Is a bioconda version planned? This would be a great help since I have already spent some time on this and am nowhere near completion.

Any ideas on these errors ? Ubuntu 16.04

Thanks.

CXX=/usr/bin/g++ echo $CXX

BOOST_ROOT=/usr/include/boost echo $BOOST_ROOT

Ubuntu 16.04 packages

sudo apt install liblz4-dev sudo apt install liblzma-dev

cd /mnt/ngsnfs/tools git clone --recursive https://github.com/DecodeGenetics/graphtyper.git

cmake .. -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Checking if C linker supports --verbose -- Checking if C linker supports --verbose - yes -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Checking if CXX linker supports --verbose -- Checking if CXX linker supports --verbose - yes -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Build type: -- Building in release mode. -- Using GCC -- CXX flags are: -march=core2 -mtune=generic -W -Wall -std=c++11 -DSEQAN_USE_HTSLIB=1 -DSEQAN_HAS_ZLIB=1 -O3 -DNDEBUG -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -lrt -- Checking for zlib -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") -- Checking for bzip2 -- Found BZip2: /mnt/ngsnfs/tools/miniconda2/lib/libbz2.a (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Checking for Boost -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Boost version: 1.58.0 -- Found the following Boost libraries: -- iostreams -- log -- thread -- serialization -- system -- regex -- log_setup -- date_time -- filesystem -- chrono -- atomic -- snappy target location is /mnt/ngsnfs/tools/graphtyper/snappy/.libs/libsnappy.a -- htslib target location is /mnt/ngsnfs/tools/graphtyper/htslib/libhts.a -- StatGen target location is /mnt/ngsnfs/tools/graphtyper/statgen/libStatGen.a -- Performing Test LZ4_GOOD_VERSION -- Performing Test LZ4_GOOD_VERSION - Success -- Found LZ4: /usr/lib/x86_64-linux-gnu/liblz4.so
-- Found LZ4: /usr/lib/x86_64-linux-gnu/liblz4.so -- Compiling graphtyper's source files -- Configuring done -- Generating done -- Build files have been written to: /mnt/ngsnfs/tools/graphtyper/release-build rcug@hpc01:/mnt/ngsnfs/tools/graphtyper/release-build$ rcug@hpc01:/mnt/ngsnfs/tools/graphtyper/release-build$ rcug@hpc01:/mnt/ngsnfs/tools/graphtyper/release-build$ make -j16 graphtyper Scanning dependencies of target project_sparsehash Scanning dependencies of target project_snappy Scanning dependencies of target project_statgen Scanning dependencies of target project_htslib [ 3%] Creating directories for 'project_snappy' [ 3%] Creating directories for 'project_sparsehash' [ 3%] Creating directories for 'project_statgen' [ 5%] Creating directories for 'project_htslib' [ 7%] No download step for 'project_snappy' [ 7%] No download step for 'project_sparsehash' [ 7%] No download step for 'project_statgen' [ 8%] No download step for 'project_htslib' [ 16%] No patch step for 'project_sparsehash' [ 16%] No update step for 'project_statgen' [ 16%] No patch step for 'project_snappy' [ 16%] No update step for 'project_sparsehash' [ 16%] No patch step for 'project_statgen' [ 16%] No update step for 'project_snappy' [ 18%] No update step for 'project_htslib' [ 18%] No patch step for 'project_htslib' [ 21%] Performing configure step for 'project_snappy' [ 22%] No configure step for 'project_statgen' [ 22%] Performing configure step for 'project_sparsehash' [ 23%] No configure step for 'project_htslib' [ 25%] Performing build step for 'project_statgen' [ 26%] Performing build step for 'project_htslib' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... ar: u' modifier ignored sinceD' is the default (see U') yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... 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... /mnt/ngsnfs/tools/graphtyper/snappy/autogen.sh: 10: /mnt/ngsnfs/tools/graphtyper/snappy/autogen.sh: libtoolize: not found CMakeFiles/project_snappy.dir/build.make:105: recipe for target '../snappy/src/project_snappy-stamp/project_snappy-configure' failed make[3]: *** [../snappy/src/project_snappy-stamp/project_snappy-configure] Error 127 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/project_snappy.dir/all' failed make[2]: *** [CMakeFiles/project_snappy.dir/all] Error 2 make[2]: *** Waiting for unfinished jobs.... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 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 dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -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 memcpy... yes checking for memmove... 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 uint16_t... yes checking for u_int16_t... yes checking for __uint16... no checking for long long... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking how to run the C++ preprocessor... g++ -E checking google/malloc_extension.h usability... no checking google/malloc_extension.h presence... no checking for google/malloc_extension.h... no checking whether the compiler implements namespaces... yes checking the location of hash_map... <tr1/unordered_map> checking how to include hash_fun directly... <tr1/functional> configure: creating ./config.status config.status: creating Makefile config.status: creating src/config.h config.status: executing depfiles commands test/sam.c: In function ‘faidx1’: test/sam.c:186:5: warning: ‘faidx_fetch_nseq’ is deprecated: Please use faidx_nseq instead [-Wdeprecated-declarations] n = faidx_fetch_nseq(fai); ^ In file included from test/sam.c:32:0: ./htslib/faidx.h:94:9: note: declared here int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead"); ^ [ 27%] Performing build step for 'project_sparsehash' /mnt/ngsnfs/tools/graphtyper/sparsehash/missing: line 52: aclocal-1.11: command not found WARNING:aclocal-1.11' is missing on your system. You should only need it if you modified acinclude.m4' orconfigure.ac'. You might want to install the Automake' andPerl' packages. Grab them from any GNU archive site. cd . && /bin/bash /mnt/ngsnfs/tools/graphtyper/sparsehash/missing --run automake-1.11 --gnu /mnt/ngsnfs/tools/graphtyper/sparsehash/missing: line 52: automake-1.11: command not found WARNING: automake-1.11' is missing on your system. You should only need it if you modifiedMakefile.am', acinclude.m4' orconfigure.ac'. You might want to install the Automake' andPerl' packages. Grab them from any GNU archive site. aclocal.m4:16: warning: this file was generated for autoconf 2.68. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically autoreconf'. running CONFIG_SHELL=/bin/bash /bin/bash /mnt/ngsnfs/tools/graphtyper/sparsehash/configure --no-create --no-recursion checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ar:u' modifier ignored since D' is the default (seeU') /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for g++... g++ checking whether the C++ compiler works... [ 28%] No install step for 'project_htslib' [ 30%] Completed 'project_htslib' yes checking for C++ compiler default output file name... a.out checking for suffix of executables... [ 30%] Built target project_htslib

