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Old 03-07-2014, 10:31 AM   #1
Agrias
Junior Member
 
Location: New Mexico

Join Date: Aug 2013
Posts: 2
Default Trinity installation error on Mac OSX Marvericks

I would like to install trinity on my iMac witn Mac OSX 10.9.2 (Mavericks).
After untaring trinity (trinityrnaseq_r20131110), $ make command gives an error.
below is in the terminal window:
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
&& ./configure --prefix=`pwd` && /Applications/Xcode.app/Contents/Developer/usr/bin/make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
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
Making install in src
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT Fasta_entry.o -MD -MP -MF ".deps/Fasta_entry.Tpo" -c -o Fasta_entry.o Fasta_entry.cpp; \
then mv -f ".deps/Fasta_entry.Tpo" ".deps/Fasta_entry.Po"; else rm -f ".deps/Fasta_entry.Tpo"; exit 1; fi
clang: warning: argument unused during compilation: '-fopenmp'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT IRKE_run.o -MD -MP -MF ".deps/IRKE_run.Tpo" -c -o IRKE_run.o IRKE_run.cpp; \
then mv -f ".deps/IRKE_run.Tpo" ".deps/IRKE_run.Po"; else rm -f ".deps/IRKE_run.Tpo"; exit 1; fi
clang: warning: argument unused during compilation: '-fopenmp'
IRKE_run.cpp:9:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
make[2]: *** [IRKE_run.o] Error 1
make[1]: *** [install-recursive] Error 1
make: *** [inchworm_target] Error 2

Does anyone know how to properly install trinity on Mavericks?
I have bowtie1 and bowtie2 installed on the iMac.
Thanks for your help in advance.

Agrias
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