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alekseyzimin / masurca

GNU General Public License v3.0
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Building from github release 3.3.3 does not work #116

Closed samfux84 closed 5 years ago

samfux84 commented 5 years ago

Hi,

I am trying to build masurca 3.3.3 from the release provided on github.

When running the install.sh script, I get lots of error messages:

++ pwd -P
+ ROOT=/cluster/apps/gdc/masurca/3.3.3
+ '[' -z '' ']'
+ DEST=/cluster/apps/gdc/masurca/3.3.3
+ mkdir -p dist-bin
+ PATH=/cluster/apps/gdc/swig/3.0.8/bin:/cluster/project/gdc/shared/scripts:/cluster/apps/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/cluster/apps/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/usr/lib64/qt-3.3/bin:/cluster/apps/modules/bin:/cluster/apps/gcc/4.8.2/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/apps/local:/cluster/home/sfux/bin:/cluster/apps/ansys/v170/fluent/bin:/cluster/apps/adm:/cluster/home/sfux/shellscript:/cluster/home/sfux/prog/bash:/cluster/apps/local:/cluster/apps/local:/opt/ibutils/bin:/cluster/apps/gdc/masurca/3.3.3/dist-bin
++ which make
+ ln -sf /usr/bin/make /cluster/apps/gdc/masurca/3.3.3/dist-bin/gmake
+ ln -sf /cluster/apps/gdc/masurca/3.3.3/PkgConfig.pm /cluster/apps/gdc/masurca/3.3.3/dist-bin/pkg-config
++ grep -c '^processor' /proc/cpuinfo
+ export NUM_THREADS=48
+ NUM_THREADS=48
+ BINDIR=/cluster/apps/gdc/masurca/3.3.3/bin
+ LIBDIR=/cluster/apps/gdc/masurca/3.3.3/lib
+ export PKG_CONFIG_PATH=/cluster/apps/gdc/masurca/3.3.3/lib/pkgconfig:
+ PKG_CONFIG_PATH=/cluster/apps/gdc/masurca/3.3.3/lib/pkgconfig:
+ cd global-1
+ ./configure --prefix=/cluster/apps/gdc/masurca/3.3.3 --bindir=/cluster/apps/gdc/masurca/3.3.3/bin --libdir=/cluster/apps/gdc/masurca/3.3.3/lib
checking build system type... x86_64-unknown-linux-gnu
checking host 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... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... /cluster/apps/gcc/4.8.2/bin/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 /cluster/apps/gcc/4.8.2/bin/gcc accepts -g... yes
checking for /cluster/apps/gcc/4.8.2/bin/gcc option to accept ISO C89... none needed
checking whether /cluster/apps/gcc/4.8.2/bin/gcc understands -c and -o together... yes
checking dependency style of /cluster/apps/gcc/4.8.2/bin/gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by /cluster/apps/gcc/4.8.2/bin/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... 3458764513820540925
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 /cluster/apps/gcc/4.8.2/bin/gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... /cluster/apps/gcc/4.8.2/bin/cpp
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 /cluster/apps/gcc/4.8.2/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for /cluster/apps/gcc/4.8.2/bin/gcc option to produce PIC... -fPIC -DPIC
checking if /cluster/apps/gcc/4.8.2/bin/gcc PIC flag -fPIC -DPIC works... yes
checking if /cluster/apps/gcc/4.8.2/bin/gcc static flag -static works... yes
checking if /cluster/apps/gcc/4.8.2/bin/gcc supports -c -o file.o... yes
checking if /cluster/apps/gcc/4.8.2/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /cluster/apps/gcc/4.8.2/bin/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 gcc... (cached) /cluster/apps/gcc/4.8.2/bin/gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether /cluster/apps/gcc/4.8.2/bin/gcc accepts -g... (cached) yes
checking for /cluster/apps/gcc/4.8.2/bin/gcc option to accept ISO C89... (cached) none needed
checking whether /cluster/apps/gcc/4.8.2/bin/gcc understands -c and -o together... (cached) yes
checking dependency style of /cluster/apps/gcc/4.8.2/bin/gcc... (cached) gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether /cluster/apps/gcc/4.8.2/bin/g++ accepts -g... yes
checking dependency style of /cluster/apps/gcc/4.8.2/bin/g++... gcc3
checking how to run the C++ preprocessor... /cluster/apps/gcc/4.8.2/bin/g++ -E