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 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 dependency style of gcc... ar: u' modifier ignored sinceD' is the default (see U') gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... ar:u' modifier ignored since D' is the default (seeU') /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for memcpy... yes checking for memmove... 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... ar: u' modifier ignored sinceD' is the default (see U') yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for uint16_t... yes checking for u_int16_t... yes checking for __uint16... no checking for long long... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking how to run the C++ preprocessor... g++ -E checking google/malloc_extension.h usability... no checking google/malloc_extension.h presence... no checking for google/malloc_extension.h... no checking whether the compiler implements namespaces... yes checking the location of hash_map... <tr1/unordered_map> checking how to include hash_fun directly... <tr1/functional> configure: creating ./config.status ar:u' modifier ignored since D' is the default (seeU') [ 31%] No install step for 'project_statgen' /bin/bash ./config.status [ 32%] Completed 'project_statgen' [ 32%] Built target project_statgen config.status: creating Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: creating src/config.h config.status: src/config.h is unchanged

Hey Colin. Thank you for reporting your problem.

It seems to you are missing Autotools and Automake. Try:

sudo apt-get install autotools-dev
sudo apt-get install automake

and then make graphtyper again. I will leave the issue open, please let me know if you get into more problems.

I am not familiar with bioconda. I will look into if I can add Graphtyper there.

Best regards, Hannes

Hi Hannes, thanks.

Unfortunately both these tools/libs were installed.

sudo apt install autotools-dev [sudo] password for rcug: Reading package lists... Done Building dependency tree
Reading state information... Done autotools-dev is already the newest version (20150820.1). autotools-dev set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 84 not upgraded. rcug@hpc01:~$ sudo apt install automake Reading package lists... Done Building dependency tree
Reading state information... Done automake is already the newest version (1:1.15-4ubuntu1). 0 upgraded, 0 newly installed, 0 to remove and 84 not upgraded.

Could they be untested versions ?

