Hi Stephane, Just delete gff3.o from kent/src/lib/makefile until we get this fixed. The module is new and not currently used by anything else in the tree.
Cheers, Mark Stephane Plaisance <[email protected]> writes: > I modified all the env variables as proposed but failed to build libs > (below a copy of the errors returned) > I am not able to fish the origin of this myself please help > I would like to use a lot of Jim's executables on my laptop for genome > annotations and more. > > Your help would be very welcome > > Thanks > > Stephane > ========== > did all exactly as in > http://bergman-lab.blogspot.com/2009_03_01_archive.html > only diff I see is MySQL version: 5.1.34 / OS X 10.5.7 > (MBP 2,4GHz intel core duo) > > ====== > # added to .profile and sourced > MACHTYPE=i386 # (was i386-apple-darwin9.0) > OSTYPE=darwin # (was darwin9.0) > > # obtained from mysql_config --libs (-L'/sw/lib/mysql' -lmysqlclient - > lz -lm -L/sw/lib) > MYSQLLIBS='/sw/lib/mysql/libmysqlclient.a -lz -lm -L/sw/lib' > > # obtainede from mysql_config --include > MYSQLINC=/sw/include/mysql > > export MACHTYPE OSTYPE MYSQLINC MYSQLLIBS > ======= > > BUILDING STEPS > > 1) >~/bin/jksrc/kent/src/lib$ make > ... > gff3.c:8:20: error: values.h: No such file or directory > gff3.c: In function gff3FileOpen: > gff3.c:864: error: MAXINT undeclared (first use in this function) > gff3.c:864: error: (Each undeclared identifier is reported only once > gff3.c:864: error: for each function it appears in.) > make: *** [gff3.o] Error 1 > > 2) >~/bin/jksrc/kent/src/lib$ cd ../jkOwnLib/ > >~/bin/jksrc/kent/src/jkOwnLib$ make > ... > no error message here OK! > > 3) >~/bin/jksrc/kent/src/jkOwnLib$ cd .. > >~/bin/jksrc/kent/src$ make > gcc -O -Wall -Werror -Wformat -Wimplicit -Wreturn-type - > Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - > D_GNU_SOURCE -DMACHTYPE_i386 -Wall -Werror -Wformat -Wimplicit - > Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc - > I../../../../inc -I../../../../../inc -o gff3.o -c gff3.c > gff3.c:8:20: error: values.h: No such file or directory > gff3.c: In function gff3FileOpen: > gff3.c:864: error: MAXINT undeclared (first use in this function) > gff3.c:864: error: (Each undeclared identifier is reported only once > gff3.c:864: error: for each function it appears in.) > make[1]: *** [gff3.o] Error 1 > make: *** [topLibs] Error 2 > > nothing in /bin/i386 > > HELP! > > -- > email: [email protected] > BITS - VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium > website: http://www.bits.vib.be/index.php > NEW! http://sites.google.com/site/dmbits/ > phone: +32 9 244 66 11, fax: +32 9 244 66 10 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
