[Bug 689870] New: Review Request: tabix - Generic indexer for TAB-delimited genome position files

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Summary: Review Request: tabix - Generic indexer for TAB-delimited genome position files

https://bugzilla.redhat.com/show_bug.cgi?id=689870

Summary: Review Request: tabix - Generic indexer for
                    TAB-delimited genome position files
           Product: Fedora
           Version: rawhide
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: medium
          Priority: medium
         Component: Package Review
        AssignedTo: [e-mail]
        ReportedBy: [e-mail]
         QAContact: [e-mail]
                CC: [e-mail], [e-mail]
   Estimated Hours: 0.0
    Classification: Fedora

Spec URL: http://verdurin.fedorapeople.org/reviews/tabix/tabix.spec
SRPM URL:
http://verdurin.fedorapeople.org/reviews/tabix/tabix-0.2.3-1.fc16.src.rpm
Description: 
Tabix indexes a TAB-delimited genome position file in.tab.bgz and
creates an index file in.tab.bgz.tbi when region is absent from the
command-line. The input data file must be position sorted and
compressed by bgzip which has a gzip(1) like interface. After
indexing, tabix is able to quickly retrieve data lines overlapping
regions specified in the format "chr:beginPos-endPos". Fast data
retrieval also works over network if URI is given as a file name and
in this case the index file will be downloaded if it is not present
locally.

[Bug 689870] Review Request: tabix - Generic indexer for TAB-delimited genome position files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=689870

Adam Huffman  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
             Blocks|                            |505154(FE-SCITECH)

[Bug 689870] Review Request: tabix - Generic indexer for TAB-delimited genome position files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=689870

--- Comment #1 from Adam Huffman  2011-04-19 06:47:50 EDT ---
New version with latest upstream release 0.2.4 available at:

http://verdurin.fedorapeople.org/reviews/tabix/tabix.spec

http://verdurin.fedorapeople.org/reviews/tabix/tabix-0.2.4-1.fc16.src.rpm

[Bug 689870] Review Request: tabix - Generic indexer for TAB-delimited genome position files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=689870

--- Comment #2 from Adam Huffman  2011-05-08 10:21:52 EDT ---
New upstream release:

http://verdurin.fedorapeople.org/reviews/tabix/tabix.spec

http://verdurin.fedorapeople.org/reviews/tabix/tabix-0.2.5-1.fc16.src.rpm

[Bug 689870] Review Request: tabix - Generic indexer for TAB-delimited genome position files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=689870

Simon Andrews  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |[e-mail]

--- Comment #3 from Simon Andrews  2011-09-21 07:12:20 EDT ---
Tried to compile this under F15, but failed with the following errors - we saw
the same thing doing a vanilla tabix install from the distributed sources.  It
looks like a missing dependency?:

$ sudo yum-builddep tabix-0.2.5-1.fc16.src.rpm
Loaded plugins: refresh-packagekit
Getting requirements for tabix-0.2.5-1.fc16.src
 --> Already installed : zlib-devel-1.2.5-3.fc15.x86_64
 --> Already installed : 4:perl-5.12.4-160.fc15.x86_64
 --> Already installed : perl-ExtUtils-MakeMaker-6.56-160.fc15.noarch
 --> Already installed : perl-Test-Simple-0.98-1.fc15.noarch
No uninstalled build requires
[andrewss@bilin1 SRPMS]$ rpmbuild --rebuild tabix-0.2.5-1.fc16.src.rpm
Installing tabix-0.2.5-1.fc16.src.rpm
warning: user mockbuild does not exist - using root
warning: group mockbuild does not exist - using root
warning: user mockbuild does not exist - using root
warning: group mockbuild does not exist - using root
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.gHV8NH
+ umask 022
+ cd /home/andrewss/rpmbuild/BUILD
+ LANG=C
+ export LANG
+ unset DISPLAY
+ cd /home/andrewss/rpmbuild/BUILD
+ rm -rf tabix-0.2.5
+ /usr/bin/bzip2 -dc /home/andrewss/rpmbuild/SOURCES/tabix-0.2.5.tar.bz2
+ /bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd tabix-0.2.5
+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.GB9jS8
+ umask 022
+ cd /home/andrewss/rpmbuild/BUILD
+ cd tabix-0.2.5
+ LANG=C
+ export LANG
+ unset DISPLAY
+ make -j2
make[1]: Entering directory `/home/andrewss/rpmbuild/BUILD/tabix-0.2.5'
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bgzf.c -o
bgzf.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  kstring.c -o
kstring.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  knetfile.c
-o knetfile.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used
[-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  index.c -o
index.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bedidx.c -o
bedidx.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  main.c -o
main.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bgzip.c -o
bgzip.o
gcc -g -Wall -O2 -fPIC  -o bgzip bgzip.o bgzf.o knetfile.o -lz
bgzf.o: In function `deflate_block':
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:311: undefined reference to
`edeflate'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:313: undefined reference to
`edeflateEnd'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:305: undefined reference to
`edeflateInit2_'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:329: undefined reference to
`edeflateEnd'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:345: undefined reference to
`ecrc32'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:346: undefined reference to
`ecrc32'
bgzf.o: In function `inflate_block':
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:380: undefined reference to
`einflateInit2_'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:385: undefined reference to
`einflate'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:391: undefined reference to
`einflateEnd'
/home/andrewss/rpmbuild/BUILD/tabix-0.2.5/bgzf.c:387: undefined reference to
`einflateEnd'
collect2: ld returned 1 exit status
make[1]: *** [bgzip] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory `/home/andrewss/rpmbuild/BUILD/tabix-0.2.5'
make: *** [all-recur] Error 1
error: Bad exit status from /var/tmp/rpm-tmp.GB9jS8 (%build)

RPM build errors:
    user mockbuild does not exist - using root
    group mockbuild does not exist - using root
    user mockbuild does not exist - using root
    group mockbuild does not exist - using root
    Bad exit status from /var/tmp/rpm-tmp.GB9jS8 (%build)

[Bug 689870] Review Request: tabix - Generic indexer for TAB-delimited genome position files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=689870

--- Comment #4 from Adam Huffman  2011-09-21 18:30:09 EDT ---
Thanks for the interest.

I normally build RPMs with mock, to ensure a clean environment and it builds
fine for me that way.

Could you give that a try?

I do need to make the compilation flags Fedora-compliant.

[Bug 689870] Review Request: tabix - Generic indexer for TAB-delimited genome position files

[Red Hat Bugzilla]

Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.

https://bugzilla.redhat.com/show_bug.cgi?id=689870

Alex Lancaster  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |[e-mail]
              Alias|                            |tabix