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  • HTSeq install

    Dear HTSeq expert(s)

    I am installing HTSeq as root user on OS: Mac OS X (snow leopard).
    I downloaded the tarbal from

    A framework to process and analyze data from high-throughput sequencing (HTS) assays


    Here is the output of the install and build command:

    Code:
    sh-3.2# ./clean
    sh-3.2# ./build_it
    swig -Wall -c++ -python StepVector.i 
    mv StepVector.py ../HTSeq
    cython HTSeq/_HTSeq.pyx -o _HTSeq.c
    make: cython: No such file or directory
    make: *** [_HTSeq.c] Error 1
    Could not import 'setuptools', falling back to 'distutils'.
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.4-x86_64-2.7
    creating build/lib.macosx-10.4-x86_64-2.7/HTSeq
    copying HTSeq/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
    copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
    copying HTSeq/StepVector.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
    copying HTSeq/_version.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
    creating build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
    copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
    copying HTSeq/scripts/qa.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
    copying HTSeq/scripts/count.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
    running build_ext
    building 'HTSeq._HTSeq' extension
    creating build/temp.macosx-10.4-x86_64-2.7
    creating build/temp.macosx-10.4-x86_64-2.7/src
    gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.4-x86_64-2.7/src/_HTSeq.o -w
    gcc: error: src/_HTSeq.c: No such file or directory
    gcc: fatal error: no input files
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    Can you please help sort the problem. What is "setuptools" seeking or how does one run that first.
    Thanks in advance
    Best,
    sarosh
    Last edited by fatakias; 04-06-2012, 06:29 AM. Reason: incomplete

  • #2
    You are not supposed to run './build_it'. Rather, install HTSeq as you would install any other Python package, by running 'python setup.py install'. And read the installation instructions, please.

    Comment


    • #3
      Hi sarosh,

      I installed HTSeq on Lion a few days ago. I got the same error message. I searched around and found a solution below:

      on the command line,
      add “export CC=gcc" into ~/.bash_profile,
      then “source ~/.bash_profile".

      I wish it would help.

      Regards,
      ngsseq

      Comment


      • #4
        HTSeq error with Ubuntu 11.10

        Hi Simon!
        I met similar problem when I tried to install HTSeq-0.5.3p3. Read the other posts on similar problem in this forum and google, not direct clear solution yet.
        Code:
        Could not import 'setuptools', falling back to 'distutils'.
        But the rest went fine. Modified the .bashrc file as suggested by ngsseq (which seems for Mac OS, but gave it shot just in case!) still did not work. My python version is 2.7.2+ Any news for this Bug? Thanks!
        Last edited by yifangt; 04-30-2012, 09:20 PM. Reason: small errors

        Comment


        • #5
          HTSeq error with Ubuntu 11.10: [SOLVED]

          Just in case anyone met the same problem. First updated my python to python3.2, still not working. Should have paid attention on the instruction (>=2.5 PYTHON <3.0). After a couple of try found out my problem is related to setuptools and python 3.2.
          1) I had setuptools3 instead of setuptools. Decided to have both.
          After this, building from the source code went well, but met problem with
          Code:
          python setup.py install
          on line 12 of setup.py. Thought of the python version.
          2) symbolic link my python to /usr/bin/python2.7.2 instead of /usr/bin/python3.2. Worked!
          And when I came back also found new version was released in another post, which does not need setuptools.
          Good luck!

          Comment


          • #6
            You don't need setuptools, distutils works just fine. (This is what a "fallback" means.)

            Comment


            • #7
              Hello, now I get a different error message pertaining to gcc. I did manage to install numpy and scipy using a super_pack script for my 64 bin MacOS 10.6. Then tried to get HTSeq going ... compiler issues linger. Can you please suggest a fix. Thank you,
              Best,
              sarosh

              Code:
              sh-3.2# cd HTSeq-0.5.3p3
              sh-3.2# python setup.py install
              running install
              running bdist_egg
              running egg_info
              writing HTSeq.egg-info/PKG-INFO
              writing top-level names to HTSeq.egg-info/top_level.txt
              writing dependency_links to HTSeq.egg-info/dependency_links.txt
              reading manifest file 'HTSeq.egg-info/SOURCES.txt'
              reading manifest template 'MANIFEST.in'
              no previously-included directories found matching 'example_data'
              no previously-included directories found matching 'test'
              warning: no previously-included files found matching 'todo.txt'
              writing manifest file 'HTSeq.egg-info/SOURCES.txt'
              installing library code to build/bdist.macosx-10.4-x86_64/egg
              running install_lib
              running build_py
              running build_ext
              building 'HTSeq._HTSeq' extension
              gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy-1.7.0.dev_3cb783e_20120427-py2.7-macosx-10.7-x86_64.egg/numpy/core/include -I/usr/local/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.4-x86_64-2.7/src/_HTSeq.o -w
              gcc: error: src/_HTSeq.c: No such file or directory
              gcc: fatal error: no input files
              compilation terminated.
              error: command 'gcc' failed with exit status 1
              Last edited by fatakias; 05-01-2012, 06:08 AM.