checking for ld used by /cluster/apps/gcc/4.8.2/bin/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 /cluster/apps/gcc/4.8.2/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /cluster/apps/gcc/4.8.2/bin/g++ option to produce PIC... -fPIC -DPIC
checking if /cluster/apps/gcc/4.8.2/bin/g++ PIC flag -fPIC -DPIC works... yes
checking if /cluster/apps/gcc/4.8.2/bin/g++ static flag -static works... yes
checking if /cluster/apps/gcc/4.8.2/bin/g++ supports -c -o file.o... yes
checking if /cluster/apps/gcc/4.8.2/bin/g++ supports -c -o file.o... (cached) yes
checking whether the /cluster/apps/gcc/4.8.2/bin/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 pthread_create in -lpthread... yes
checking for library containing clock_gettime... none required
checking for __int128... yes
checking for OpenMP flag of C++ compiler... -fopenmp
configure: Detected BOOST_ROOT; continuing with --with-boost=/cluster/apps/gdc/boost/1.55.0
checking for Boost headers version >= 1.46.0... /cluster/apps/gdc/boost/1.55.0/include
checking for Boost's header version... 1_55
checking boost/icl/interval_set.hpp usability... yes
checking boost/icl/interval_set.hpp presence... yes
checking for boost/icl/interval_set.hpp... yes
checking for _NSGetExecutablePath... no
checking if std::thread::sleep_for is supported... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for mremap... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for zlibVersion in -lz... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for __builtin_prefetch... yes
checking for architecture... Linux-amd64
checking for yaggo... /cluster/home/sfux/bin/yaggo
checking for perl... /usr/bin/perl
checking for Perl prefix... /usr
checking for Perl extension include path... /usr/lib64/perl5/CORE
checking for Perl extension target directory... $(libdir)/perl
checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
checking for Perl extensions linker flags... -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,-z,relro 
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating jellyfish/jellyfish-2.0.pc
config.status: creating MUMmer/mummer.pc
config.status: creating samtools/Makefile
config.status: creating prepare/Makefile
config.status: creating ufasta/Makefile
config.status: creating quorum/Makefile
config.status: creating SuperReads/Makefile
config.status: creating SOAPdenovo2/Makefile
config.status: creating PacBio/Makefile
config.status: creating CA8/Makefile
config.status: creating jellyfish/Makefile
config.status: creating MUMmer/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
+ make -j 48 install-special
Making install in jellyfish pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/jellyfish'
make  install-am
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/jellyfish'
  CXX      swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo
  CXXLD    bin/jellyfish
swig/perl5/swig_wrap.cpp:743:20: fatal error: EXTERN.h: No such file or directory
 #include "EXTERN.h"
                    ^
compilation terminated.
make[2]: *** [swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/jellyfish'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/jellyfish'
Making install in samtools pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/samtools'
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/samtools'
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/lib'
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/include/samtools/bcftools'
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/include/samtools'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libbam.la bcftools/libbcf.la '/cluster/apps/gdc/masurca/3.3.3/lib'
 /usr/bin/install -c -m 644 bam.h bam2bcf.h bam_endian.h bgzf.h errmod.h faidx.h kaln.h khash.h klist.h knetfile.h kprobaln.h kseq.h ksort.h kstring.h razf.h sam.h sam_header.h sample.h bam_tview.h '/cluster/apps/gdc/masurca/3.3.3/include/samtools'
