O2 -I. -c -o textutils.o textutils.c gcc -Wall -g -O2 -I. -c -o thread_pool.o thread_pool.c gcc -Wall -g -O2 -I. -c -o vcf.o vcf.c gcc -Wall -g -O2 -I. -c -o vcfutils.o vcfutils.c gcc -Wall -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -Wall -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -Wall -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -Wall -g -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -Wall -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -Wall -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -Wall -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -Wall -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -Wall -g -O2 -I. -c -o cram/files.o cram/files.c gcc -Wall -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -Wall -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -Wall -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -Wall -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -Wall -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -Wall -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -Wall -g -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c gcc -Wall -g -O2 -I. -c -o hfile_gcs.o hfile_gcs.c gcc -Wall -g -O2 -I. -c -o hfile_s3.o hfile_s3.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o 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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o ranlib libhts.a gcc -dynamiclib -install_name /usr/local/lib/libhts.2to3part5.dylib -current_version 1.9.255 -compatibility_version 2.5 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o 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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o -llzma -lbz2 -lz -lcurl ln -sf libhts.dylib libhts.2to3part5.dylib gcc -Wall -g -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/hts_endian.o test/hts_endian.c gcc -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lcurl gcc -Wall -g -O2 -I. -c -o test/fieldarith.o test/fieldarith.c gcc -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/hfile.o test/hfile.c gcc -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/pileup.o test/pileup.c gcc -pthread -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/sam.o test/sam.c gcc -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_kstring.o test/test_kstring.c gcc -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_realn.o test/test_realn.c gcc -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-regidx.o test/test-regidx.c gcc -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_view.o test/test_view.c gcc -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test_index.o test/test_index.c gcc -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread gcc -Wall -g -O2 -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -Wall -g -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lcurl -lpthread (citeseq_tools) wmnd-ibassano:htslib ibassano$ sudo make install Password: Sorry, try again. Password: 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/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi install -p libhts.dylib /usr/local/lib/libhts.1.9-149-gf5b75ff.dylib ln -sf libhts.1.9-149-gf5b75ff.dylib /usr/local/lib/libhts.dylib ln -sf libhts.1.9-149-gf5b75ff.dylib /usr/local/lib/libhts.2to3part5.dylib sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@

/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9-149-gf5b75ff#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 (citeseq_tools) wmnd-ibassano:htslib ibassano$ cd ../demuxlet/ (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ autoreconf -vfi autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS} aclocal: warning: couldn't open directory 'm4': No such file or directory autoreconf: configure.ac: tracing autoreconf: configure.ac: creating directory aux-dist autoreconf: running: glibtoolize --copy --force glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'aux-dist'. glibtoolize: copying file 'aux-dist/ltmain.sh' glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. glibtoolize: copying file 'm4/libtool.m4' glibtoolize: copying file 'm4/ltoptions.m4' glibtoolize: copying file 'm4/ltsugar.m4' glibtoolize: copying file 'm4/ltversion.m4' glibtoolize: copying file 'm4/lt~obsolete.m4' autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:45: installing 'aux-dist/compile' configure.ac:45: installing 'aux-dist/config.guess' configure.ac:45: installing 'aux-dist/config.sub' configure.ac:7: installing 'aux-dist/install-sh' configure.ac:7: installing 'aux-dist/missing' Makefile.am: installing 'aux-dist/depcomp' autoreconf: Leaving directory.' (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... aux-dist/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for g++... g++ 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 g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for int32_t... yes checking for int64_t... yes checking for C/C++ restrict keyword... restrict checking for size_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for ptrdiff_t... yes checking for error_at_line... