hello everyone,

i have rent server from school computer center, and trying to install Trinity on it via SSH. but i got the following error message:

kurban910@node9:~/trinityrnaseq-2.0.6> make
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
                && sh ./configure --prefix=`pwd`  && make install
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 for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm'
make[1]: Warning: File `Makefile' has modification time 5e+04 s in the future
Making install in src
make[2]: Entering directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm/src'
make[2]: Warning: File `.deps/string_util.Po' has modification time 4.9e+04 s in the future
g++ -DHAVE_CONFIG_H -I. -I..    -std=c++0x -pedantic -fopenmp -Wall -Wextra -Wno-deprecated -m64 -g -O2 -MT Fasta_entry.o -MD -MP -MF .deps/Fasta_entry.Tpo -c -o Fasta_entry.o Fasta_entry.cpp
cc1plus: error: unrecognized command line option "-std=c++0x"
cc1plus: error: unrecognized command line option "-fopenmp"
make[2]: *** [Fasta_entry.o] Error 1
make[2]: Leaving directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm/src'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/public/home/kurban910/trinityrnaseq-2.0.6/Inchworm'
make: *** [inchworm_target] Error 2
kurban910@node9:~/trinityrnaseq-2.0.6> 

i am still new at linux operation. could anyone give me some sugessions what have gone wrong here?

hi @iamtuttu5

did u solve the problem? when the time  i was trying to install trinity, it was truly the problem of GCC version and the IT guy who was admin in the computer center at the time said they can not update gcc compiler at that time just for me. then i contacted a friend of mine who had another server, the i checked the compiler version and it was new , and its version as shown as below:

[WHL@server ~]$ gcc -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC)

kurban@kurban-X550VC:~$

the i used his server which installed trinity successfully, then i used 50 threads and 200G memory in one night when no body using it finished my job .

sorry about this comment sent as an answer, it is because  the place where i am now has a little problem opening the biostars every time . i can only sent something this way.

It seems you are using an old version of GCC, you probably need to use a more recent one. You could have easily found that out searching a bit, when I googled for your first error ( cc1plus: error: unrecognized command line option "-std=c++0x" ) I found this StackOverflow thread, and for the second error ( cc1plus: error: unrecognized command line option "-fopenmp" ), I found this one.

Which Linux and GCC version are you using? Type the following at the terminal:

cat /etc/issue

uname -a

gcc -v

Oftentimes the system default GCC is old, but there is a newer one installed as gcc-X.Y (e.g. gcc-4.7), if such is the case you may edit the Makefile and replace gcc by gcc-X.Y (the one available at your system). You should probably ask for help for your school IT guys, they will be able to guide you through the initial difficulties and point to relevant resources.

thank you guys,

yes, the gcc version on the server is really old, its gcc 4.1 version. then i contacted with IT in the computer center. 