              Comment


              • #8
                Continued from above post - after a clean up .. Additional details provided. Can someone please suggest a fix for HTSeq install. Thanks,
                Best,
                sarosh


                Code:
                sh-3.2# sh clean
                
                sh-3.2# python setup.py install
                running install
                running bdist_egg
                running egg_info
                writing HTSeq.egg-info/PKG-INFO
                writing top-level names to HTSeq.egg-info/top_level.txt
                writing dependency_links to HTSeq.egg-info/dependency_links.txt
                file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
                reading manifest file 'HTSeq.egg-info/SOURCES.txt'
                reading manifest template 'MANIFEST.in'
                no previously-included directories found matching 'example_data'
                no previously-included directories found matching 'test'
                warning: no previously-included files found matching 'todo.txt'
                writing manifest file 'HTSeq.egg-info/SOURCES.txt'
                installing library code to build/bdist.macosx-10.4-x86_64/egg
                running install_lib
                running build_py
                file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
                creating build
                creating build/lib.macosx-10.4-x86_64-2.7
                creating build/lib.macosx-10.4-x86_64-2.7/HTSeq
                copying HTSeq/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
                copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
                copying HTSeq/_version.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq
                creating build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
                copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
                copying HTSeq/scripts/qa.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
                copying HTSeq/scripts/count.py -> build/lib.macosx-10.4-x86_64-2.7/HTSeq/scripts
                file HTSeq/StepVector.py (for module HTSeq.StepVector) not found
                running build_ext
                building 'HTSeq._HTSeq' extension
                creating build/temp.macosx-10.4-x86_64-2.7
                creating build/temp.macosx-10.4-x86_64-2.7/src
                gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy-1.7.0.dev_3cb783e_20120427-py2.7-macosx-10.7-x86_64.egg/numpy/core/include -I/usr/local/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.4-x86_64-2.7/src/_HTSeq.o -w
                gcc: error: src/_HTSeq.c: No such file or directory
                gcc: fatal error: no input files
                compilation terminated.
                error: command 'gcc' failed with exit status 1

                Comment


                • #9
                  Please start over and follow the instructions. Especially, note that the instructions do not ask you to run 'clean' or 'build_it'.

                  Comment


                  • #10
                    HTseq build error

                    Hi,

                    I am trying to install HTseq on our cluster(not root user) but it is giving me error while building.

                    PHP Code:
                    Could not import 'setuptools'falling back to 'distutils'.
                    running build
                    running build_py
                    creating build
                    creating build
                    /lib.linux-x86_64-2.6
                    creating build
                    /lib.linux-x86_64-2.6/HTSeq
                    copying HTSeq
                    /__init__.py -> build/lib.linux-x86_64-2.6/HTSeq
                    copying HTSeq
                    /_HTSeq_internal.py -> build/lib.linux-x86_64-2.6/HTSeq
                    copying HTSeq
                    /StepVector.py -> build/lib.linux-x86_64-2.6/HTSeq
                    copying HTSeq
                    /_version.py -> build/lib.linux-x86_64-2.6/HTSeq
                    creating build
                    /lib.linux-x86_64-2.6/HTSeq/scripts
                    copying HTSeq
                    /scripts/__init__.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts
                    copying HTSeq
                    /scripts/qa.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts
                    copying HTSeq
                    /scripts/count.py -> build/lib.linux-x86_64-2.6/HTSeq/scripts
                    running build_ext
                    building 
                    'HTSeq._HTSeq' extension
                    creating build
                    /temp.linux-x86_64-2.6
                    creating build
                    /temp.linux-x86_64-2.6/src
                    icc 
                    -pthread -fno-strict-aliasing -DNDEBUG --O3 -Wall -Wstrict-prototypes -fPIC -I/data/gkushwah/xulab/garima/tools/numpy-1.7.1rc1/lib/python2.6/site-packages/numpy/core/include -I/share/sw/python/current/include/python2.6 -c src/_HTSeq.-o build/temp.linux-x86_64-2.6/src/_HTSeq.-w
                    icc 
                    -pthread -shared build/temp.linux-x86_64-2.6/src/_HTSeq.-o build/lib.linux-x86_64-2.6/HTSeq/_HTSeq.so
                    building 
                    'HTSeq._StepVector' extension
                    icc 
                    -pthread -fno-strict-aliasing -DNDEBUG --O3 -Wall -Wstrict-prototypes -fPIC -I/share/sw/python/current/include/python2.6 -c src/StepVector_wrap.cxx -o build/temp.linux-x86_64-2.6/src/StepVector_wrap.-w
                    icpc 
                    -pthread -shared build/temp.linux-x86_64-2.6/src/StepVector_wrap.o src/step_vector.-o build/lib.linux-x86_64-2.6/HTSeq/_StepVector.so
                    ld
                    : /tmp/icpc4Ax1zp.orelocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
                    /tmp/icpc4Ax1zp.o: could not read symbols: Bad value
                    error: command 'icpc' failed with exit status 1 
                    Any suggestion?

                    Comment


                    • #11
                      First of all: Please give complete information, when asking a question. It is not nice that I have to guess that your are using Linux and forgot to mention this although you can see that this thread is all about Mac OS. Which Linux distribution? Which Python? Is this your desktop PC or some centrally administered server?

                      Your Python is using Intel's C compiler (icc) instead of the GNU C compiler (gcc), which is used by virtually all Linux distribution. This hence does not seem to be a standard Python installation. You will have to try again with a more standard setup or ask the person for help who had the qeustionable idea of deploying an icc-built Python.

                      Comment


                      • #12
                        Hi,

                        I want to install htseq-count on a server (unix).
                        Here http://www-huber.embl.de/users/ander...l.html#install
                        they have for linux,mac and windows but not unix.

                        Let me know if you have any idea.

                        Comment


                        • #13
                          Originally posted by alexGrenoble View Post
                          Hi,

                          I want to install htseq-count on a server (unix).
                          Here http://www-huber.embl.de/users/ander...l.html#install
                          they have for linux,mac and windows but not unix.

                          Let me know if you have any idea.
                          linux is a unix-like OS. So use the linux version.

                          Comment

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