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