Hello Kurban

Me also going through the same condtition that you been through

I am also accessing server system for running trinity , I am getting this errorr

tuttu@kau:~/ngs/trinityrnaseq-2.1.1$ sudo make
[sudo] password for tuttu:
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
                && sh ./configure --prefix=`pwd`  && make install
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 for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory `/home/jinu/ngs/trinityrnaseq-2.1.1/Inchworm'
Making install in src
make[2]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
make[3]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
test -z "/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/bin" || /bin/mkdir -p "/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/bin"
  /usr/bin/install -c inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats '/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
make[2]: Leaving directory `/home/tutu/ngs/trinityrnaseq-2.1.1/Inchworm/src'
make[2]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[3]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[2]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
make[1]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Inchworm'
cd Chrysalis && make UNSUPPORTED=yes
make[1]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Chrysalis'
make[1]: Nothing to be done for `all'.tu
make[1]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/Chrysalis'
cd trinity-plugins && make trinity_essentials
make[1]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins'
tar xvf "htslib.github.Aug182015.tar.gz" && cd htslib && make
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htslib/tbx.c
htslib/README.md
htslib/htsfile.1
htslib/config.h.in
htslib/LICENSE
htslib/htslib/
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htslib/htslib/kfunc.h
htslib/htslib/faidx.h
htslib/htslib/khash.h
htslib/htslib/ksort.h
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htslib/htslib/regidx.h
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htslib/htslib/synced_bcf_reader.h
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htslib/htslib/kstring.h
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htslib/htslib/bgzf.h
htslib/hfile_irods.c
htslib/htslib.pc.in
htslib/htslib_vars.mk
htslib/test/
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htslib/test/xx#minimal.sam
htslib/test/c1#noseq.sam
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htslib/test/ce#1.sam
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htslib/test/xx#tlen2.sam
htslib/test/ce#unmap.sam
htslib/test/sam.c
htslib/test/c1#pad3.sam
htslib/test/c1#pad1.sam
htslib/test/ce#large_seq.sam
htslib/test/test_view.pl
htslib/test/c2.fa.fai
htslib/test/c1#pad2.sam
htslib/test/xx#unsorted.sam
htslib/test/ce#5.sam
htslib/test/c1#clip.sam
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htslib/test/xx#blank.sam
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htslib/test/xx#rg.sam
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htslib/test/xx.fa
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htslib/test/xx#triplet.sam
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htslib/test/cross_validate.sh
htslib/test/ce#unmap1.sam
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htslib/test/auxf.fa
htslib/test/test-vcf-sweep.out
htslib/test/c2.fa
htslib/test/fieldarith.c
htslib/test/ce.fa.fai
htslib/test/c2#pad.sam
htslib/test/ce#supp.sam
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htslib/test/fieldarith.sam
htslib/test/auxf.fa.fai
htslib/test/c1#unknown.sam
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htslib/tabix.c
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htslib/cram/open_trace_file.h
htslib/cram/thread_pool.c
htslib/cram/zfio.c
htslib/cram/zfio.h
htslib/cram/string_alloc.h
htslib/cram/vlen.c
htslib/cram/rANS_byte.h
htslib/cram/mFILE.c
htslib/cram/cram_encode.c
htslib/cram/cram_codecs.h
htslib/cram/cram_external.c
htslib/cram/string_alloc.c
htslib/cram/rANS_static.c
htslib/cram/open_trace_file.c
htslib/cram/files.c
htslib/cram/cram_samtools.h
htslib/cram/rANS_static.h
htslib/cram/sam_header.c
htslib/cram/cram_structs.h
htslib/cram/cram_index.c
htslib/cram/cram_decode.c
htslib/cram/pooled_alloc.h
htslib/cram/mFILE.h
htslib/cram/cram_stats.h
htslib/cram/os.h
htslib/cram/pooled_alloc.c
htslib/cram/cram_encode.h
htslib/cram/cram_index.h
htslib/cram/cram_stats.c
htslib/cram/cram_codecs.c
htslib/cram/vlen.h
htslib/cram/cram_samtools.c
htslib/cram/cram_decode.h
htslib/cram/sam_header.h
htslib/cram/thread_pool.h
htslib/cram/misc.h
htslib/cram/cram.h
htslib/cram/cram_io.c
htslib/Makefile
htslib/hfile.c
htslib/README
htslib/knetfile.c
htslib/bgzf.c
htslib/faidx.c
htslib/vcf.c
htslib/kstring.c
htslib/synced_bcf_reader.c
htslib/bgzip.c
htslib/hts_internal.h
htslib/.gitignore
htslib/hts.c
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htslib/htslib.mk
htslib/kfunc.c
htslib/.travis.yml
htslib/regidx.c
htslib/vcf.5
htslib/md5.c
htslib/NEWS
htslib/vcf_sweep.c
htslib/vcfutils.c
htslib/config.h
htslib/htsfile.c
htslib/faidx.5
htslib/.gitattributes
make[2]: git: Command not found
make[2]: Entering directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins/htslib'
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
In file included from bgzf.c:39:0:
htslib/bgzf.h:34:18: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
                  ^
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins/htslib'
make[1]: *** [htslib_target] Error 2
make[1]: Leaving directory `/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity-plugins'
make: *** [trinity_essentials] Error 2

I tried the commands mentioned by h.mon in this page

cat /etc/issue

uname -a

gcc -v

It outputs the following

tuttu@kau:~$ cat /etc/issue
Ubuntu 14.04.3 LTS \n \l

tuttu@kau:~$ uname -a
Linux jntbgri 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

tuttu@kau:~$  gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04)