Unconfigured Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • Agrias
    Junior Member
    • Aug 2013
    • 2

    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

Latest Articles

Collapse

  • SEQadmin2
    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by SEQadmin2


    I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.


    Here are nine questions we think about, in roughly the order they matter, before...
    Today, 07:11 AM
  • SEQadmin2
    From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
    by SEQadmin2


    Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.


    The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
    ...
    06-02-2026, 10:05 AM
  • SEQadmin2
    Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
    by SEQadmin2


    With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.


    Introduction

    Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
    05-22-2026, 06:42 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 06:09 AM
0 responses
16 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-09-2026, 11:58 AM
0 responses
36 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-05-2026, 10:09 AM
0 responses
42 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 06-04-2026, 08:59 AM
0 responses
49 views
0 reactions
Last Post SEQadmin2  
Working...