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Permissions problems with executables (Mac)

John Nash
2011-12-14
2013-04-18
  • John Nash
    John Nash
    2011-12-14

    Good afternoon,

    I'm a glutton for punishment so instead of installing the Mac binary, as usual I checked out the latest svn version and made it.

    My procedure:

    Xcode is installed and up-to-date, macports is installed and up-to-date.  All of the required packages are installed and up-to-date. I've probably done this successfully 30 times on 6 computers in the last 3 weeks (hence the query).

    ## Install io_lib:
    cd ~/staden_install
    svn co https://staden.svn.sourceforge.net/svnroot/staden/io_lib/trunk io_lib.trunk
    cd io_lib.trunk
    ./bootstrap
    ./configure --prefix=/usr/local/staden --disable-shared
    make
    make check
    sudo make install
    

    So far so good.

    cd ~/staden_install
    svn co https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk staden.trunk
    cd staden.trunk/src 
    ./bootstrap
    mkdir install.macosx
    cd install.macosx
    ../configure --disable-rpath --prefix=/usr/local/staden --with-io_lib=/usr/local/staden --with-png=/opt/local/  --with-lzma=/opt/local/ --with-tcl=/opt/local/lib --with-tk=/opt/local/lib --with-tklib=/usr/local/lib/tklib0.5/ --with-itcl=/opt/local/lib/itcl3.4/ --with-itk=/opt/local/lib/itk3.3/ --with-iwidgets=/opt/local/lib/iwidgets/
    make
    sudo make install
    

    Everything is as normal, except the execute permissions are not set for most of the staden programs in /usr/local/staden/bin

    I fixed it by issuing sudo chmod 755 /usr/local/staden/bin/* but it's not what usually happens. Bug? John-screwup?  Anybody else seen this?

    A la prochaine
    John

     
  • James Bonfield
    James Bonfield
    2011-12-15

    Ah, was this specifically the wrapper script programs, like gap5, trev, etc, and not binaries like makeSCF, vector_clip and so on?

    I changed how those were built, coming from a ".in" file to allow auto-generation with the appropriate name of the Tcl interpreter as it tends to differ per platform. So it's probably my error. I'll take a look at the build system. It worked for me fine, but maybe I already had copies of them so the make install was preserving old permissions.

    For what it's worth, I've been experimenting with building a set of Mac binaries complete with some .app bundles. It's work in progress but take a look at ftp://ftp.sanger.ac.uk/pub/jkb/staden.mac.dmg (or something very similar- typed out by memory).

    James

     
  • John Nash
    John Nash
    2011-12-15

    James: you are absolutely correct in your description up the the first paragraph above.

    I'll have a peek at the DMGs soon - I just ordered several mac minis for technician use in the bioinformatics hub.  This will save me some compilation time.  Seeing as my systems are all pretty much the same, I could probably tarball /usr/local/staden/* and re-deploy but I have never really kept a tarball handy, it was always easier to pull the source from svn and make.

    Thanks
    John