#278 Build failure, file and directory permissions in TIGR

consensus
closed-wont-fix
Brian Walenz
None
5
2014-08-01
2014-07-31
David Mathog
No

When make is run on trunk downloaded 2014_07_30 it runs along normally and then fails like this:

############################## AS_RUN ##############################
cp: cannot create regular file `/home/mathog/wgs_project/wgs_trunk_2014_07_30/Linux-amd64/bin/TIGR/.svn/prop-base/AsmLib.pm.svn-base': Permission denied
cp: cannot create regular file `/home/mathog/wgs_project/wgs_trunk_2014_07_30/Linux-amd64/bin/TIGR/.svn/prop-base/Foundation.pm.svn-base': Permission denied
cp: cannot create regular file `/home/mathog/wgs_project/wgs_trunk_2014_07_30/Linux-amd64/bin/TIGR/.svn/text-base/AsmLib.pm.svn-base': Permission denied
cp: cannot create regular file `/home/mathog/wgs_project/wgs_trunk_2014_07_30/Linux-amd64/bin/TIGR/.svn/text-base/Foundation.pm.svn-base': Permission denied
cp: cannot create regular file `/home/mathog/wgs_project/wgs_trunk_2014_07_30/Linux-amd64/bin/TIGR/.svn/entries': Permission denied
make[1]: *** [TIGR] Error 1
make: *** [all] Error 1

ls -al shows that I own those directories and files. However the TIGR directory had protections 644, and the files listed above, which were actually created, had protections 444.

When I built this from trunk on 2014_07_03 this didn't happen.

Discussion

  • David Mathog
    David Mathog
    2014-07-31

    Ran the make as "root" in the same place, and it worked fine.

     
  • Brian Walenz
    Brian Walenz
    2014-08-01

    1) We were uselessly copying the subversion checkout files to the install. Fixed. Not the problem here, just wasted space.

    2) The problem here is that somehow the TIGR/ directory lost the 'x' bit, making directory operations not possible. Root essentially ignored the permissions, so it worked. I don't have any idea how it lost the bit. There is nothing in the assembler code that does this.

    You probably want to set the TIGR directory back to 755, else the last step in the assembler, caqc, will fail leaving you with a mostly useless asm.qc report.

     
  • Brian Walenz
    Brian Walenz
    2014-08-01

    • status: open --> closed-wont-fix
    • assigned_to: Brian Walenz
     
  • David Mathog
    David Mathog
    2014-08-01

    It must be from one (or both) of these:

    ./src/AS_RUN/.svn/text-base/Makefile.svn-base:
    ./src/AS_RUN/Makefile:

    which both have:

    TIGR: asmQC/TIGR
            @mkdir $(LOCAL_BIN)/TIGR
            @cp $</AsmLib.pm $(LOCAL_BIN)/TIGR
            @cp $</Foundation.pm $(LOCAL_BIN)/TIGR
    

    That should probably be

    TIGR: asmQC/TIGR
            @mkdir $(LOCAL_BIN)/TIGR
            @chmod 755 $(LOCAL_BIN)/TIGR
            @cp $</AsmLib.pm $(LOCAL_BIN)/TIGR
            @cp $</Foundation.pm $(LOCAL_BIN)/TIGR
            @chmod 775 $(LOCAL_BIN)/TIGR/*.pm