sudo apt show automake Package: automake Version: 1:1.15-4ubuntu1 Priority: optional Section: devel Source: automake-1.15 Origin: Ubuntu Maintainer: Ubuntu Developers ubuntu-devel-discuss@lists.ubuntu.com Original-Maintainer: Eric Dorland eric@debian.org Bugs: https://bugs.launchpad.net/ubuntu/+filebug Installed-Size: 1.529 kB Provides: automake-1.15, automaken Depends: autoconf (>= 2.65), autotools-dev (>= 20020320.1) Suggests: autoconf-doc, gnu-standards Conflicts: automake (<< 1:1.4-p5-1), automake1.10-doc, automake1.5 (<< 1.5-2), automake1.6 (<< 1.6.1-4) Homepage: https://www.gnu.org/software/automake/ Task: ubuntu-sdk-libs-tools, ubuntu-sdk Supported: 5y Download-Size: 510 kB APT-Manual-Installed: yes APT-Sources: http://de.archive.ubuntu.com/ubuntu xenial/main amd64 Packages Description: Tool for generating GNU Standards-compliant Makefiles Automake is a tool for automatically generating Makefile.in's from files calledMakefile.am'. . The goal of Automake is to remove the burden of Makefile maintenance from the back of the individual GNU maintainer (and put it on the back of the Automake maintainer). . The Makefile.am' is basically a series ofmake' macro definitions (with rules being thrown in occasionally). The generated `Makefile.in's are compliant with the GNU Makefile standards. . Automake 1.15 fails to work in a number of situations that Automake 1.4, 1.6, 1.7, 1.8, 1.9, 1.10, 1.11 and 1.14 did, so previous versions are available as separate packages.

sudo apt show autotools-dev Package: autotools-dev Version: 20150820.1 Priority: optional Section: devel Origin: Ubuntu Maintainer: Ubuntu Developers ubuntu-devel-discuss@lists.ubuntu.com Original-Maintainer: Henrique de Moraes Holschuh hmh@debian.org Bugs: https://bugs.launchpad.net/ubuntu/+filebug Installed-Size: 155 kB Enhances: cdbs, debhelper Homepage: http://savannah.gnu.org/projects/config/ Task: ubuntu-sdk-libs-tools, ubuntu-sdk Supported: 5y Download-Size: 39,8 kB APT-Manual-Installed: yes APT-Sources: http://de.archive.ubuntu.com/ubuntu xenial/main amd64 Packages Description: Update infrastructure for config.{guess,sub} files This package installs an up-to-date version of config.guess and config.sub, used by the automake and libtool packages. It provides the canonical copy of those files for other packages as well. . It also documents in /usr/share/doc/autotools-dev/README.Debian.gz best practices and guidelines for using autoconf, automake and friends on Debian packages. This is a must-read for any developers packaging software that uses the GNU autotools, or GNU gettext. . Additionally this package provides seamless integration into Debhelper or CDBS, allowing maintainers to easily update config.{guess,sub} files in their packages.

Hey Colin. Thank you for a quick reply.

We have tested compiling Graphtyper on a Ubuntu 16.04 so the versions of these libraries should match. But I suspect that I might have missed the dependency "libtool". I have now added it to the README. Can you try for me:

sudo apt-get install libtool

and then make graphtyper yet again.

Best regards, Hannes

Ditto on the quick reply, thanks.

