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Bedtools 2.24.0 errors while decompressing .tar

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  • Bedtools 2.24.0 errors while decompressing .tar

    When I decompress bedtools 2.24.0:

    Code:
    tar -zxvf ./bedtools-2.24.0.tar.gz
    I get several errors:

    Code:
    tar: bedtools2/src/utils/aux: Cannot mkdir: Protocol error
    tar: bedtools2/src/utils/aux: Cannot mkdir: Protocol error
    tar: bedtools2/src/utils/aux/BedtoolsDriver.cpp: Cannot open: No such file or directory
    tar: bedtools2/src/utils/aux: Cannot mkdir: Protocol error
    tar: bedtools2/src/utils/aux/BedtoolsDriver.h: Cannot open: No such file or directory
    tar: bedtools2/src/utils/aux: Cannot mkdir: Protocol error
    tar: bedtools2/src/utils/aux/Makefile: Cannot open: No such file or directory
    tar: Exiting with failure status due to previous errors
    Make therefore doesn't finish when it looks for these files in /src/utils/aux. I have tried re-downloading using wget and directly from the website (right-click-->save-as), and decompressing with 7zip in Windows instead of tar in Ubuntu. The 7zip gui gave no errors but make gave the same errors that it couldn't find files in /src/utils/aux. I have no problems with the previous version of bedtools 2.23.0 which I can decompress, make, and run bedtools with no errors.

  • #2
    Must be something on your end. Did not have any problems with download/compilation (2.24.0) just now.

    Comment


    • #3
      Windows refuses to create files or directories with names like aux, as it reserves such filenames to refer to IIRC your serial port.

      So alas you're straight out of luck with 2.24.0 on Windows. You'd need to download the tarball on another machine, rename src/utils/aux and fix up the makefiles, and transfer the fixed up tree back to your Windows machine.

      I've reported this as a bedtools bug, and I imagine Aaron will rename this directory for 2.25. In the meantime, it might be easiest just to wait with 2.23.0...

      Comment


      • #4
        Originally posted by jmarshall View Post
        Windows refuses to create files or directories with names like aux, as it reserves such filenames to refer to IIRC your serial port.
        Cool I didn't know about that. I'm actually using bedtools in an Ubuntu VM under Windows but was working in a shared folder so it was trying to to untar and create the aux folders on a Windows drive. Once I switched to a folder within the VM it worked fine. Thanks for the help.

        Comment

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