Problem compiling

[david vilanova]

Hi, I´m trying to use metabat however i have a coupe of problems. I have downloaded the binary static version provided here but it looks like some libraries are still shared...

#!

 ./metabat 
./metabat: /usr/lib64/libgomp.so.1: version `GOMP_4.0' not found (required by ./metabat)

I have tried to compile myself downloading the master release from here as well. I have libboost_1_5-9 properly installed and found.

Got this problem:

#!


g++ -o src/metabat.o -c -O3 -Wall -g -fopenmp -DNDEBUG -I/home/david/work/libs/include src/metabat.cpp
src/metabat.cpp:55: error: using ‘typename’ outside of template
src/metabat.cpp:56: error: using ‘typename’ outside of template
src/metabat.cpp:57: error: using ‘typename’ outside of template
scons: *** [src/metabat.o] Error 1
scons: building terminated because of errors.

How can i move forward ?

[Don Kang]

Can you paste your command line and entire output for building MetaBAT?

[david vilanova]

#!
cd berkeleylab-metabat-5583d6a5ce3d
scons PREFIX=/home/david/work/david/sources/metabat install

#!


scons: Reading SConscript files ...
Building with custom install of htslib / samtools
checking for gcc... gcc
checking whether the C compiler works... yes

checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
make: Nothing to be done for `all'.
mkdir -p -m 755 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/bin /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/include /home/david/work/david/source
s/berkeleylab-metabat-5583d6a5ce3d/samtools/include/htslib /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/sam
tools/share/man/man1 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/share/man/man5 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/pkgconfig
install -p -m 644 libhts.so /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/libhts.so.1.2.1
ln -sf libhts.so.1.2.1 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/libhts.so
ln -sf libhts.so.1.2.1 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/libhts.so.1
sed -e 's#@includedir@#/home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/include#g;s#@libdir@#/home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib#g;s#@PACK
AGE_VERSION@#1.2.1#g' htslib.pc.in > /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/pkgconfig/htslib.pc
chmod 644 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/pkgconfig/htslib.pc
install -p bgzip htsfile tabix /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/bin
install -p -m 644 htslib/*.h /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/include/htslib
install -p -m 644 libhts.a /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/lib/libhts.a
install -p -m 644 htsfile.1 tabix.1 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/share/man/man5
make: Nothing to be done for `all'.
mkdir -p -m 755 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/bin /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/share/man/man1
install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.
pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /home/david/work/david/sources/ber
keleylab-metabat-5583d6a5ce3d/samtools/bin
install -p -m 644 samtools.1 /home/david/work/david/sources/berkeleylab-metabat-5583d6a5ce3d/samtools/share/man/man1
Found from environment BOOST_ROOT=/home/david/work/lib/
Found boost libs in /home/david/work/lib//lib
setting boost include to /home/david/work/lib//include
setting boost lib to /home/david/work/lib//lib
Found static library boost_program_options as /home/david/work/lib//lib/libboost_program_options.a
Found static library boost_serialization as /home/david/work/lib//lib/libboost_serialization.a
Found static library boost_graph as /home/david/work/lib//lib/libboost_graph.a
Found static library bam as samtools/lib/libbam.a
Found static library hts as samtools/lib/libhts.a
Found static library boost_system as /home/david/work/lib//lib/libboost_system.a
Found static library bam as samtools/lib/libbam.a
Found static library hts as samtools/lib/libhts.a
scons: done reading SConscript files.
scons: Building targets ...
/home/david/work/sources/berkeleylab-metabat-5583d6a5ce3d/jgi_summarize_bam_contig_depths --outputDepth test/contigs.fa.depth.txt test/contigs-1000.fastq.bam
Output depth matrix to test/contigs.fa.depth.txt
Output matrix to test/contigs.fa.depth.txt
Opening bam: test/contigs-1000.fastq.bam
Consolidating headers
Processing bam files
Thread 0 processing: contigs-1000.fastq.bam
Thread 0 finished: contigs-1000.fastq.bam with 1000 reads and 1000 readsWellMapped
Creating depth matrix file: test/contigs.fa.depth.txt
Closing most bam files
Closing last bam file
Finished
g++ -o src/metabat.o -c -O3 -Wall -g -fopenmp -DNDEBUG -I/home/dvilanova/work/lib/include src/metabat.cpp
src/metabat.cpp:55: error: using ‘typename’ outside of template
src/metabat.cpp:56: error: using ‘typename’ outside of template
src/metabat.cpp:57: error: using ‘typename’ outside of template
scons: *** [src/metabat.o] Error 1

#!

 g++ --version
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Looks like a compiler sort of standard issue ?

[Don Kang]

Yes. It needs g++ >= 4.6

[Rob Egan]

I just pushed a change to allow it to compile further, but without g++ >=4.6 the application will not be multi-threaded. We don't have g++4.4 installed anywhere easy to check whether this fully fixes your issue.

[david vilanova]

good to know. I will follow your recommendations and will compile with higher version >=4.6 thanks

[david vilanova]

Had another install with g++4.9.1 and compiled properly. Great !!!

[Silas Kieser]

Is there any solution for osx?

I get the following problem with the to prebuild libraries:

dyld: Library not loaded: /usr/local/opt/gcc@4.9/lib/gcc/4.9/libgomp.1.dylib
  Referenced from: /Users/silas/Documents/Debug_atlas/conda_envs/66f3e419/bin/jgi_summarize_bam_contig_depths
  Reason: image not found

[Rob Egan]

Hi Silas, I can not reproduce the error you see. And I suspect that you may be running a different version of OSX than I have access to at the moment. Have you tried running the docker container? That should work and is the easiest path to executing, imo.