Unconfigured Ad

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

    #1

    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
    Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
    by SEQadmin2



    CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

    Despite this, “CRISPR helped turn genome editing from a specialized technique into
    ...
    07-31-2026, 11:01 AM
  • SEQadmin2
    Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
    by SEQadmin2


    Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

    The systematic characterization of the human proteome has
    ...
    07-20-2026, 11:48 AM
  • SEQadmin2
    Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
    by SEQadmin2



    Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
    ...
    07-09-2026, 11:10 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 08-03-2026, 10:13 AM
0 responses
20 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-31-2026, 02:55 AM
0 responses
34 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-24-2026, 12:17 PM
0 responses
24 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-23-2026, 11:41 AM
0 responses
21 views
0 reactions
Last Post SEQadmin2  
Working...