Need help compiling GapFiller

[jmarshall]

GapFiller's src/Makefile.am has been updated to account for a linking change in the last few years (cf ld --add-needed), but unfortunately the rest of its build infrastructure has not been regenerated accordingly.

So before running configure, you need to run autoreconf yourself to regenerate src/Makefile.in etc:

autoreconf
./configure
make

You will need to have autoconf and automake available.

Having fixed this, you may get undefined symbol errors about __ks_insertsort_off(), packInt16(), packInt32(), and unpackInt16(). To fix these, find the __ks_insertsort_##name() definition in src/samtools/ksort.h and the three *packInt*() definitions in src/samtools/bgzf.c, and change "inline" to "static inline".

[GenoMax]

I suggest that you google "/lib/x86_64-linux-gnu/libz.so.1: error adding symbols: DSO missing from command line" and see some of the suggestions that come up.

[robalba1]

Just tried "make clean" followed by ./configure LIBS="-lz" and then a make again and that did not solve the problem. It still throws the same error(s).

[GenoMax]

Have you tried a "make clean" followed by ./configure LIBS="-lz" and then a make again?

[robalba1]

Hi GenoMax,

Thanks for the rapid reply. I appreciate it very much

I previously looked at http://seqanswers.com/forums/showthread.php?t=47998, and many other suggested solutions for errors that appear similar to the one I get. I tried ./configure LIBS="-lz" previously and it did not solve my problem. That said, in my makefile the LIBS line reads: LIBS = -lz.

I installed the zlib previously, and $locate zlib indicates that it is installed. That does not mean I installed the zlib correctly or that I am pointing to it correctly.

Can I safely assume that a zlib installation, for this purpose, follows a typical linux install process?

Rob

[GenoMax]

See if this helps: http://seqanswers.com/forums/showthread.php?t=47998

If you have zlib missing from your system then you would need to install it first.

[robalba1]

Hello,

I have been unsuccessful compiling GapFiller on my ThinkMate genomics workstation (Ubuntu 16.04 OS). I think it is a library link issue, but am not 100% certain of that. I am probably overlooking something obvious.

The output from my ./configure and my make commands is below.

Any guidance would be greatly appreciated.

Rob





rob@linux:~/.linuxbrew/Cellar/gapfiller-2.1.1$ ./configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
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 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... 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 dependency style of gcc... gcc3
checking whether gcc and cc understand -c and -o together... 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 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 for stdbool.h that conforms to C99... yes
checking for _Bool... no
checking for inline... inline
checking for size_t... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking iostream usability... yes
checking iostream presence... yes
checking for iostream... yes
checking fstream usability... yes
checking fstream presence... yes
checking for fstream... yes
checking string usability... yes
checking string presence... yes
checking for string... yes
checking vector usability... yes
checking vector presence... yes
checking for vector... yes
checking exception usability... yes
checking exception presence... yes
checking for exception... yes
checking sstream usability... yes
checking sstream presence... yes
checking for sstream... yes
checking how to print strings... printf
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 whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-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
file: compiled magic version [524] does not match with shared library magic version [528]
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 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 for Boost headers version >= 1.40.0... yes
checking for Boost's header version...
checking for the toolset name used by Boost for g++... configure: WARNING: could not figure out which toolset name to use for g++