It now seems to have a problem with libboost if I can interpret this correctly

rcug@hpc01:/mnt/ngsnfs/tools/graphtyper/release-build$ make -j 8 graphtyper [ 5%] Creating directories for 'project_statgen' [ 5%] Creating directories for 'project_sparsehash' [ 5%] Creating directories for 'project_snappy' [ 5%] Creating directories for 'project_htslib' [ 8%] No download step for 'project_htslib' [ 8%] No download step for 'project_snappy' [ 8%] No download step for 'project_statgen' [ 8%] No download step for 'project_sparsehash' [ 11%] No update step for 'project_statgen' [ 18%] No patch step for 'project_statgen' [ 18%] No update step for 'project_sparsehash' [ 18%] No patch step for 'project_snappy' [ 18%] No update step for 'project_snappy' [ 18%] No patch step for 'project_htslib' [ 18%] No update step for 'project_htslib' [ 18%] No patch step for 'project_sparsehash' [ 20%] No configure step for 'project_statgen' [ 23%] Performing configure step for 'project_snappy' [ 23%] No configure step for 'project_htslib' [ 23%] Performing configure step for 'project_sparsehash' [ 25%] Performing build step for 'project_statgen' [ 26%] Performing build step for 'project_htslib' ar: u' modifier ignored sinceD' is the default (see U') [ 27%] No install step for 'project_htslib' [ 28%] Completed 'project_htslib' [ 28%] Built target project_htslib ar:u' modifier ignored since D' is the default (seeU') ar: u' modifier ignored sinceD' is the default (see U') ar:u' modifier ignored since D' is the default (seeU') ar: u' modifier ignored sinceD' is the default (see U') ar:u' modifier ignored since D' is the default (seeU') [ 30%] No install step for 'project_statgen' [ 31%] Completed 'project_statgen' [ 31%] Built target project_statgen 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 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 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 dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -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 memcpy... yes checking for memmove... 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 uint16_t... yes checking for u_int16_t... yes checking for uint16... no checking for long long... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking how to run the C++ preprocessor... g++ -E checking google/malloc_extension.h usability... no checking google/malloc_extension.h presence... no checking for google/malloc_extension.h... /usr/share/automake-1.15/am/ltlibrary.am: warning: 'libsnappy.la': linking libtool libraries using a non-POSIX /usr/share/automake-1.15/am/ltlibrary.am: archiver requires 'AM_PROG_AR' in 'configure.ac' Makefile.am:4: while processing Libtool library 'libsnappy.la' no checking whether the compiler implements namespaces... yes checking the location of hash_map... 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 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 style of include used by make... GNU 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... <tr1/unordered_map> checking how to include hash_fun directly... 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 whether gcc understands -c and -o together... <tr1/functional> yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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)... configure: creating ./config.status /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... config.status: creating Makefile config.status: creating src/config.h @ checking for strip... config.status: src/config.h is unchanged strip checking for ranlib... config.status: executing depfiles commands ranlib checking command to parse /usr/bin/nm -B output from gcc object... [ 32%] Performing build step for 'project_sparsehash' ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 [ 33%] No install step for 'project_sparsehash' [ 35%] Completed 'project_sparsehash' [ 35%] Built target project_sparsehash checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -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 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 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 for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 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 whether byte ordering is bigendian... no checking for size_t... yes checking for ssize_t... yes checking for stdint.h... (cached) yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking sys/mman.h usability... yes checking sys/mman.h presence... yes checking for sys/mman.h... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking byteswap.h usability... yes checking byteswap.h presence... yes checking for byteswap.h... yes checking sys/byteswap.h usability... no checking sys/byteswap.h presence... no checking for sys/byteswap.h... no checking sys/endian.h usability... no checking sys/endian.h presence... no checking for sys/endian.h... no checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for mmap... yes checking for 'gtest-config'... checking for gtest-config... no no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gflags... no checking if the compiler supports builtin_expect... yes checking if the compiler supports builtin_ctzll... yes checking for zlibVersion in -lz... yes checking for lzo1x_1_15_compress in -llzo2... no checking for lzf_compress in -llzf... no checking for fastlz_compress in -lfastlz... no checking for qlz_compress in -lquicklz... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating snappy-stubs-public.h config.status: creating snappy.pc config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands [ 36%] Performing build step for 'project_snappy' config.status: creating config.h config.status: config.h is unchanged libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c snappy-c.cc -fPIC -DPIC -o .libs/snappy-c.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-stubs-internal.lo -MD -MP -MF .deps/snappy-stubs-internal.Tpo -c snappy-stubs-internal.cc -fPIC -DPIC -o .libs/snappy-stubs-internal.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c snappy.cc -fPIC -DPIC -o .libs/snappy.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-c.lo -MD -MP -MF .deps/snappy-c.Tpo -c snappy-c.cc -o snappy-c.