Hi Mahmud, I believe it is a real problem that ti_bgzf_tell is undeclared at that point. Two more things to double-check:
1. When compiling with USE_TABIX=1, do you also have KNETFILE_HOOKS=1 ? (This will also require that you patch samtools if you also use USE_BAM=1.) 2. Does your TABIXDIR variable point to the recompiled patched installation of tabix? (or, if you have set them separately, TABIXINC and TABIXLIB variables) Sorry for the inconvenience. Angie ----- Original Message ----- > From: "Mahmud Siddiqi" <[email protected]> > To: [email protected] > Sent: Friday, December 2, 2011 2:56:09 PM > Subject: [Genome-mirror] Errors compiling from source, function ti_bgzf_tell > Update -- > > Error is related to tabix, not samtools. > > USE_BAM=1 compiles without errors. > > USE_TABIX=1 returns the "implicit declaration of function > ti_bgzf_tell" > error below. > > I have patched the tabix source code with the appropriate KNET_HOOKS > file; tabix > compiles without errors. tabix is version 0.2.5, obtained from > SourceForge. > > Is this an actual error, or a warning that can be safely ignored > (i.e., > remove -Wimplicit > from the gcc options in common.mk)? > > Help greatly appreciated... > Mahmud > > - - - - - - - > > > Hello everyone, > > I'm attempting to set up a mirror site, and compiling from source. I > get > the following when I attempt the build: > > linefile.c:261: warning: implicit declaration of function > ti_bgzf_tell > gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 > -DCOLOR32 -DUSE_BAM -DKNETFILE_HOOKS -DUSE_TABIX -DKNETFILE_HOOKS > -Wall > -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc > -I../../../inc -I../../../../inc -I../../../../../inc > -I/usr/include/libpng12 -I/mnt/raid5/samtools-0.1.18 > -I/mnt/raid5/tabix-0.2.5 -I/usr/include/mysql -o gbWarn.o -c gbWarn.c > make[2]: *** [compile] Error 1 > make[1]: *** [cartReset.alpha] Error 2 > make[2]: *** [compile] Error 1 > make[1]: *** [hgConvert.alpha] Error 2 > make[2]: *** [compile] Error 1 > make[1]: *** [hgBlat.alpha] Error 2 > make[2]: *** [compile] Error 1 > make[1]: *** [das.alpha] Error 2 > make: *** [cgi-alpha] Error 2 > > > and the build fails. The solution has so far eluded me. The only > reference > I have found to ti_bgzf_tell is in regards to samtools and tabix, but > I > have already applied the KNETFILE_HOOKS patches and recompiled both of > them as instructed. I have removed -Werror in common.mk . > > My system is RHEL6.1, x86_64, gcc version 4.4.5 20110214 (Red Hat > 4.4.5-6). > Any help will be greatly appreciated. > > Mahmud > > -- > Mahmud Siddiqi, PhD > Carnegie Institution/Embryology > > _______________________________________________ > Genome-mirror mailing list > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
