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?
What is your GCC version?
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, 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.