Question: error with trinity installation
0
gravatar for Kurban
3.9 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

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?

 

ADD COMMENTlink modified 3.3 years ago • written 3.9 years ago by Kurban170
1

What is your GCC version?

ADD REPLYlink written 3.9 years ago by arnstrm1.7k
1
gravatar for Kurban
3.3 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

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.

 

ADD COMMENTlink written 3.3 years ago by Kurban170
0
gravatar for h.mon
3.9 years ago by
h.mon24k
Brazil
h.mon24k wrote:

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.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by h.mon24k
0
gravatar for Kurban
3.9 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

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. 

ADD COMMENTlink written 3.9 years ago by Kurban170
0
gravatar for iamtuttu5
3.3 years ago by
iamtuttu540
United States
iamtuttu540 wrote:

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
htslib/
htslib/tbx.c
htslib/README.md
htslib/htsfile.1
htslib/config.h.in
htslib/LICENSE
htslib/htslib/
htslib/htslib/khash_str2int.h
htslib/htslib/kfunc.h
htslib/htslib/faidx.h
htslib/htslib/khash.h
htslib/htslib/ksort.h
htslib/htslib/tbx.h
htslib/htslib/vcf.h
htslib/htslib/regidx.h
htslib/htslib/hts.h
htslib/htslib/hfile.h
htslib/htslib/vcfutils.h
htslib/htslib/synced_bcf_reader.h
htslib/htslib/hts_defs.h
htslib/htslib/kstring.h
htslib/htslib/kseq.h
htslib/htslib/vcf_sweep.h
htslib/htslib/knetfile.h
htslib/htslib/sam.h
htslib/htslib/klist.h
htslib/htslib/cram.h
htslib/htslib/bgzf.h
htslib/hfile_irods.c
htslib/htslib.pc.in
htslib/htslib_vars.mk
htslib/test/
htslib/test/c1.fa.fai
htslib/test/xx#minimal.sam
htslib/test/c1#noseq.sam
htslib/test/ce.fa
htslib/test/c1.fa
htslib/test/ce#unmap2.sam
htslib/test/ce#2.sam
htslib/test/test-vcf-api.out
htslib/test/ce#5b.sam
htslib/test/xx#tlen.sam
htslib/test/test-vcf-api.c
htslib/test/ce#1.sam
htslib/test/test-regidx.c
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
htslib/test/xx#large_aux.sam
htslib/test/xx#blank.sam
htslib/test/c1#bounds.sam
htslib/test/ce#tag_padded.sam
htslib/test/hfile.c
htslib/test/xx#pair.sam
htslib/test/ce#tag_depadded.sam
htslib/test/xx#rg.sam
htslib/test/test.pl
htslib/test/xx.fa
htslib/test/auxf#values.sam
htslib/test/xx#triplet.sam
htslib/test/compare_sam.pl
htslib/test/xx#large_aux2.sam
htslib/test/cross_validate.sh
htslib/test/ce#unmap1.sam
htslib/test/xx.fa.fai
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
htslib/test/test-vcf-sweep.c
htslib/test/test_view.c
htslib/test/fieldarith.sam
htslib/test/auxf.fa.fai
htslib/test/c1#unknown.sam
htslib/sam.c
htslib/INSTALL
htslib/hfile_net.c
htslib/configure.ac
htslib/tabix.c
htslib/sam.5
htslib/cram/
htslib/cram/cram_io.h
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
htslib/tabix.1
htslib/config.mk.in
htslib/hfile_internal.h
htslib/.git/
htslib/.git/branches/
htslib/.git/packed-refs
htslib/.git/HEAD
htslib/.git/description
htslib/.git/info/
htslib/.git/info/exclude
htslib/.git/refs/
htslib/.git/refs/heads/
htslib/.git/refs/heads/develop
htslib/.git/refs/remotes/
htslib/.git/refs/remotes/origin/
htslib/.git/refs/remotes/origin/cram_index_fix454
htslib/.git/refs/remotes/origin/HEAD
htslib/.git/refs/remotes/origin/develop
htslib/.git/refs/tags/
htslib/.git/FETCH_HEAD
htslib/.git/index
htslib/.git/logs/
htslib/.git/logs/HEAD
htslib/.git/logs/refs/
htslib/.git/logs/refs/heads/
htslib/.git/logs/refs/heads/develop
htslib/.git/logs/refs/remotes/
htslib/.git/logs/refs/remotes/origin/
htslib/.git/logs/refs/remotes/origin/cram_index_fix454
htslib/.git/logs/refs/remotes/origin/HEAD
htslib/.git/logs/refs/remotes/origin/develop
htslib/.git/config
htslib/.git/hooks/