 /usr/bin/install -c -m 644 bcftools/bcf.h bcftools/kmin.h bcftools/prob1.h '/cluster/apps/gdc/masurca/3.3.3/include/samtools/bcftools'
libtool: install: /usr/bin/install -c .libs/libbam.so.0.0.0 /cluster/apps/gdc/masurca/3.3.3/lib/libbam.so.0.0.0
libtool: install: (cd /cluster/apps/gdc/masurca/3.3.3/lib && { ln -s -f libbam.so.0.0.0 libbam.so.0 || { rm -f libbam.so.0 && ln -s libbam.so.0.0.0 libbam.so.0; }; })
libtool: install: (cd /cluster/apps/gdc/masurca/3.3.3/lib && { ln -s -f libbam.so.0.0.0 libbam.so || { rm -f libbam.so && ln -s libbam.so.0.0.0 libbam.so; }; })
libtool: install: /usr/bin/install -c .libs/libbam.lai /cluster/apps/gdc/masurca/3.3.3/lib/libbam.la
libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.so.0.0.0 /cluster/apps/gdc/masurca/3.3.3/lib/libbcf.so.0.0.0
libtool: install: (cd /cluster/apps/gdc/masurca/3.3.3/lib && { ln -s -f libbcf.so.0.0.0 libbcf.so.0 || { rm -f libbcf.so.0 && ln -s libbcf.so.0.0.0 libbcf.so.0; }; })
libtool: install: (cd /cluster/apps/gdc/masurca/3.3.3/lib && { ln -s -f libbcf.so.0.0.0 libbcf.so || { rm -f libbcf.so && ln -s libbcf.so.0.0.0 libbcf.so; }; })
libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.lai /cluster/apps/gdc/masurca/3.3.3/lib/libbcf.la
libtool: install: /usr/bin/install -c .libs/libbam.a /cluster/apps/gdc/masurca/3.3.3/lib/libbam.a
libtool: install: chmod 644 /cluster/apps/gdc/masurca/3.3.3/lib/libbam.a
libtool: install: ranlib /cluster/apps/gdc/masurca/3.3.3/lib/libbam.a
libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.a /cluster/apps/gdc/masurca/3.3.3/lib/libbcf.a
libtool: install: chmod 644 /cluster/apps/gdc/masurca/3.3.3/lib/libbcf.a
libtool: install: ranlib /cluster/apps/gdc/masurca/3.3.3/lib/libbcf.a
libtool: finish: PATH="/cluster/apps/gdc/swig/3.0.8/bin:/cluster/project/gdc/shared/scripts:/cluster/apps/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/cluster/apps/lsf/10.1/linux2.6-glibc2.3-x86_64/bin:/usr/lib64/qt-3.3/bin:/cluster/apps/modules/bin:/cluster/apps/gcc/4.8.2/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/apps/local:/cluster/home/sfux/bin:/cluster/apps/ansys/v170/fluent/bin:/cluster/apps/adm:/cluster/home/sfux/shellscript:/cluster/home/sfux/prog/bash:/cluster/apps/local:/cluster/apps/local:/opt/ibutils/bin:/cluster/apps/gdc/masurca/3.3.3/dist-bin:/sbin" ldconfig -n /cluster/apps/gdc/masurca/3.3.3/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /cluster/apps/gdc/masurca/3.3.3/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c samtools '/cluster/apps/gdc/masurca/3.3.3/bin'
libtool: install: /usr/bin/install -c .libs/samtools /cluster/apps/gdc/masurca/3.3.3/bin/samtools
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/samtools'
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/samtools'
Making install in prepare pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/prepare'
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/prepare'
make[2]: Nothing to be done for `install-data-am'.
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c finalFusion '/cluster/apps/gdc/masurca/3.3.3/bin'
libtool: install: /usr/bin/install -c finalFusion /cluster/apps/gdc/masurca/3.3.3/bin/finalFusion
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/prepare'
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/prepare'
Making install in ufasta pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/ufasta'
make  install-am
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/ufasta'
make[3]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/ufasta'
make[3]: Nothing to be done for `install-data-am'.
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c ufasta '/cluster/apps/gdc/masurca/3.3.3/bin'
libtool: install: /usr/bin/install -c ufasta /cluster/apps/gdc/masurca/3.3.3/bin/ufasta
make[3]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/ufasta'
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/ufasta'
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/ufasta'
