pbCalResStdGlobal is a program we use during Proteome Browser database build pipeline. Ordinary users do not need it.
Fan. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Smirnov, Ivan Sent: Friday, March 05, 2010 4:41 PM To: Hiram Clawson Cc: [email protected] Subject: Re: [Genome] hgTrackDb errors Hi Hiram, here my gcc -v Using built-in specs. Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.3.3-5ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.3 --program-suffix=-4.3 --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --enable-mpfr --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 4.3.3 (Ubuntu 4.3.3-5ubuntu4) I tried your idea of playing with compilation options and found that removing -Werror magically converted errors into warnings and compilation went through. What is this pbCalResStdGlobal function is needed for anyway? Ivan ________________________________________ From: Hiram Clawson [[email protected]] Sent: Thursday, March 04, 2010 9:59 AM To: Smirnov, Ivan Cc: [email protected] Subject: Re: [Genome] hgTrackDb errors Good Morning Ivan: It appears your compiler is a newer version. I would be curious to see the output of: $ gcc -v You can get rid of the option that makes warnings become fatal by removing some options from the src/inc/common.mk file. Compile this program pbCalResStdGlobal.c and take a look at the compile command, something like this: gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_PNG -DUSE_BAM -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/hive/data/outside/samtools/samtools/x86_64 -o pbCalResStdGlobal.o -c pbCalResStdGlobal.c Try repeating that command on your command line with one of those -W arguments removed to see if it will work. One of those arguments is causing the build to fail. --Hiram Smirnov, Ivan wrote: > It worked! Thanks.. > But then it broke again: > > pbCalResStdGlobal.c: In function main: > pbCalResStdGlobal.c:233: error: ignoring return value of "system", declared with attribute warn_unused_result > pbCalResStdGlobal.c:237: error: ignoring return value of "system", declared with attribute warn_unused_result > pbCalResStdGlobal.c:240: error: ignoring return value of "fgets", declared with attribute warn_unused_result > pbCalResStdGlobal.c:247: error: ignoring return value of "system", declared with attribute warn_unused_result > pbCalResStdGlobal.c:258: error: ignoring return value of "fgets", declared with attribute warn_unused_result > pbCalResStdGlobal.c:262: error: ignoring return value of "fgets", declared with attribute warn_unused_result > pbCalResStdGlobal.c:268: error: ignoring return value of "fgets", declared with attribute warn_unused_result > pbCalResStdGlobal.c:272: error: ignoring return value of "fgets", declared with attribute warn_unused_result > make[2]: *** [pbCalResStdGlobal.o] Error 1 > make[2]: Leaving directory `/home/ivan/setupGB/kent/src/hg/protein/pbCalResStdGlobal' > make[1]: *** [pbCalResStdGlobal.utils] Error 2 > make[1]: Leaving directory `/home/ivan/setupGB/kent/src/hg/protein' > make: *** [protein.utils] Error 2 > > Ivan > ________________________________________ > From: Ann Zweig [[email protected]] > Sent: Wednesday, March 03, 2010 1:55 PM > To: Smirnov, Ivan > Cc: [email protected] > Subject: Re: [Genome] hgTrackDb errors > > Hello Ivan, > > One of our developers suggests that you change that line to: > > safef(previous, sizeof(previous), "%s", row[0]); > > then recompile. Be sure to let us know if this does not fix the problem. > > In the future, please send emails specific to your mirror site to this mailing > list: [email protected]. > > > Regards, > > ---------- > Ann Zweig > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
