hyunminkang
commented
4 years ago Isn't demuxlet binary created? I do not see any error messages.
Hyun.
Hyun Min Kang, Ph.D. Associate Professor of Biostatistics University of Michigan, Ann Arbor Email : hmkang@umich.edu
On Tue, Sep 24, 2019 at 1:19 PM Vinay Kartha notifications@github.com wrote:
Hi, as it appears with some others, I too am getting errors when trying to install demuxlet on an Ubuntu machine.
I made sure htslibs was downloaded and installed in the "sibling" folder, within the same parent directory as my demuxlet downloaded folder. After running the initial /.configure command (output pasted below), I ran make and see the following error (also pasted below):
demuxlet$ sudo ./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... /bin/mkdir -p checking for gawk... gawk 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 for style of include used by make... GNU 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... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking 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... yes 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-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes 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... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /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 https://github.com/file support... @ 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... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no 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++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so 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
demuxlet$ sudo make make all-am make[1]: Entering directory '/mnt/bin/demuxlet' 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: In member function ‘void param::message(const char*, ...)’: params.cpp:77:17: warning: format not a string literal and no format arguments [-Wformat-security] ::printf(buf); ^ 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 In file included from hts_utils.cpp:25:0: ../htslib/htslib/hfile.h: In function ‘ssize_t hwrite(hFILE, const void, size_t)’: ../htslib/htslib/hfile.h:261:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (fp->limit - fp->begin < nbytes){
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 bcf_filtered_reader.cpp: In member function ‘void BCFFilteredReader::init_params()’: bcf_filtered_reader.cpp:57:53: warning: ‘scol’ may be used uninitialized in this function [-Wmaybe-uninitialized] std::string id = tsv_sex_map.str_field_at(scol); ^ 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: In function ‘void filters_set_genotype_string(filter_t*, bcf1_t*, token_t*)’: filter.cpp:649:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( str.l - plen > blen ) ~~~~~~~~~~~~~^~~~~~ filter.cpp: In function ‘int filters_init1(filter_t*, char*, int, token_t*)’: filter.cpp:1318:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i=0; i<tmp.l; i++) ~^~~~~~ filter.cpp:1443:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( end - tmp.s != strlen(tmp.s) ) ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ filter.cpp: In function ‘filter_t* filter_init(bcf_hdr_t*, const char*)’: filter.cpp:1639:26: warning: ‘ival’ may be used uninitialized in this function [-Wmaybe-uninitialized] if ( out[ival].tok_type!=TOK_VAL || !out[ival].key ) ^ filter.cpp:1617:38: warning: ‘ival’ may be used uninitialized in this function [-Wmaybe-uninitialized] if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival].is_str = 0; } ^ filter.cpp:1623:26: warning: ‘itok’ may be used uninitialized in this function [-Wmaybe-uninitialized] if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and; ^ 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 /bin/bash ./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 ../htslib/libhts.a -lpthread -llzma -lbz2 -lgomp /usr/lib/x86_64-linux-gnu/libcurl.so -lcrypto -lz -pthread make[1]: Leaving directory '/mnt/bin/demuxlet' Any input would be appreciated, as I try to get this up and running! — You are receiving this because you are subscribed to this thread. 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Hi, as it appears with some others, I too am getting errors when trying to install demuxlet on an Ubuntu machine.
I made sure htslibs was downloaded and installed in the "sibling" folder, within the same parent directory as my demuxlet downloaded folder. After running the initial /.configure command (output pasted below), I ran make and see the following error (also pasted below):
demuxlet$ sudo ./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... /bin/mkdir -p checking for gawk... gawk 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 for style of include used by make... GNU 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... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking 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... yes 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-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes 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... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /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... @ 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... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no 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++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so 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
demuxlet$ sudo make make all-am make[1]: Entering directory '/mnt/bin/demuxlet' 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: In member function ‘void param::message(const char*, ...)’: params.cpp:77:17: warning: format not a string literal and no format arguments [-Wformat-security] ::printf(buf); ^ 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 In file included from hts_utils.cpp:25:0: ../htslib/htslib/hfile.h: In function ‘ssize_t hwrite(hFILE, const void, size_t)’: ../htslib/htslib/hfile.h:261:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (fp->limit - fp->begin < nbytes){