Making install in quorum pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/quorum'
make  install-am
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/quorum'
  CXX      src/error_correct_reads.o
  CXX      src/create_database.o
  CXX      src/merge_mate_pairs.o
  CXXLD    split_mate_pairs
  GEN      quorum
src/merge_mate_pairs.cc:4:40: fatal error: jellyfish/stream_manager.hpp: No such file or directory
 #include <jellyfish/stream_manager.hpp>
                                        ^
compilation terminated.
src/create_database.cc:23:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src/merge_mate_pairs.o] Error 1
/make[2]: usr*** Waiting for unfinished jobs..../
bin/ld: cannot find -ljellyfish-2.0
collect2: error: ld returned 1 exit status
make[2]: *** [src/create_database.o] Error 1
make[2]: *** [split_mate_pairs] Error 1
src/error_correct_reads.cc:25:36: fatal error: jellyfish/atomic_gcc.hpp: No such file or directory
 #include <jellyfish/atomic_gcc.hpp>
                                    ^
compilation terminated.
make[2]: *** [src/error_correct_reads.o] Error 1
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/quorum'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/quorum'
Making install in SuperReads pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SuperReads'
make  install-am
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SuperReads'
  AR       libutils.a
  CXX      src/error_corrected2frg.o
  CXX      src/create_k_unitigs_large_k.o
  CXX      src/sorted_merge.o
  CXX      src/create_k_unitigs_large_k2.o
  CXX      src/bloom_query.o
  CXX      src/filter_overlap_file.o
  CXX      src/rename_filter_fastq.o
  CXX      src/read_parser.o
  CXX      src2/findMatchesBetweenKUnitigsAndReads.o
  CXX      src2/createKUnitigMaxOverlaps.o
mkdir -p src/
  CXX      src2/getSuperReadInsertCountsFromReadPlacementFile.o
  CXX      src2/joinKUnitigs_v3.o
  CXX      src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o
  CXX      src2/collectReadSequencesForLocalGapClosing.o
  CXX      src2/runByDirectory.o
sed -e 's,[@]bindir[@],/cluster/apps/gdc/masurca/3.3.3/bin,g' \
    -e 's,[@]libdir[@],/cluster/apps/gdc/masurca/3.3.3/lib,g' \
    -e 's,[@]PERL_EXT_DIR[@],/cluster/apps/gdc/masurca/3.3.3/lib/perl,g' < src/MasurcaPaths.pm.in > src/MasurcaPaths.pm
src2/findMatchesBetweenKUnitigsAndReads.cc:31:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src2/findMatchesBetweenKUnitigsAndReads.o] Error 1
make[2]: *** Waiting for unfinished jobs....
chmod +x src/MasurcaPaths.pm
src/rename_filter_fastq.cc:21:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
src/error_corrected2frg.cc:24:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
src/bloom_query.cc:2:37: fatal error: jellyfish/mapped_file.hpp: No such file or directory
 #include <jellyfish/mapped_file.hpp>
                                     ^
compilation terminated.
make[2]: *** [src/rename_filter_fastq.o] Error 1
make[2]: *** [src/error_corrected2frg.o] Error 1
make[2]: *** [src/bloom_query.o] Error 1
src/filter_overlap_file.cc:23:35: fatal error: jellyfish/jellyfish.hpp: No such file or directory
 #include <jellyfish/jellyfish.hpp>
                                   ^
compilation terminated.
src2/createKUnitigMaxOverlaps.cc:65:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src/filter_overlap_file.o] Error 1
make[2]: *** [src2/createKUnitigMaxOverlaps.o] Error 1
In file included from ./include/jflib/multiplexed_parser.hpp:26:0,
                 from ./src/read_parser.hpp:24,
                 from src/read_parser.cc:19:
./include/jflib/pool.hpp:22:41: fatal error: jellyfish/circular_buffer.hpp: No such file or directory
 #include <jellyfish/circular_buffer.hpp>
                                         ^
compilation terminated.
src2/getSuperReadInsertCountsFromReadPlacementFile.cc:27:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src/read_parser.o] Error 1
