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.
