The commit <https://sourceforge.net/p/sashimi/code/7460/>fixed the problem. Thx! Great software, Great team.
On Monday, November 21, 2016 at 11:46:15 AM UTC-8, Jimmy Eng wrote: > > I found the offending code causing the buffer overflow issue in > InteractParser.cpp and committed the fix to trunk (revision 7460). > > On Thu, Nov 17, 2016 at 2:12 PM, Roden Luo <[email protected] > <javascript:>> wrote: > >> Sorry guys, there are problems by installing TPPv5 in this way. >> >> 1. I cannot run comet, the same problem as described here >> <https://groups.google.com/forum/#!topic/comet-ms/Tw_toe0SMHE>. >> >> 2. I can run command 'xinteract -OA -PPM -Nbasename basename.pep.xml' for >> a file less than 60M with no reported error and shows job completed. But >> when I run it for a 71M file, it is interrupted by buffer overflow error >> while calling "InteractParser". Below is the error log. >> >> Any help would be much appreciated. Thx! >> Roden >> >> ========== >> # Error log begins >> >> $ /usr/local/tpp/bin/xinteract -OA -PPM -N20161103_Illumina_GulCAspN_01 >> 20161103_Illumina_GulCAspN_01.pep.xml >> >> /usr/local/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build >> 201611162218-exported (Linux-x86_64)) >> PPM mode in Accurate Mass Model ... >> naming output file interact-20161103_Illumina_GulCAspN_01.pep.xml >> >> running: "/usr/local/tpp/bin/InteractParser >> 'interact-20161103_Illumina_GulCAspN_01.pep.xml' >> '20161103_Illumina_GulCAspN_01.pep.xml' -L'7'" >> file 1: 20161103_Illumina_GulCAspN_01.pep.xml >> SUCCESS: CORRECTED data file >> /home/roden/tpp_test_run/20161103_Illumina_GulCAspN_01.mzXML in >> msms_run_summary tag ... >> SUCCESS: CORRECTED data file >> /home/roden/tpp_test_run/20161103_Illumina_GulCAspN_01.mzXML in >> msms_run_summary tag ... >> processed altogether 21262 results >> *** buffer overflow detected ***: /usr/local/tpp/bin/InteractParser >> terminated >> ======= Backtrace: ========= >> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f1b913737e5] >> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f1b9141456c] >> /lib/x86_64-linux-gnu/libc.so.6(+0x116570)[0x7f1b91412570] >> /lib/x86_64-linux-gnu/libc.so.6(+0x115ad9)[0x7f1b91411ad9] >> /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x80)[0x7f1b913776b0] >> /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0xc90)[0x7f1b91349e00] >> /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7f1b91411b64] >> /lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7f1b91411abd] >> /usr/local/tpp/bin/InteractParser[0x412b5c] >> /usr/local/tpp/bin/InteractParser[0x40db8c] >> /usr/local/tpp/bin/InteractParser[0x40adaa] >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f1b9131c830] >> /usr/local/tpp/bin/InteractParser[0x40c8e9] >> ======= Memory map: ======== >> 00400000-00642000 r-xp 00000000 fc:00 23731550 >> /usr/local/tpp/bin/InteractParser >> 00841000-0086b000 r--p 00241000 fc:00 23731550 >> /usr/local/tpp/bin/InteractParser >> 0086b000-008a9000 rw-p 0026b000 fc:00 23731550 >> /usr/local/tpp/bin/InteractParser >> 008a9000-008af000 rw-p 00000000 00:00 0 >> 00a7f000-04d7a000 rw-p 00000000 00:00 0 >> [heap] >> 7f1b8b8f9000-7f1b8c2fa000 rw-p 00000000 00:00 0 >> 7f1b8c2fa000-7f1b8ccfb000 rw-p 00000000 00:00 0 >> 7f1b8ccfb000-7f1b8d6fc000 rw-p 00000000 00:00 0 >> 7f1b8eafe000-7f1b8eaff000 ---p 00000000 