Hmm, I don't recall that htmldoc was being built on linux by default. On windows I know it isn't. You most likely don't need it so could remove it from the build process.
-Joe On Mon, Jan 12, 2015 at 2:58 PM, Brian Hampton <[email protected]> wrote: > 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]> >> 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]. >>> 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. >>> >> >> >> >> -- >> Joe Slagel >> Institute for Systems Biology >> [email protected] >> >> -- > 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. > -- Joe Slagel Institute for Systems Biology [email protected] -- 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.