checking boost/iostreams/device/file_descriptor.hpp usability... yes
checking boost/iostreams/device/file_descriptor.hpp presence... yes
checking for boost/iostreams/device/file_descriptor.hpp... yes
checking for the Boost iostreams library... yes
checking boost/program_options.hpp usability... yes
checking boost/program_options.hpp presence... yes
checking for boost/program_options.hpp... yes
checking for the Boost program_options library... yes
checking for 64 bit architecture... yes
======================================
Compiling with 64 bit
======================================
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
rob@linux:~/.linuxbrew/Cellar/gapfiller-2.1.1$ make
Making all in src
make[1]: Entering directory '/home/rob/.linuxbrew/Cellar/gapfiller-2.1.1/src'
/bin/bash ../libtool --tag=CXX --mode=link g++ -O0 -g3 -fpermissive -DDEBUG -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -m64 -DCPU_64 -lboost_program_options -lboost_iostreams-mt -o GapFiller_debug GapFiller_debug-GapFiller.o data_structures/GapFiller_debug-Hash.o data_structures/GapFiller_debug-Reads.o data_structures/GapFiller_debug-Contig.o data_structures/GapFiller_debug-Contig_layout.o data_structures/GapFiller_debug-Layout_list.o data_structures/GapFiller_debug-Layout_vector.o io/GapFiller_debug-Auto_Unzip.o io/GapFiller_debug-Auto_Zip.o io/GapFiller_debug-Fastq.o io/GapFiller_debug-Sam.o io/GapFiller_debug-Binary.o errors/GapFiller_debug-Data_Exception.o errors/GapFiller_debug-Data_Not_Found.o errors/GapFiller_debug-File_Not_Found.o errors/GapFiller_debug-Generic_Exception.o errors/GapFiller_debug-Incorrect_Format.o options/GapFiller_debug-Menu.o options/GapFiller_debug-Options.o options/GapFiller_debug-Singleton.o modules/GapFiller_debug-Assembly.o modules/GapFiller_debug-Assembly_only_sequence.o modules/GapFiller_debug-Assembly_store_layout.o samtools/GapFiller_debug-bam_aux.o samtools/GapFiller_debug-bam_import.o samtools/GapFiller_debug-bam_pileup.o samtools/GapFiller_debug-bam_index.o samtools/GapFiller_debug-bam.o samtools/GapFiller_debug-bgzf.o samtools/GapFiller_debug-faidx.o samtools/GapFiller_debug-knetfile.o samtools/GapFiller_debug-kstring.o samtools/GapFiller_debug-razf.o samtools/GapFiller_debug-sam.o samtools/GapFiller_debug-sam_header.o
libtool: link: g++ -O0 -g3 -fpermissive -DDEBUG -Wall -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -m64 -DCPU_64 -o GapFiller_debug GapFiller_debug-GapFiller.o data_structures/GapFiller_debug-Hash.o data_structures/GapFiller_debug-Reads.o data_structures/GapFiller_debug-Contig.o data_structures/GapFiller_debug-Contig_layout.o data_structures/GapFiller_debug-Layout_list.o data_structures/GapFiller_debug-Layout_vector.o io/GapFiller_debug-Auto_Unzip.o io/GapFiller_debug-Auto_Zip.o io/GapFiller_debug-Fastq.o io/GapFiller_debug-Sam.o io/GapFiller_debug-Binary.o errors/GapFiller_debug-Data_Exception.o errors/GapFiller_debug-Data_Not_Found.o errors/GapFiller_debug-File_Not_Found.o errors/GapFiller_debug-Generic_Exception.o errors/GapFiller_debug-Incorrect_Format.o options/GapFiller_debug-Menu.o options/GapFiller_debug-Options.o options/GapFiller_debug-Singleton.o modules/GapFiller_debug-Assembly.o modules/GapFiller_debug-Assembly_only_sequence.o modules/GapFiller_debug-Assembly_store_layout.o samtools/GapFiller_debug-bam_aux.o samtools/GapFiller_debug-bam_import.o samtools/GapFiller_debug-bam_pileup.o samtools/GapFiller_debug-bam_index.o samtools/GapFiller_debug-bam.o samtools/GapFiller_debug-bgzf.o samtools/GapFiller_debug-faidx.o samtools/GapFiller_debug-knetfile.o samtools/GapFiller_debug-kstring.o samtools/GapFiller_debug-razf.o samtools/GapFiller_debug-sam.o samtools/GapFiller_debug-sam_header.o -lboost_program_options -lboost_iostreams-mt
/usr/bin/ld: samtools/GapFiller_debug-bam_import.o: undefined reference to symbol 'gzdopen'
//lib/x86_64-linux-gnu/libz.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:608: recipe for target 'GapFiller_debug' failed
make[1]: *** [GapFiller_debug] Error 1
make[1]: Leaving directory '/home/rob/.linuxbrew/Cellar/gapfiller-2.1.1/src'
Makefile:298: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1