Thanks very much! No worries, I'll get your changes through SVN. It's quite great of you to come back with a fix so quickly! I'll follow up if it doesn't work for me for some reason.
Thanks! Eric On Dec 20, 2012 1:49 PM, "Joseph Slagel" <[email protected]> wrote: > Brian, Eric, > > I just checked into the TPP trunk a fix that corrects the issue. It > turned out to be an invalid use of strcpy() which doesn't seem to manifest > itself on older versions of glibc/gcc and the platforms we regularly use. > > I can provide a patch for your source if you need it or you can get it > from our SourceForge subversion repository. > > -Joe > > > On Fri, Dec 14, 2012 at 6:38 PM, Eric Paniagua <[email protected]>wrote: > >> I am seeing a similar misbehavior in a new Linux installation of TPP >> 4.6.1. While I haven't systematically investigated this apparent >> path-rewriting bug yet (I'm doing RCA on different irregularity in Pep3D), >> I have noted an (awfully crude) workaround to at least get to see some >> images. >> >> 1. Attempt to run Pep3D as usual (through Petunia in my case). >> 2. Replace each missing character with 2 copies of that character. >> 3. Click "Generate Pep3D Images" >> >> In my case, step 2 appears to act as a left inverse for the path mutation >> process which is deleting characters. >> >> Hopefully that is helpful to someone. I would be curious to know about >> cases where this temporary workaround fails, as they may be helpful to know >> when debugging. >> >> I, too, would be grateful to hear from anyone who has sorted this out or >> is attempting to fix it. I can provide more detailed system and >> configuration info for my installation if it would be helpful. >> >> Thanks, >> Eric Paniagua >> Informatics Software Developer >> Cold Spring Harbor Laboratory >> >> On Dec 7, 2012 9:44 AM, "Brian Hampton" <[email protected]> wrote: >> > >> > I am seeing a strange behavior in TPP 4.6.1 (also saw same in 4.5.2) >> Linux install. When I click on the link to generate a Ped3D image of >> either an .mzXML file or a pep.xml file it will re-write the file name and >> then not be able to generate the Pep3D image cause a file with that name >> doesn't exist. For example: >> > >> > /usr/local/tpp/data/projects/s-aorta-1/121205_Saorta1_Guan-6.mzXML is >> the input file to Pep3D and it will re-write the file name to: >> > >> > /usr/local/tpp/data/projects/s-aorta-1/121205_Sarta1_Guan-6.mzXML and >> then fail cause that file doesn't exist. Note the missing "o". >> > >> > If I keep clicking the button to generate the Pep3D image it will >> continue to delete certain letters and then I got this: >> > >> > >> /usr/local/tpp/data/projects/s-aorta-1/121205_Saa1_Guan-6.mzXMLmzRange=Full >> > >> > The mzXML files are generated by MSConvert on a PC from a thermo .raw >> file no options other than 32 bit. >> > >> > Any clues? >> > >> > Thanks in advance, >> > >> > Brian >> > >> > -- >> > You received this message because you are subscribed to the Google >> Groups "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> [email protected]. >> > For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
