busted tape archive (i.e. tar error)

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    • August 1, 2011 at 4:48 pm #997
      mmulqueen
      Participant

        I’ve just downloaded the full Rosetta 3.3 bundle (twice, to be sure), but it’s not a valid tar file.

        >> tar tf rosetta3.3_bundles.tgz
        rosetta3.3/
        rosetta3.3/Antibody-3.3.tgz
        rosetta3.3/rosetta3.3_fragments.tgz
        rosetta3.3/new_apps.note
        rosetta3.3/protocol_capture-3.3.tgz
        rosetta3.3/rosetta3.3_database.tgz
        rosetta3.3/foldit-3.3.tgz
        rosetta3.3/release.note
        rosetta3.3/rosetta3.3_demos.tgz
        rosetta3.3/BioTools-3.3.tgz
        rosetta3.3/README.Copyrights
        rosetta3.3/rosetta3.3_source.tgz
        rosetta3.3/README.version
        rosetta3.3/rosetta3.3_manual.tgz

        gzip: stdin: invalid compressed data–crc error
        tar: Child returned status 1
        tar: Error is not recoverable: exiting now

        Same error when I unpack with tar xfz. Solutions??

        Thanks.

        Andreas

      • August 1, 2011 at 7:25 pm #5916
        Anonymous

          I’m waiting for it to download to verify myself; in the meantime have you tried getting just the code and database tarballs and seeing if they work?

        • August 1, 2011 at 8:29 pm #5918
          Anonymous

            I can confirm that tar spits an error, but not that the error appears to mean anything – what does untar looks correct to me. The individual tarballs appear to work as well. I’ve let the webmaster know to take a look.

          • August 2, 2011 at 4:02 pm #5924
            mmulqueen
            Participant

              The tar archive is most definitely bust. The Rosetta database is not just incomplete, it’s rudimentary:

              admin@csb1 in rosetta3.3: du -hs rosetta_database_separate/ rosetta_database_bundle/
              379M rosetta_database_separate/
              108M rosetta_database_incomplete/

              Could the developers please have a look at this and tell me which other packages I have to download separately to complete the installation? And fix rosetta3.3_bundles.tgz as well?

              Thanks.

              Andreas

            • August 8, 2011 at 12:13 am #5941
              Anonymous

                Eran has updated the tarball – let us know if it works or not for you.

              • August 2, 2011 at 9:19 am #5922
                mmulqueen
                Participant

                  I guess I should not have got discouraged so easily. The tar file might unpack properly, despite the errors. The containing tgz files also seem to unpack, also with errors.

                  admin@computer in rosetta3.3: for i in *.tgz
                  > do
                  > tar zfx $i
                  > done
                  tar: Skipping to next header

                  gzip: stdin: invalid compressed data–crc error

                  gzip: stdin: invalid compressed data–length error
                  tar: Child returned status 1
                  tar: Error is not recoverable: exiting now

                  gzip: stdin: invalid compressed data–crc error
                  tar: Child returned status 1
                  tar: Error is not recoverable: exiting now

                  admin@computer in rosetta3.3: cd rosetta_source
                  admin@computer in rosetta_source: external/scons-local/scons.py -j4 bin mode=release

                  Compilation segfaults on RHEL 6.1. I’m submitting a report…

                  Andreas

                • August 2, 2011 at 7:33 pm #5928
                  Anonymous

                    379 sounds about right. The developer database is currently 768 MB. SVN doubles the file footprint of all files, so that would be 384.

                    I’ve brought this to the attention of the guy who administers this, but I suspect he’s currently traveling: RosettaCON is the latter half of this week.

                  • August 2, 2011 at 7:44 pm #5929
                    Anonymous

                      Other packages: if you’re on Ubuntu, some other user has helpfully compiled a list:

                      “make sure all build dependencies are available
                      sudo apt-get install debhelper scons zlib1g-dev quilt build-essential”
                      http://www.rosettacommons.org/content/debian-med-sharing-rosetta-build-experience-debian-and-ubuntu#comment-3167

                      I know that scons is not actually needed (we supply an embedded scons). I don’t use quilt or debhelper so I assume it’s not essential (I think they matter for the other stuff in that thread). build-essential supplies the compiler, and zlib1g-dev is necessary. I assume you can figure out the RHEL packages from that information?

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