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy-stubs-internal.lo -MD -MP -MF .deps/snappy-stubs-internal.Tpo -c snappy-stubs-internal.cc -o snappy-stubs-internal.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -g -O2 -MT snappy.lo -MD -MP -MF .deps/snappy.Tpo -c snappy.cc -o snappy.o >/dev/null 2>&1 libtool: link: rm -fr .libs/libsnappy.a .libs/libsnappy.la .libs/libsnappy.lai .libs/libsnappy.so .libs/libsnappy.so.1 .libs/libsnappy.so.1.3.0 libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o .libs/snappy.o .libs/snappy-sinksource.o .libs/snappy-stubs-internal.o .libs/snappy-c.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -g -O2 -Wl,-soname -Wl,libsnappy.so.1 -o .libs/libsnappy.so.1.3.0 libtool: link: (cd ".libs" && rm -f "libsnappy.so.1" && ln -s "libsnappy.so.1.3.0" "libsnappy.so.1") libtool: link: (cd ".libs" && rm -f "libsnappy.so" && ln -s "libsnappy.so.1.3.0" "libsnappy.so") libtool: link: ar cru .libs/libsnappy.a snappy.o snappy-sinksource.o snappy-stubs-internal.o snappy-c.o ar: u' modifier ignored sinceD' is the default (see U') libtool: link: ranlib .libs/libsnappy.a libtool: link: ( cd ".libs" && rm -f "libsnappy.la" && ln -s "../libsnappy.la" "libsnappy.la" ) libtool: link: g++ -g -O2 -o .libs/snappy_unittest snappy_unittest-snappy_unittest.o snappy_unittest-snappy-test.o ./.libs/libsnappy.so -lz [ 37%] No install step for 'project_snappy' [ 38%] Completed 'project_snappy' [ 38%] Built target project_snappy [ 40%] Creating directories for 'project_rocksdb' [ 41%] No download step for 'project_rocksdb' [ 43%] No patch step for 'project_rocksdb' [ 43%] No update step for 'project_rocksdb' [ 45%] No configure step for 'project_rocksdb' [ 46%] Performing build step for 'project_rocksdb' [ 47%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/absolute_position.cpp.o [ 48%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/constructor.cpp.o [ 51%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/genotype.cpp.o [ 51%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/genomic_region.cpp.o [ 55%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/haplotype.cpp.o [ 55%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/graph_serialization.cpp.o [ 55%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/graph.cpp.o [ 56%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/haplotype_calls.cpp.o [ 57%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/haplotype_extractor.cpp.o [ 58%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/label.cpp.o [ 60%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/reference_depth.cpp.o [ 61%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/ref_node.cpp.o [ 62%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/sequence_extractor.cpp.o [ 63%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/var_node.cpp.o [ 65%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/graph/var_record.cpp.o [ 66%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/index/indexer.cpp.o [ 67%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/index/mem_index.cpp.o [ 68%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/index/rocksdb.cpp.o [ 70%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/aligner.cpp.o GEN util/build_version.cc [ 70%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/alignment.cpp.o [ 72%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/caller.cpp.o [ 72%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/discovery.cpp.o [ 73%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/genotype_paths.cpp.o [ 75%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/graph_swapper.cpp.o [ 76%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/path.cpp.o [ 77%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/sample_call.cpp.o [ 78%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/segment.cpp.o [ 80%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/segment_calling.cpp.o [ 81%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/var_stats.cpp.o [ 82%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/variant.cpp.o [ 83%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/variant_candidate.cpp.o GEN util/build_version.cc CC db/builder.o [ 85%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/variant_map.cpp.o CC db/column_family.o [ 86%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/variant_support.cpp.o [ 87%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/vcf.cpp.o [ 88%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/vcf_operations.cpp.o [ 90%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/typer/vcf_writer.cpp.o CC db/compacted_db_impl.o [ 91%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/adapter_removal.cpp.o CC db/compaction.o [ 92%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/io.cpp.o CC db/compaction_iterator.o CC db/compaction_job.o [ 93%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/kmer_help_functions.cpp.o CC db/compaction_picker.o CC db/convenience.o [ 95%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/type_conversions.cpp.o [ 95%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/sam_reader.cpp.o CC db/db_filesnapshot.o CC db/db_impl.o CC db/db_impl_readonly.o [ 96%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/options.cpp.o CC db/db_impl_experimental.o CC db/db_impl_add_file.o CC db/db_iter.o CC db/experimental.o CC db/event_helpers.o CC db/flush_job.o CC db/flush_scheduler.o CC db/forward_iterator.o CC db/internal_stats.o CC db/managed_iterator.o CC db/memtable.o CC db/memtable_list.o CC db/repair.o CC db/table_cache.o CC db/transaction_log_impl.o CC db/version_builder.o CC db/version_edit.o CC db/version_set.o CC db/wal_manager.o CC db/write_batch.o CC db/write_thread.o CC db/xfunc_test_points.o CC memtable/hash_cuckoo_rep.o [ 96%] Built target graphtyper_objects CC memtable/hash_linklist_rep.o CC memtable/hash_skiplist_rep.o CC memtable/skiplistrep.o CC memtable/vectorrep.o CC table/adaptive_table_factory.o CC table/block_based_filter_block.o CC table/block_based_table_builder.o CC table/block_based_table_factory.o CC table/block_based_table_reader.o CC table/block.o CC table/cuckoo_table_builder.o CC table/cuckoo_table_factory.o CC table/cuckoo_table_reader.o CC table/format.o