Hi Jose, Whoops, pardon me!
I thought that link would work. Instead, you can visit http://genome-source.cse.ucsc.edu/gitweb/ and navigate to the appropriate file. Or just update your source tree. Sorry for the non-link! -- Brooke Rhead UCSC Genome Bioinformatics Group On 02/03/11 18:12, Brooke Rhead wrote: > Hi Jose, > > The problem you reported has been fixed in the latest source code. You > can see the fix here: > > http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=commitdiff;h=dae4e0aa5ea2ca7d8322580278a017d31230138b > > (scroll down to the diff in the last file . . . the first few files are > some new tests related to the fix.) > > Thanks again for reporting the problem! > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 02/02/11 22:52, Brooke Rhead wrote: >> Hi Jose, >> >> Thank you for this report. One of our engineers is working on it, and >> the fix should be ready soon. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 02/02/11 00:24, Jose R. Valverde wrote: >>> Hi, >>> >>> this is Jose R Valverde, from CNB/CSIC in Spain. >>> >>> I have run into a "bug" in the software that popped up while >>> running ldHgGene, and which resulted in the program crashing with a >>> segmentation violation while converting a data file from GFF to GenePred >>> format. >>> >>> Using a debugger I could trace the problem to kent/src/lib/gff.c, >>> line 100, where the library makes use of the strcpy function which is >>> unsafe and, with this dataset, resulted in a buffer overrun of nameBuf. >>> The solution I used was to change >>> >>> strcpy(nameBuf, groupName); >>> by >>> strncpy(nameBuf, groupName,511); >>> >>> This allowed me to complete the run, but I am not sure -as I haven't >>> dwelt deeper in the code- if it is a good fix for, if groupName exceeds >>> nameBuf size and is truncated on output, it might do more harm than >>> good. My problem is the scarcity of documentation on the formats and >>> logic of the program, which would require me a long dive into the code >>> to find out, so if you could confirm and definitely fix the problem, I'd >>> be most grateful. >>> >>> Sincerely. >>> >>> jr >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
