This question isn't critical, but I'm curious: why is it that the TPP comes with a version of X! Tandem that's about three years older than the current version?
On May 14, 2:53 pm, Jesse J <[email protected]> wrote: > Thanks, that worked out, both with installing TPP and fixing Tandem. > > On May 14, 1:41 pm, Natalie Tasman <[email protected]> > wrote: > > > > > Thank you, David. Ubuntu 10 users (or any other system), please feel free > > to add notes or pages to the wiki. Email me if you need an account there. > > > :) > > > Natalie > > > On Fri, May 14, 2010 at 12:06 PM, David Trudgian < > > > [email protected]> wrote: > > > Hi Jesse, > > > > This problem occurs because recent versions of g++ need the headet file > > > stdint.h included explicitly to use the types the error messages are > > > complaining about. You can fix the problem by adding the following line to > > > the file extern/xtandem/src/saxhandler.h > > > > #include <stdint.h> > > > > Put it under the other #include statements that are already there. If you > > > try to compile again then it should work fine. > > > > @Natalie - I inadvertently committed this change to trunk in the commit > > > for > > > my ASAPRatio changes, so it's in trunk. > > > > DT > > > > Dr. David Trudgian, Bioinformatician in Proteomics, University of Oxford. > > > Tel: (+44) (01865 2)87807 (CCMP - Mon-Thu) > > > Tel: (+44) (01865 2)75557 (Dunn - Friday ) > > > > ________________________________________ > > > From: [email protected] > > > [[email protected]] > > > On Behalf Of Jesse J [[email protected]] > > > Sent: 14 May 2010 18:17 > > > To: spctools-discuss > > > Subject: [spctools-discuss] Installing X! Tandem Under Linux > > > > I've been running some of the TPP tools under wine, but I'm trying now > > > to run them as Linux programs, or more specifically, Ubuntu 10.04. I > > > was following the instructions on the Wiki page for installing TPP > > > under Linux (http://tools.proteomecenter.org/wiki/index.php? > > > title=TPP_4.2.1:_Installing_on_Ubuntu_9.04) but I ran into a problem > > > after the second 'make -j5': > > > > In file included from saxgamlhandler.h:140, > > > from loadmspectrum.h:235, > > > from loadmspectrum.cpp:143: > > > saxhandler.h:240: error: ‘uint32_t’ has not been declared > > > saxhandler.h:241: error: ‘uint64_t’ does not name a type > > > make[3]: *** [linuxloadmspectrum.o] Error 1 > > > make[3]: Leaving directory `/usr/local/src/tpp-4.2.1/extern/xtandem/ > > > src' > > > make[2]: *** [default] Error 2 > > > make[2]: Leaving directory `/usr/local/src/tpp-4.2.1/extern/xtandem/ > > > src' > > > make[1]: *** [xtandem] Error 2 > > > make[1]: Leaving directory `/usr/local/src/tpp-4.2.1/src' > > > make: *** [default] Error 2 > > > > I got this same error when I tried earlier to install X! Tandem by > > > itself, but trying to resolve it just got me into more problems. > > > Hoping I could just skip this, I did the next step in the > > > instructions, which was 'make install', but then I got into another > > > problem: > > > > # Create Directories > > > mkdir -p /usr/local/apps/tpp/ > > > mkdir -p /usr/local/apps/tpp/bin/ > > > mkdir -p /usr/local/apps/tpp/cgi-bin/ > > > mkdir -p /usr/local/apps/tpp/schema/ > > > # Copy all source executables and configuration files to their > > > location > > > cp -f /usr/local/src/tpp-4.2.1/src/../build/linux/ > > > ASAPRatioPeptideParser /usr/local/apps/tpp/bin/ > > > cp: cannot stat `/usr/local/src/tpp-4.2.1/src/../build/linux/ > > > ASAPRatioPeptideParser': No such file or directory > > > make: *** [install-linux-xml] Error 1 > > > > I'm not sure if this problem is related or not, but I'm really not > > > sure how to fix it. Has anyone else come across this problem? > > > > -- > > > 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]<spctools-discuss%[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]<spctools-discuss%[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 > > athttp://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 > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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