CC table/full_filter_block.o CC table/meta_blocks.o CC table/sst_file_writer.o CC table/plain_table_builder.o CC table/plain_table_factory.o CC table/plain_table_index.o CC table/plain_table_key_coding.o CC table/plain_table_reader.o CC table/persistent_cache_helper.o CC table/table_properties.o CC table/two_level_iterator.o CC util/bloom.o CC utilities/blob_db/blob_db.o CC utilities/checkpoint/checkpoint.o CC utilities/memory/memory_util.o CC utilities/options/options_util.o CC utilities/transactions/optimistic_transaction_impl.o CC utilities/transactions/optimistic_transaction_db_impl.o CC utilities/transactions/transaction_base.o CC utilities/transactions/transaction_db_impl.o CC utilities/transactions/transaction_impl.o CC utilities/transactions/transaction_util.o CC utilities/ttl/db_ttl_impl.o CC utilities/date_tiered/date_tiered_db_impl.o CC utilities/write_batch_with_index/write_batch_with_index.o CC utilities/write_batch_with_index/write_batch_with_index_internal.o CC util/cf_options.o CC util/options.o CC util/options_helper.o CC util/options_parser.o CC util/thread_status_updater_debug.o CC tools/ldb_cmd.o CC tools/sst_dump_tool.o AR librocksdb.a ar: creating librocksdb.a [ 97%] No install step for 'project_rocksdb' [ 98%] Completed 'project_rocksdb' [ 98%] Built target project_rocksdb [ 98%] Building CXX object src/CMakeFiles/graphtyper.dir/main.cpp.o [100%] Linking CXX executable ../bin/graphtyper CMakeFiles/graphtyper.dir/main.cpp.o: In functionvoid boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator >::aligned_write(wchar_t const, long)': main.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x85): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const, unsigned long, std::cxx11::basic_string<char, std::char_traits, std::allocator >&, std::locale const&)' main.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x147): undefined reference to boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)' CMakeFiles/graphtyper.dir/main.cpp.o: In functionvoid boost::log::v2_mt_posix::type_dispatcher::callback_base::trampoline<boost::log::v2_mt_posix::binder1st<boost::log::v2_mt_posix::output_fun, boost::log::v2_mt_posix::expressions::aux::stream_ref<boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator > >&>, std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator > >(void*, std::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&)': main.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7cxx1112basic_stringIwSBIwESaIwEEEEEvPvRKT0[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7cxx1112basic_stringIwSBIwESaIwEEEEEvPvRKT0]+0x6e): undefined reference to boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)' CMakeFiles/graphtyper.dir/main.cpp.o: In functionboost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend >::consume(boost::log::v2_mt_posix::record_view const&)': main.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0xb9): undefined reference to `boost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/graphtyper.dir/main.cpp.o: In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)': main.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0xb9): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/graphtyper.dir/main.cpp.o: In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)': main.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0xd6): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/graphtyper.dir/main.cpp.o: In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)': main.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0xd6): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/graphtyper_objects.dir/graph/genomic_region.cpp.o: In function void gyper::GenomicRegion::serialize<boost::archive::binary_oarchive>(boost::archive::binary_oarchive&, unsigned int)': genomic_region.cpp:(.text._ZN5gyper13GenomicRegion9serializeIN5boost7archive15binary_oarchiveEEEvRT_j[_ZN5gyper13GenomicRegion9serializeIN5boost7archive15binary_oarchiveEEEvRT_j]+0x5c): undefined reference toboost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/graphtyper_objects.dir/graph/genomic_region.cpp.o: In function void gyper::GenomicRegion::serialize<boost::archive::binary_iarchive>(boost::archive::binary_iarchive&, unsigned int)': genomic_region.cpp:(.text._ZN5gyper13GenomicRegion9serializeIN5boost7archive15binary_iarchiveEEEvRT_j[_ZN5gyper13GenomicRegion9serializeIN5boost7archive15binary_iarchiveEEEvRT_j]+0x51): undefined reference toboost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive, char, std::char_traits >::load(std::cxx11::basic_string<char, std::char_traits, std::allocator >&)' CMakeFiles/graphtyper_objects.dir/graph/graph_serialization.cpp.o: In function boost::archive::detail::common_iarchive<boost::archive::binary_iarchive>::vload(boost::archive::class_name_type&)': graph_serialization.cpp:(.text._ZN5boost7archive6detail15common_iarchiveINS0_15binary_iarchiveEE5vloadERNS0_15class_name_typeE[_ZN5boost7archive6detail15common_iarchiveINS0_15binary_iarchiveEE5vloadERNS0_15class_name_typeE]+0x3): undefined reference toboost::archive::basic_binary_iarchive::load_override(boost::archive::class_name_type&, int)' CMakeFiles/graphtyper_objects.dir/graph/graph_serialization.cpp.o: In function boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::vsave(boost::archive::class_name_type const&)': graph_serialization.cpp:(.text._ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE[_ZN5boost7archive6detail15common_oarchiveINS0_15binary_oarchiveEE5vsaveERKNS0_15class_name_typeE]+0x7d): undefined reference toboost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive, char, std::char_traits >::save(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)' collect2: error: ld returned 1 exit status src/CMakeFiles/graphtyper.dir/build.make:195: recipe for target 'bin/graphtyper' failed make[3]: [bin/graphtyper] Error 1 CMakeFiles/Makefile2:278: recipe for target 'src/CMakeFiles/graphtyper.dir/all' failed make[2]: [src/CMakeFiles/graphtyper.dir/all] Error 2 CMakeFiles/Makefile2:290: recipe for target 'src/CMakeFiles/graphtyper.dir/rule' failed make[1]: [src/CMakeFiles/graphtyper.dir/rule] Error 2 Makefile:238: recipe for target 'graphtyper' failed make: [graphtyper] Error 2

