args.I errors

Issue #248 resolved
Xinxin Peng
created an issue

The installation of rpy2 was interrupted at the gcc compiling stage. It seems that the problem is due to the unsuitable string after the paramter -I.

=============
gcc ... - I / b i n / R / l i b 6 4 / R / i n c l u d e

gcc: I: No such file or directory
gcc: b: No such file or directory
gcc: i: No such file or directory
gcc: n: No such file or directory
gcc: R: No such file or directory
gcc: l: No such file or directory
gcc: i: No such file or directory
gcc: b: No such file or directory
gcc: 6: No such file or directory
gcc: 4: No such file or directory
gcc: R: No such file or directory
gcc: i: No such file or directory
gcc: n: No such file or directory
gcc: c: No such file or directory
gcc: l: No such file or directory
gcc: u: No such file or directory
gcc: d: No such file or directory
gcc: e: No such file or directory
gcc: cannot specify -o with -c or -S with multiple files
error: command 'gcc' failed with exit status 1
=============

Thanks for your help.

Comments (8)

  1. Laurent Gautier

    Hi,

    At first sight the behavior is looking rather unexpected: the problem is that the argument to gcc (-I/some/include/directory) is broken down into it constituting letters, including the -I (becoming - I). The latter is handled by setuptools / distutils and it is surprising to see this.

    More information (more of what is printed to the console when trying to install) would be required to try figuring out what is happening.

  2. Xinxin Peng reporter

    I have just noted that there are some warnings before the interruption.

    reading manifest file 'rpy2.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching 'README' anywhere in distribution
    warning: no previously-included files matching '*patch*' found anywhere in distribution
    warning: no previously-included files matching '*diff*' found anywhere in distribution
    warning: no previously-included files matching '.hg' found anywhere in distribution
    warning: no files found matching 'MANIFEST'
    warning: no files found matching 'MPL_LICENSE'
    warning: no files found matching 'GPL_LICENSE'
    warning: no files found matching 'LGPL_LICENSE'
    no previously-included directories found matching 'dist'
    warning: no files found matching 'doc/source/rpy2_logo.png'
    writing manifest file 'rpy2.egg-info/SOURCES.txt'
    installing library code to build/bdist.linux-x86_64/egg
    running install_lib
    running build_py
    running build_ext
    building 'rpy2.rinterface._rinterface' extension
    

    Thanks a lot.

  3. Laurent Gautier

    The warnings are nothing we can be proud of, yet they are harmless.

    What would be helpful to debug is the rest of the output to the console, such as the report of the warnings issued by R and the details of the include and libraries guessed by setup.py calling R CMD config.

  4. Xinxin Peng reporter

    Here I paste all the output to the console.

    R version 3.1.1 (2014-07-10) -- "Sock it to Me"
    /bin/R/lib64/R/bin/R CMD config --ldflags
    setup.py:134: UserWarning: R emitting a warning: WARNING: ignoring environment value of R_HOME
      warnings.warn("R emitting a warning: %s" % output[0])
    /bin/R/lib64/R/bin/R CMD config --cppflags
    setup.py:203: UserWarning: No include specified
      warnings.warn('No include specified')
    setup.py:214: UserWarning: No libraries as -l arguments to the compiler.
      warnings.warn('No libraries as -l arguments to the compiler.')
    
        Compilation parameters for rpy2's C components:
            include_dirs    = []
            library_dirs    = []
            libraries       = []
            extra_link_args = ['-', 'W', 'l', ',', '-', '-', 'e', 'x', 'p', 'o', 'r', 't', '-', 'd', 'y', 'n', 'a', 'm', 'i', 'c', '-', 'f', 'o', 'p', 'e', 'n', 'm', 'p', '-', 'L', '/', 'b', 'i', 'n', '/', 'R','/', 'l', 'i', 'b', '6', '4', '/', 'R', '/', 'l', 'i', 'b', '-', 'l', 'R', '-', 'l', 'r', 't', '-', 'l', 'd', 'l', '-', 'l', 'm']
    
    running install
    running bdist_egg
    running egg_info
    writing requirements to rpy2.egg-info/requires.txt
    writing rpy2.egg-info/PKG-INFO
    writing top-level names to rpy2.egg-info/top_level.txt
    writing dependency_links to rpy2.egg-info/dependency_links.txt
    R version 3.1.1 (2014-07-10) -- "Sock it to Me"
    reading manifest file 'rpy2.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching 'README' anywhere in distribution
    warning: no previously-included files matching '*patch*' found anywhere in distribution
    warning: no previously-included files matching '*diff*' found anywhere in distribution
    warning: no previously-included files matching '.hg' found anywhere in distribution
    warning: no files found matching 'MANIFEST'
    warning: no files found matching 'MPL_LICENSE'
    warning: no files found matching 'GPL_LICENSE'
    warning: no files found matching 'LGPL_LICENSE'
    no previously-included directories found matching 'dist'
    warning: no files found matching 'doc/source/rpy2_logo.png'
    writing manifest file 'rpy2.egg-info/SOURCES.txt'
    installing library code to build/bdist.linux-x86_64/egg
    running install_lib
    running build_py
    running build_ext
    building 'rpy2.rinterface._rinterface' extension
    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/bin/Python/include/python2.7 -c ./rpy/rinterface/_rinterface.c -o build/temp.linux-x86_64-2.7/./rpy/rinterface/_rinterface.o - I / b i n / R 3 1 1 / l i b 6 4 / R / i n c l u d e
    gcc: I: No such file or directory
    gcc: b: No such file or directory
    gcc: i: No such file or directory
    gcc: n: No such file or directory
    gcc: R: No such file or directory
    gcc: l: No such file or directory
    gcc: i: No such file or directory
    gcc: b: No such file or directory
    gcc: 6: No such file or directory
    gcc: 4: No such file or directory
    gcc: R: No such file or directory
    gcc: i: No such file or directory
    gcc: n: No such file or directory
    gcc: c: No such file or directory
    gcc: l: No such file or directory
    gcc: u: No such file or directory
    gcc: d: No such file or directory
    gcc: e: No such file or directory
    gcc: cannot specify -o with -c or -S with multiple files
    error: command 'gcc' failed with exit status 1
    
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