htslib/.git/hooks/update.sample
htslib/.git/hooks/pre-commit.sample
htslib/.git/hooks/pre-push.sample
htslib/.git/hooks/applypatch-msg.sample
htslib/.git/hooks/pre-applypatch.sample
htslib/.git/hooks/post-update.sample
htslib/.git/hooks/pre-rebase.sample
htslib/.git/hooks/commit-msg.sample
htslib/.git/hooks/prepare-commit-msg.sample
htslib/.git/ORIG_HEAD
htslib/.git/objects/
htslib/.git/objects/c4/
htslib/.git/objects/c4/dcd9310892b5d6ce73bd4d432f2cdb5d185b86
htslib/.git/objects/d7/
htslib/.git/objects/d7/5415141386bd7af4a3b0c18ce9c72b58c0895e
htslib/.git/objects/f7/
htslib/.git/objects/f7/9045536b9bb89666bedf7ee665503a0d9bad2a
htslib/.git/objects/d0/
htslib/.git/objects/d0/4c125779fc55599e27217ea16bfa81eb329ce0
htslib/.git/objects/77/
htslib/.git/objects/77/e93b8f53693557080d7eb7dc819f81ec02364e
htslib/.git/objects/77/8653c5935e1a7ded2305db8eb8d9b2b027f6d5
htslib/.git/objects/a5/
htslib/.git/objects/a5/25f1dcd387ed9c498651d9ca52f7f2b3f7cbd2
htslib/.git/objects/35/
htslib/.git/objects/35/aa79fce8592f9fb6b9cc398035e8d3b8f61216
htslib/.git/objects/pack/
htslib/.git/objects/pack/pack-8b94c94d585cec4f62afce453de1b8cc15451ed0.idx
htslib/.git/objects/pack/pack-8b94c94d585cec4f62afce453de1b8cc15451ed0.pack
htslib/.git/objects/c7/
htslib/.git/objects/c7/54ea68af5c2b729639f4c900c53e5e4096e736
htslib/.git/objects/81/
htslib/.git/objects/81/e6a04ea0d63e72eb80b704e4bef9d7c602097c
htslib/.git/objects/9e/
htslib/.git/objects/9e/62c629a55841a79ef98d70329cd19d3ab6e7b2
htslib/.git/objects/44/
htslib/.git/objects/44/94fa66822f0fad7f9715ed6925939295f3e87a
htslib/.git/objects/44/128b6e6d073f5026b6ad1b19309e35607fd06b
htslib/.git/objects/7e/
htslib/.git/objects/7e/a4c18f0f50926e0105ea9e5a42accf5ff5f7ff
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htslib/.git/objects/b8/
htslib/.git/objects/b8/59b9b01afc995480fb5308f04598982f677009
htslib/.git/objects/6f/
htslib/.git/objects/6f/68c606364c438a4d176acc5d7b664468e7d472
htslib/.git/objects/info/
htslib/.git/objects/23/
htslib/.git/objects/23/ba31e625abe185d3d1e46e911f9c8fd8a0963b
htslib/.git/objects/d1/
htslib/.git/objects/d1/aedf5ce3686ec0bc2b7295a8995643a3340e2b
htslib/.git/objects/8c/
htslib/.git/objects/8c/2d8ff9cd4673bf397b6281a77514caa00c5735
htslib/.git/objects/88/
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htslib/.git/objects/fe/
htslib/.git/objects/fe/fcbcabcbd770ab3fa8c20aeb3ae1769824c8d1
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htslib/.git/objects/28/616da42f9f07650a279e07c887ece24cf2b3f4
htslib/.git/objects/13/
htslib/.git/objects/13/b38fb0a3127ae1ec555ca1fd722004a7dba0af
htslib/.git/objects/c9/
htslib/.git/objects/c9/ce386ad3a01d0bb2df4cad26f0f377feead353
htslib/.git/objects/73/
htslib/.git/objects/73/2a5763f9bfeea52ff21b5238334786e5cc3e6a
htslib/.git/objects/45/
htslib/.git/objects/45/baa0e2c299aff7b5934d31c62431348b372174
htslib/.git/objects/7f/
htslib/.git/objects/7f/323b8eac960ac516ab3d0f7121b3914365e82e
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htslib/.git/objects/ec/c32eb4cf8d13e9c2705200e67402763d1a4b4d
htslib/.git/objects/29/
htslib/.git/objects/29/d9613036d807c86c4fa95b45190c5edd083cab
htslib/.git/objects/2e/
htslib/.git/objects/2e/9e19050ec2bc6a1904705a7d8cca52a9320b39
htslib/.git/objects/4b/
htslib/.git/objects/4b/646a70bf88bc0995b5be8f7a8e8511f53cfbf7
htslib/.git/objects/4b/2ad4f539779b519d20c6a9cdb5b9e786544a8b
htslib/.git/objects/8a/
htslib/.git/objects/8a/1d073707280c815607e35293bb9079616c7272
htslib/.git/objects/4c/
htslib/.git/objects/4c/82a74420393b253b34f6a8dfd28d190a1b7579
htslib/.git/objects/7d/
htslib/.git/objects/7d/beffcdcac3279b308ca26a9daa2af1a87f9a91
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)

 

 

 

 

ADD COMMENTlink written 3.3 years ago by iamtuttu540
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