Hi. We are getting very close... thank you for your patience :)

But there seems to be problem linking to boost. Can you check for me if Boost was compiled using the same GCC compiler?

If you have the "strings" utility you can check it with:

$ strings -a $BOOST_ROOT/lib/libboost_log.so | grep GNU
GCC: (GNU) 5.4.0

Best regards, Hannes

Hi Hannes, thanks for all your help.

libtool was definitely helpful by the way.

Boost is the precompiled Ubuntu 16.04 version and does not include the path /lib/

ls /usr/include/boost/

accumulators cstdlib.hpp algorithm current_function.hpp align cxx11_char_types.hpp aligned_storage.hpp date_time align.hpp date_time.hpp any.hpp detail archive dynamic_bitset array.hpp dynamic_bitset_fwd.hpp asio dynamic_bitset.hpp asio.hpp enable_shar assert.hpp endian assign exception assign.hpp exception_ptr.hpp atomic filesystem atomic.hpp filesystem.hpp bimap flyweight bimap.hpp flyweight.hpp bind foreach_fwd.hpp bind.hpp foreach.hpp blank_fwd.hpp format blank.hpp format.hpp call_traits.hpp function cast.hpp functional cerrno.hpp functional.hpp checked_delete.hpp function_equal.hpp chrono function.hpp chrono.hpp function_ou circular_buffer function_types circular_buffer_fwd.hpp fusion circular_buffer.hpp generator_iterator.hpp compatibility geometry compressed_pair.hpp geometry.hpp concept get_pointer.hpp concept_archetype.hpp gil concept_check graph concept_check.hpp heap config icl config.hpp implicit_cast.hpp container indirect_reference.hpp context integer core integer_fwd.hpp coroutine integer.hpp crc.hpp integer_traits.hpp cregex.hpp interprocess cstdfloat.hpp intrusive cstdint.hpp intrusive_ptr.hpp io parameter signals2 io_fwd.hpp parameter.hpp signals2.hpp iostreams pending signals.hpp is_placeholder.hpp phoenix smart_ptr iterator phoenix.hpp smart_ptr.hpp iterator_adaptors.hpp pointee.hpp sort iterator.hpp pointer_cast.hpp spirit lambda pointer_to_other.hpp spirit.hpp last_value.hpp polygon statechart ed_from_this.hpp lexical_cast polymorphic_cast.hpp static_assert.hpp lexical_cast.hpp polymorphic_pointer_cast.hpp swap.hpp limits.hpp pool system locale predef test locale.hpp predef.h thread local_function preprocessor thread.hpp local_function.hpp preprocessor.hpp throw_exception.hpp lockfree program_options timer log program_options.hpp timer.hpp logic progress.hpp token_functions.hpp make_shared.hpp property_map token_iterator.hpp make_unique.hpp property_tree tokenizer.hpp math proto tr1 math_fwd.hpp ptr_container tti mem_fn.hpp python tuple memory_order.hpp python.hpp type_erasure move random type.hpp tput_iterator.hpp mpi random.hpp type_index mpi.hpp range type_index.hpp mpl range.hpp typeof msm ratio type_traits multi_array ratio.hpp type_traits.hpp multi_array.hpp rational.hpp units multi_index ref.hpp unordered multi_index_container_fwd.hpp regex unordered_map.hpp multi_index_container.hpp regex_fwd.hpp unordered_set.hpp multiprecision regex.h utility next_prior.hpp regex.hpp utility.hpp noncopyable.hpp scoped_array.hpp uuid nondet_random.hpp scoped_ptr.hpp variant none.hpp scope_exit.hpp variant.hpp none_t.hpp serialization version.hpp non_type.hpp shared_array.hpp visit_each.hpp numeric shared_container_iterator.hpp wave operators.hpp shared_ptr.hpp wave.hpp optional signal.hpp weak_ptr.hpp optional.hpp signals xpressive

