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
