Entering edit mode
9.9 years ago
Kurban
▴
230
Hello everyone,
I have rented a 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 suggestions what have gone wrong here?
What is your GCC version?
Hi @iamtuttu5
Did you solve the problem? When 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, then I checked the compiler version and it was new , and its version as shown as below:
Then 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.
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
I tried the commands mentioned by h.mon in this page
It outputs the following