Have I installed all the necessary boost packages? (see installed below)

sudo apt list boost Listing... Done dm-writeboost-dkms/xenial-updates,xenial-updates 2.1.1-1ubuntu1 all libboost-all-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-atomic-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-atomic1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-atomic1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-chrono-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-chrono1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-chrono1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-context-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-context1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-context1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-coroutine-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-coroutine1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-coroutine1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-date-time-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-date-time1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-date-time1.58.0/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed,automatic] libboost-dbg/xenial 1.58.0.1ubuntu1 amd64 libboost-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-doc/xenial,xenial 1.58.0.1ubuntu1 all libboost-exception-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-exception1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-filesystem-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-filesystem1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-filesystem1.58.0/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed,automatic] libboost-geometry-utils-perl/xenial 0.15-2build2 amd64 libboost-graph-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-graph-parallel-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-graph-parallel1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-graph-parallel1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-graph1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-graph1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-iostreams-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-iostreams1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-iostreams1.58.0/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed,automatic] libboost-locale-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-locale1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-locale1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-log-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-log1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-log1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-math-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-math1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-math1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-mpi-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-mpi-python-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-mpi-python1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-mpi-python1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-mpi1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-mpi1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-program-options-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-program-options1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-program-options1.58.0/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed,automatic] libboost-python-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-python1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-python1.58.0/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed,automatic] libboost-random-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-random1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-random1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-regex-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-regex1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-regex1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-serialization-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-serialization1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-serialization1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-signals-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-signals1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-signals1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-system-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-system1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-system1.58.0/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed,automatic] libboost-test-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-test1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-test1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-thread-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-thread1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-thread1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-timer-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-timer1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-timer1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-tools-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-wave-dev/xenial 1.58.0.1ubuntu1 amd64 libboost-wave1.58-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost-wave1.58.0/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost1.58-all-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost1.58-dbg/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libboost1.58-dev/xenial-updates,now 1.58.0+dfsg-5ubuntu3.1 amd64 [installed] libboost1.58-doc/xenial-updates,xenial-updates 1.58.0+dfsg-5ubuntu3.1 all libboost1.58-tools-dev/xenial-updates 1.58.0+dfsg-5ubuntu3.1 amd64 libodb-boost-2.4/xenial-updates 2.4.0-1build0~16.04.1 amd64 libodb-boost-dev/xenial-updates 2.4.0-1build0~16.04.1 amd64 pianobooster/xenial 0.6.4.0-1 amd64 pianobooster-dbg/xenial 0.6.4.0-1 amd64 python-rosboost-cfg/xenial,xenial 1.12.5-4 all writeboost/xenial,xenial 1.20150630-1 all

Thanks, Colin

Hey Colin. I see you have installed libboost1.58-all-dev which should include everything you need.

Can you try for me:

export LD_LIBRARY_PATH=/usr/lib/:$LD_LIBRARY_PATH

and then try making again?

If that does not work, can you show me the output of ls -l /usr/lib/libboost*.so?

And although I don't think it is the cause of the problem, you may also want to try to set

export BOOST_ROOT=/usr

and try making again.

Best regards, Hannes

Hi,

after using both export commands recompiling failed like before.

There are no libboost files in /usr/lib/

Looking further:

find /usr/lib -name "libboost*" /usr/lib/x86_64-linux-gnu/libboost_python-py35.so.1.58.0 /usr/lib/x86_64-linux-gnu/libboost_date_time.so.1.58.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.58.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.58.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.58.0 /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.58.0

Colin

Hey Colin, thanks.

This is very odd, something seems to be wrong with the Boost installation on your system. For example, before you listed that the package libboost-log1.58-dev was installed but you are missing its files (see: https://packages.ubuntu.com/xenial/amd64/libboost-log1.58-dev/filelist).

Can you try reinstalling libboost1.58-all-dev?

Best regards, Hannes

Hey again.

Sorry, I see now that the list you sent me before was not a list of all your installed packages, but rather only a few of those packages are installed. You need to install libboost1.58-all-dev.

Because CMake might have put in cache that you don't have Boost library files, can you install libboost1.58-all-dev and then start the build process from the beginning?

Best, Hannes

Hi Hannes,

that did the trick, thanks, after removing the directory, recloning and recompiling.

I'll run the tests to check things are working.

[ 97%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/sam_reader.cpp.o [ 98%] Building CXX object src/CMakeFiles/graphtyper_objects.dir/utilities/options.cpp.o [ 98%] Built target graphtyper_objects Scanning dependencies of target graphtyper [ 98%] Building CXX object src/CMakeFiles/graphtyper.dir/main.cpp.o [100%] Linking CXX executable ../bin/graphtyper [100%] Built target graphtyper

Colin

Hey Colin. That's awesome!

If you want to run Graphtyper on some data I recommend to use this pipeline.

Cheers, Hannes

DecodeGenetics / graphtyper

multiple errors while compiling. #2

Ubuntu 16.04 packages