make[2]: *** [src2/getSuperReadInsertCountsFromReadPlacementFile.o] Error 1
src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.cc:27:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o] Error 1
src2/collectReadSequencesForLocalGapClosing.cc:19:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src2/collectReadSequencesForLocalGapClosing.o] Error 1
src2/joinKUnitigs_v3.cc:48:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src2/joinKUnitigs_v3.o] Error 1
In file included from src/create_k_unitigs_large_k.cc:25:0:
./src/create_k_unitigs_common.hpp:21:37: fatal error: jellyfish/thread_exec.hpp: No such file or directory
 #include <jellyfish/thread_exec.hpp>
                                     ^
compilation terminated.
make[2]: *** [src/create_k_unitigs_large_k.o] Error 1
src2/runByDirectory.cc:20:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src2/runByDirectory.o] Error 1
src/create_k_unitigs_large_k2.cc:24:35: fatal error: jellyfish/jellyfish.hpp: No such file or directory
 #include <jellyfish/jellyfish.hpp>
                                   ^
compilation terminated.
make[2]: *** [src/create_k_unitigs_large_k2.o] Error 1
src/sorted_merge.cc:29:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src/sorted_merge.o] Error 1
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SuperReads'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SuperReads'
Making install in SOAPdenovo2 pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SOAPdenovo2'
  CC       standardPregraph/libstandard63_a-readseq1by1.o
  CXX      sparsePregraph/libsparse63_a-build_preArc.o
  CXX      sparsePregraph/libsparse63_a-io_func.o
  CC       standardPregraph/libstandard127_a-readseq1by1.o
  CXX      sparsePregraph/libsparse127_a-build_preArc.o
  CXX      sparsePregraph/libsparse127_a-io_func.o
  AR       libstandard63.a
  AR       libstandard127.a
  AR       libsparse63.a
  GEN      SOAPdenovo-63mer
  AR       libsparse127.a
  GEN      SOAPdenovo-127mer
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SOAPdenovo2'
make[2]: Nothing to be done for `install-data-am'.
 /usr/bin/mkdir -p '/cluster/apps/gdc/masurca/3.3.3/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c SOAPdenovo-63mer SOAPdenovo-127mer '/cluster/apps/gdc/masurca/3.3.3/bin'
libtool: install: /usr/bin/install -c SOAPdenovo-63mer /cluster/apps/gdc/masurca/3.3.3/bin/SOAPdenovo-63mer
libtool: install: /usr/bin/install -c SOAPdenovo-127mer /cluster/apps/gdc/masurca/3.3.3/bin/SOAPdenovo-127mer
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SOAPdenovo2'
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/SOAPdenovo2'
Making install in PacBio pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/PacBio'
make  install-am
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/PacBio'
  CXX      src_jf_aligner/jf_aligner.o
  CXX      src_jf_aligner/pb_aligner.o
  CXX      src_jf_aligner/superread_parser.o
  CXX      src_jf_aligner/coarse_aligner.o
  CXX      src_jf_aligner/fine_aligner.o
  CXX      src_jf_aligner/create_mega_reads.o
  CXX      src_jf_aligner/longest_path_overlap_graph2.o
  CXX      src_jf_aligner/overlap_graph.o
  CXX      src_jf_aligner/coords_parsing.o
  CXX      src_jf_aligner/merge_coords.o
  CXXLD    bin/get_super_read_sizes
  CXXLD    bin/findGapsInCoverageOfPacbios
In file included from src_jf_aligner/superread_parser.cc:6:0:
./src_jf_aligner/superread_parser.hpp:8:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src_jf_aligner/superread_parser.o] Error 1
make[2]: *** Waiting for unfinished jobs....
In file included from src_jf_aligner/jf_aligner.cc:8:0:
./src_jf_aligner/superread_parser.hpp:8:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src_jf_aligner/jf_aligner.o] Error 1
In file included from src_jf_aligner/create_mega_reads.cc:8:0:
./src_jf_aligner/superread_parser.hpp:8:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src_jf_aligner/create_mega_reads.o] Error 1
