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.
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
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
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)
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.
New Version release: http://iski.tv/tabix.spec http://iski.tv/tabix-0.2.6-1.fc17.src.rpm
hi, I taking the review i have do yesterday this package before to see your request. Mine works : http://bioinfornatics.fedorapeople.org/tabix.spec These statement should be remove for fedora 16 and higther : _________________ BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) rm -rf %{buildroot} %clean rm -rf %{buildroot} _________________ thanks to merge our works
Note: todo -> not use static lib
I generally maintain EPEL5 branches where possible, which is why I keep those statements. I'll take a look at your .spec and combine the two this weekend.
ok no problem To save some time you should contact upstream for not use static library. Because it is a no-go . Currently is possible to edit the makefile to use a shared library. But as fedora want to be close to upstream this job should be done by upstream one day
ping
reporter seem to be not anymore interested by packaging
I haven't been working in this field for over two years now, so it would be better for someone else to adopt this package.