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking whether sys/types.h defines makedev... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for gethostname... yes checking for memset... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for strtol... yes checking for gzopen in -lz... yes checking for erf in -lm... yes checking for erfc in -lm... yes checking build system type... x86_64-apple-darwin18.5.0 checking host system type... x86_64-apple-darwin18.5.0 checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert x86_64-apple-darwin18.5.0 file names to x86_64-apple-darwin18.5.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin18.5.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ autoreconf -vfi autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS} autoreconf: configure.ac: tracing autoreconf: running: glibtoolize --copy --force glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'aux-dist'. glibtoolize: copying file 'aux-dist/ltmain.sh' glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. glibtoolize: copying file 'm4/libtool.m4' glibtoolize: copying file 'm4/ltoptions.m4' glibtoolize: copying file 'm4/ltsugar.m4' glibtoolize: copying file 'm4/ltversion.m4' glibtoolize: copying file 'm4/lt~obsolete.m4' autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoconf --force autoreconf: running: /usr/local/Cellar/autoconf/2.69/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:45: installing 'aux-dist/compile' configure.ac:7: installing 'aux-dist/missing' Makefile.am: installing 'aux-dist/depcomp' autoreconf: Leaving directory.' (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ ./configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... aux-dist/install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make sets $(MAKE)... (cached) yes checking for g++... g++ 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 g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for int32_t... yes checking for int64_t... yes checking for C/C++ restrict keyword... restrict checking for size_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for ptrdiff_t... yes checking for error_at_line... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking whether sys/types.h defines makedev... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for gethostname... yes checking for memset... yes checking for pow... yes checking for select... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for strtol... yes checking for gzopen in -lz... yes checking for erf in -lm... yes checking for erfc in -lm... yes checking build system type... x86_64-apple-darwin18.5.0 checking host system type... x86_64-apple-darwin18.5.0 checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert x86_64-apple-darwin18.5.0 file names to x86_64-apple-darwin18.5.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin18.5.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.5.0 dyld checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands (citeseq_tools) wmnd-ibassano:demuxlet ibassano$ make /Library/Developer/CommandLineTools/usr/bin/make all-am g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT Error.o -MD -MP -MF .deps/Error.Tpo -c -o Error.o Error.cpp mv -f .deps/Error.Tpo .deps/Error.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT PhredHelper.o -MD -MP -MF .deps/PhredHelper.Tpo -c -o PhredHelper.o PhredHelper.cpp mv -f .deps/PhredHelper.Tpo .deps/PhredHelper.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT params.o -MD -MP -MF .deps/params.Tpo -c -o params.o params.cpp params.cpp:77:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security] ::printf(buf); ^~~ params.cpp:77:14: note: treat the string as an argument to avoid this ::printf(buf); ^ "%s", 1 warning generated. mv -f .deps/params.Tpo .deps/params.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT hts_utils.o -MD -MP -MF .deps/hts_utils.Tpo -c -o hts_utils.o hts_utils.cpp mv -f .deps/hts_utils.Tpo .deps/hts_utils.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_ordered_reader.o -MD -MP -MF .deps/bcf_ordered_reader.Tpo -c -o bcf_ordered_reader.o bcf_ordered_reader.cpp mv -f .deps/bcf_ordered_reader.Tpo .deps/bcf_ordered_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval.o -MD -MP -MF .deps/interval.Tpo -c -o interval.o interval.cpp mv -f .deps/interval.Tpo .deps/interval.