Hi Joe, I was headed down that track thanks to your updated INSTALL_LINUX document which contains updated info compared to previous releases of TPP.
After installing libgd2-xpm-dev it compiles successfully. Thanks a bunch! I also noticed the following output, and after install, the 4.8 pipeline seems to be working. Should I be worried about the below? root@nautilus:/usr/local/src/TPP-4.8.0/trans_proteomic_pipeline/src# make all > make-output.txt 2>&1 *** buffer overflow detected ***: ../htmldoc/htmldoc terminated ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x73e0f)[0x2b8046285e0f] /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x2b804631d71c] /lib/x86_64-linux-gnu/libc.so.6(+0x10a5e0)[0x2b804631c5e0] ../htmldoc/htmldoc[0x419424] ../htmldoc/htmldoc[0x429649] ../htmldoc/htmldoc[0x4033f3] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x2b8046233ec5] ../htmldoc/htmldoc[0x40539d] ======= Memory map: ======== 00400000-00442000 r-xp 00000000 08:11 32638885 /usr/local/src/TPP-4.8.0/trans_proteomic_pipeline/extern/htmldoc/htmldoc/htmldoc 00641000-00642000 r--p 00041000 08:11 32638885 /usr/local/src/TPP-4.8.0/trans_proteomic_pipeline/extern/htmldoc/htmldoc/htmldoc 00642000-00644000 rw-p 00042000 08:11 32638885 /usr/local/src/TPP-4.8.0/trans_proteomic_pipeline/extern/htmldoc/htmldoc/htmldoc 00644000-00657000 rw-p 00000000 00:00 0 0220c000-02663000 rw-p 00000000 00:00 0 [heap] 2b804534f000-2b8045372000 r-xp 00000000 08:01 4457979 /lib/x86_64-linux-gnu/ld-2.19.so 2b8045372000-2b8045375000 rw-p 00000000 00:00 0 2b8045380000-2b8045418000 rw-p 00000000 00:00 0 2b8045571000-2b8045572000 r--p 00022000 08:01 4457979 /lib/x86_64-linux-gnu/ld-2.19.so 2b8045572000-2b8045573000 rw-p 00023000 08:01 4457979 /lib/x86_64-linux-gnu/ld-2.19.so 2b8045573000-2b8045574000 rw-p 00000000 00:00 0 2b8045574000-2b8045599000 r-xp 00000000 08:01 4456701 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 2b8045599000-2b8045798000 ---p 00025000 08:01 4456701 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 2b8045798000-2b8045799000 r--p 00024000 08:01 4456701 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 2b8045799000-2b804579a000 rw-p 00025000 08:01 4456701 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 2b804579a000-2b80457b2000 r-xp 00000000 08:01 4456734 /lib/x86_64-linux-gnu/libz.so.1.2.8 2b80457b2000-2b80459b1000 ---p 00018000 08:01 4456734 /lib/x86_64-linux-gnu/libz.so.1.2.8 2b80459b1000-2b80459b2000 r--p 00017000 08:01 4456734 /lib/x86_64-linux-gnu/libz.so.1.2.8 2b80459b2000-2b80459b3000 rw-p 00018000 08:01 4456734 /lib/x86_64-linux-gnu/libz.so.1.2.8 2b80459b3000-2b80459f6000 r-xp 00000000 08:11 4460709 /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2 2b80459f6000-2b8045bf6000 ---p 00043000 08:11 4460709 /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2 2b8045bf6000-2b8045bf7000 r--p 00043000 08:11 4460709 /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2 2b8045bf7000-2b8045bf8000 rw-p 00044000 08:11 4460709 /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2 2b8045bf8000-2b8045c08000 rw-p 00000000 00:00 0 2b8045c08000-2b8045cee000 r-xp 00000000 08:11 4458972 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 2b8045cee000-2b8045eed000 ---p 000e6000 08:11 4458972 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 2b8045eed000-2b8045ef5000 r--p 000e5000 08:11 4458972 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 2b8045ef5000-2b8045ef7000 rw-p 000ed000 08:11 4458972 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 2b8045ef7000-2b8045f0c000 rw-p 00000000 00:00 0 2b8045f0c000-2b8046011000 r-xp 00000000 08:01 4456483 /lib/x86_64-linux-gnu/libm-2.19.so 2b8046011000-2b8046210000 ---p 00105000 08:01 4456483 /lib/x86_64-linux-gnu/libm-2.19.so 2b8046210000-2b8046211000 r--p 00104000 08:01 4456483 /lib/x86_64-linux-gnu/libm-2.19.so 2b8046211000-2b8046212000 rw-p 00105000 08:01 4456483 /lib/x86_64-linux-gnu/libm-2.19.so 2b8046212000-2b80463cd000 r-xp 00000000 08:01 4457982 /lib/x86_64-linux-gnu/libc-2.19.so 2b80463cd000-2b80465cd000 ---p 001bb000 08:01 4457982 /lib/x86_64-linux-gnu/libc-2.19.so 2b80465cd000-2b80465d1000 r--p 001bb000 08:01 4457982 /lib/x86_64-linux-gnu/libc-2.19.so 2b80465d1000-2b80465d3000 rw-p 001bf000 08:01 4457982 /lib/x86_64-linux-gnu/libc-2.19.so 2b80465d3000-2b80465d8000 rw-p 00000000 00:00 0 2b80465d8000-2b80465ee000 r-xp 00000000 08:01 4456597 /lib/x86_64-linux-gnu/libgcc_s.so.1 2b80465ee000-2b80467ed000 ---p 00016000 08:01 4456597 /lib/x86_64-linux-gnu/libgcc_s.so.1 2b80467ed000-2b80467ee000 rw-p 00015000 08:01 4456597 /lib/x86_64-linux-gnu/libgcc_s.so.1 2b80467ee000-2b8046ab7000 r--p 00000000 08:11 4458993 /usr/lib/locale/locale-archive 7ffffaa57000-7ffffaa78000 rw-p 00000000 00:00 0 [stack] 7ffffabfe000-7ffffac00000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] On Monday, January 12, 2015 at 4:56:43 PM UTC-5, [email protected] wrote: > > Hi Brian, > > Do you have the GD dev library installed? and if so you may need to add > its location to the makefile as a "-I". Under ubuntu I think you can > install it via > > apt-get install libgd2-dev > > -Joe > > > On Mon, Jan 12, 2015 at 11:54 AM, Brian Hampton <[email protected] > <javascript:>> wrote: > >> Hello, >> >> I'm trying to compile TPP 4.8.0 on Ubuntu 14.04. I've successfully >> compiled versions up to 4.7.1 (currently running) but am getting a fatal >> error when it gets to compiling the XPressPeptideUpdateParserMain.o >> >> Any help greatly appreciated. >> >> Brian >> >> Here is the last couple of lines from the output: >> >> /usr/local/src/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/XPressPeptideUpdateParserMain.o >> >> Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx >> >> Quantitation/XPress/XPressPeptideUpdateParser/XPressPeptideUpdateParserMain.cxx:46:16: >> >> fatal error: gd.h: No such file or directory >> >> #include "gd.h" >> >> ^ >> >> compilation terminated. >> >> make: *** >> [/usr/local/src/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/XPressPeptideUpdateParserMain.o] >> >> Error 1 >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] <javascript:> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