In file included from ./include/jflib/multiplexed_parser.hpp:26:0,
                 from ./src_jf_aligner/coords_parsing.hpp:10,
                 from src_jf_aligner/merge_coords.cc:7:
./include/jflib/pool.hpp:22:41: fatal error: jellyfish/circular_buffer.hpp: No such file or directory
 #include <jellyfish/circular_buffer.hpp>
                                         ^
compilation terminated.
In file included from src_jf_aligner/longest_path_overlap_graph2.cc:9:0:
./src_jf_aligner/output_file.hpp:9:29: fatal error: jellyfish/err.hpp: No such file or directory
 #include <jellyfish/err.hpp>
                             ^
compilation terminated.
make[2]: *** [src_jf_aligner/merge_coords.o] Error 1
make[2]: *** [src_jf_aligner/longest_path_overlap_graph2.o] Error 1
/In file included from ./include/jflib/multiplexed_parser.hpp:26:0,
                 from ./src_jf_aligner/coords_parsing.hpp:10,
                 from src_jf_aligner/coords_parsing.cc:4:
./include/jflib/pool.hpp:22:41: fatal error: jellyfish/circular_buffer.hpp: No such file or directory
 #include <jellyfish/circular_buffer.hpp>
                                         ^
usr/bin/ldcompilation terminated.
: cannot find -ljellyfish-2.0
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -ljellyfish-2.0
collect2: error: ld returned 1 exit status
make[2]: *** [src_jf_aligner/coords_parsing.o] Error 1
make[2]: *** [bin/findGapsInCoverageOfPacbios] Error 1
make[2]: *** [bin/get_super_read_sizes] Error 1
In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
                 from src_jf_aligner/pb_aligner.cc:8:
./src_jf_aligner/jf_aligner.hpp:14:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
In file included from ./src_jf_aligner/fine_aligner.hpp:7:0,
                 from src_jf_aligner/fine_aligner.cc:4:
./src_jf_aligner/jf_aligner.hpp:14:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src_jf_aligner/fine_aligner.o] Error 1
make[2]: *** [src_jf_aligner/pb_aligner.o] Error 1
In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
                 from ./src_jf_aligner/coarse_aligner.hpp:10,
                 from src_jf_aligner/coarse_aligner.cc:4:
./src_jf_aligner/jf_aligner.hpp:14:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src_jf_aligner/coarse_aligner.o] Error 1
In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
                 from ./src_jf_aligner/overlap_graph.hpp:9,
                 from src_jf_aligner/overlap_graph.cc:4:
./src_jf_aligner/jf_aligner.hpp:14:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 #include <jellyfish/mer_dna.hpp>
                                 ^
compilation terminated.
make[2]: *** [src_jf_aligner/overlap_graph.o] Error 1
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/PacBio'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/PacBio'
Making install in MUMmer pwd /cluster/apps/gdc/masurca/3.3.3/global-1
make[1]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/MUMmer'
make  install-am
make[2]: Entering directory `/cluster/apps/gdc/masurca/3.3.3/global-1/MUMmer'
  CXXLD    libumdmummer.la
  CXX      swig/perl5/swig_perl5_mummer_la-swig_wrap.lo
swig/perl5/swig_wrap.cpp:743:20: fatal error: EXTERN.h: No such file or directory
 #include "EXTERN.h"
                    ^
compilation terminated.
make[2]: *** [swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/MUMmer'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/cluster/apps/gdc/masurca/3.3.3/global-1/MUMmer'
make: *** [install-special] Error 2
samfux84 commented 5 years ago

Could solve the problem by changing the perl version

VimacN commented 5 years ago

Hi, I have the same issue. Could you explain how you changed the perl version?

Thanks.

samfux84 commented 5 years ago

On our cluster, we have a perl installation that comes with the operating system. I just installed a newer perl version with perlbrew (https://perlbrew.pl/) in user space.

VimacN commented 5 years ago

Thanks it worked!