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT interval_tree.o -MD -MP -MF .deps/interval_tree.Tpo -c -o interval_tree.o interval_tree.cpp mv -f .deps/interval_tree.Tpo .deps/interval_tree.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.cpp mv -f .deps/utils.Tpo .deps/utils.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genome_interval.o -MD -MP -MF .deps/genome_interval.Tpo -c -o genome_interval.o genome_interval.cpp mv -f .deps/genome_interval.Tpo .deps/genome_interval.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT reference_sequence.o -MD -MP -MF .deps/reference_sequence.Tpo -c -o reference_sequence.o reference_sequence.cpp mv -f .deps/reference_sequence.Tpo .deps/reference_sequence.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_chunked_reader.o -MD -MP -MF .deps/bcf_chunked_reader.Tpo -c -o bcf_chunked_reader.o bcf_chunked_reader.cpp mv -f .deps/bcf_chunked_reader.Tpo .deps/bcf_chunked_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT genomeChunk.o -MD -MP -MF .deps/genomeChunk.Tpo -c -o genomeChunk.o genomeChunk.cpp mv -f .deps/genomeChunk.Tpo .deps/genomeChunk.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sam_filtered_reader.o -MD -MP -MF .deps/sam_filtered_reader.Tpo -c -o sam_filtered_reader.o sam_filtered_reader.cpp mv -f .deps/sam_filtered_reader.Tpo .deps/sam_filtered_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT sc_drop_seq.o -MD -MP -MF .deps/sc_drop_seq.Tpo -c -o sc_drop_seq.o sc_drop_seq.cpp mv -f .deps/sc_drop_seq.Tpo .deps/sc_drop_seq.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT bcf_filtered_reader.o -MD -MP -MF .deps/bcf_filtered_reader.Tpo -c -o bcf_filtered_reader.o bcf_filtered_reader.cpp mv -f .deps/bcf_filtered_reader.Tpo .deps/bcf_filtered_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.cpp filter.cpp:1637:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i; ^~~~~~~~ filter.cpp:1639:22: note: uninitialized use occurs here if ( out[ival].tok_type!=TOK_VAL || !out[ival].key ) ^~~~ filter.cpp:1637:18: note: remove the 'if' if its condition is always true else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NE, ival = ++i; ^~~~~~~~ ~ filter.cpp:1631:31: note: initialize the variable 'ival' to silence this warning int itok = i, ival; ^ = 0 filter.cpp:1615:23: warning: variable 'ival' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = ... ^~~~~~~~~~~~~~~ filter.cpp:1617:34: note: uninitialized use occurs here if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { ... ^~~~ filter.cpp:1615:18: note: remove the 'if' if its condition is always true ...if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1; ^~~~~~~~~~~~~~~ ~ filter.cpp:1611:27: note: initialize the variable 'ival' to silence this warning int itok, ival; ^ = 0 filter.cpp:1615:23: warning: variable 'itok' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = ... ^~~~~~~~~~~~~~~ filter.cpp:1623:22: note: uninitialized use occurs here if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].... ^~~~ filter.cpp:1615:18: note: remove the 'if' if its condition is always true ...if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1; ^~~~~~~~~~~~~~~ ~ filter.cpp:1611:21: note: initialize the variable 'itok' to silence this warning int itok, ival; ^ = 0 3 warnings generated. mv -f .deps/filter.Tpo .deps/filter.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT tsv_reader.o -MD -MP -MF .deps/tsv_reader.Tpo -c -o tsv_reader.o tsv_reader.cpp mv -f .deps/tsv_reader.Tpo .deps/tsv_reader.Po g++ -DHAVE_CONFIG_H -I. -I ../htslib/ -I ../../htslib/htslib -pipe -DSTDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 -g -O2 -MT cmd_cram_demuxlet.o -MD -MP -MF .deps/cmd_cram_demuxlet.Tpo -c -o cmd_cram_demuxlet.o cmd_cram_demuxlet.cpp mv -f .deps/cmd_cram_demuxlet.Tpo .deps/cmd_cram_demuxlet.Po /bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -o demuxlet Error.o PhredHelper.o params.o hts_utils.o bcf_ordered_reader.o interval.o interval_tree.o utils.o genome_interval.o reference_sequence.o bcf_chunked_reader.o genomeChunk.o sam_filtered_reader.o sc_drop_seq.o bcf_filtered_reader.o filter.o tsv_reader.o cmd_cram_demuxlet.o ../htslib/libhts.a -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto -lz libtool: link: g++ -g -O2 -o demuxlet Error.o PhredHelper.o params.o hts_utils.o bcf_ordered_reader.o interval.o interval_tree.o utils.o genome_interval.o reference_sequence.o bcf_chunked_reader.o genomeChunk.o sam_filtered_reader.o sc_drop_seq.o bcf_filtered_reader.o filter.o tsv_reader.o cmd_cram_demuxlet.o -Wl,-bind_at_load ../htslib/libhts.a -lpthread -llzma -lbz2 -lgomp -lcurl -lcrypto -lz ld: library not found for -lgomp clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: [demuxlet] Error 1 make: [all] Error 2 (citeseq_tools) wmnd-ibassano:demuxlet ibassano$

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