00:00 0 >> 7f1b8eaff000-7f1b8f2ff000 rw-p 00000000 00:00 0 >> 7f1b90602000-7f1b90903000 rw-p 00000000 00:00 0 >> 7f1b912fc000-7f1b914bb000 r-xp 00000000 fc:00 23597357 >> /lib/x86_64-linux-gnu/libc-2.23.so >> 7f1b914bb000-7f1b916bb000 ---p 001bf000 fc:00 23597357 >> /lib/x86_64-linux-gnu/libc-2.23.so >> 7f1b916bb000-7f1b916bf000 r--p 001bf000 fc:00 23597357 >> /lib/x86_64-linux-gnu/libc-2.23.so >> 7f1b916bf000-7f1b916c1000 rw-p 001c3000 fc:00 23597357 >> /lib/x86_64-linux-gnu/libc-2.23.so >> 7f1b916c1000-7f1b916c5000 rw-p 00000000 00:00 0 >> 7f1b916c5000-7f1b916db000 r-xp 00000000 fc:00 23593495 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f1b916db000-7f1b918da000 ---p 00016000 fc:00 23593495 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f1b918da000-7f1b918db000 rw-p 00015000 fc:00 23593495 >> /lib/x86_64-linux-gnu/libgcc_s.so.1 >> 7f1b918db000-7f1b919e3000 r-xp 00000000 fc:00 23597349 >> /lib/x86_64-linux-gnu/libm-2.23.so >> 7f1b919e3000-7f1b91be2000 ---p 00108000 fc:00 23597349 >> /lib/x86_64-linux-gnu/libm-2.23.so >> 7f1b91be2000-7f1b91be3000 r--p 00107000 fc:00 23597349 >> /lib/x86_64-linux-gnu/libm-2.23.so >> 7f1b91be3000-7f1b91be4000 rw-p 00108000 fc:00 23597349 >> /lib/x86_64-linux-gnu/libm-2.23.so >> 7f1b91be4000-7f1b91d56000 r-xp 00000000 fc:00 23726109 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 >> 7f1b91d56000-7f1b91f56000 ---p 00172000 fc:00 23726109 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 >> 7f1b91f56000-7f1b91f60000 r--p 00172000 fc:00 23726109 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 >> 7f1b91f60000-7f1b91f62000 rw-p 0017c000 fc:00 23726109 >> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 >> 7f1b91f62000-7f1b91f66000 rw-p 00000000 00:00 0 >> 7f1b91f66000-7f1b91f6d000 r-xp 00000000 fc:00 23597352 >> /lib/x86_64-linux-gnu/librt-2.23.so >> 7f1b91f6d000-7f1b9216c000 ---p 00007000 fc:00 23597352 >> /lib/x86_64-linux-gnu/librt-2.23.so >> 7f1b9216c000-7f1b9216d000 r--p 00006000 fc:00 23597352 >> /lib/x86_64-linux-gnu/librt-2.23.so >> 7f1b9216d000-7f1b9216e000 rw-p 00007000 fc:00 23597352 >> /lib/x86_64-linux-gnu/librt-2.23.so >> 7f1b9216e000-7f1b92186000 r-xp 00000000 fc:00 23597356 >> /lib/x86_64-linux-gnu/libpthread-2.23.so >> 7f1b92186000-7f1b92385000 ---p 00018000 fc:00 23597356 >> /lib/x86_64-linux-gnu/libpthread-2.23.so >> 7f1b92385000-7f1b92386000 r--p 00017000 fc:00 23597356 >> /lib/x86_64-linux-gnu/libpthread-2.23.so >> 7f1b92386000-7f1b92387000 rw-p 00018000 fc:00 23597356 >> /lib/x86_64-linux-gnu/libpthread-2.23.so >> 7f1b92387000-7f1b9238b000 rw-p 00000000 00:00 0 >> 7f1b9238b000-7f1b923a4000 r-xp 00000000 fc:00 23593592 >> /lib/x86_64-linux-gnu/libz.so.1.2.8 >> 7f1b923a4000-7f1b925a3000 ---p 00019000 fc:00 23593592 >> /lib/x86_64-linux-gnu/libz.so.1.2.8 >> 7f1b925a3000-7f1b925a4000 r--p 00018000 fc:00 23593592 >> /lib/x86_64-linux-gnu/libz.so.1.2.8 >> 7f1b925a4000-7f1b925a5000 rw-p 00019000 fc:00 23593592 >> /lib/x86_64-linux-gnu/libz.so.1.2.8 >> 7f1b925a5000-7f1b925cb000 r-xp 00000000 fc:00 23597353 >> /lib/x86_64-linux-gnu/ld-2.23.so >> 7f1b926bc000-7f1b927b8000 rw-p 00000000 00:00 0 >> 7f1b927c7000-7f1b927ca000 rw-p 00000000 00:00 0 >> 7f1b927ca000-7f1b927cb000 r--p 00025000 fc:00 23597353 >> /lib/x86_64-linux-gnu/ld-2.23.so >> 7f1b927cb000-7f1b927cc000 rw-p 00026000 fc:00 23597353 >> /lib/x86_64-linux-gnu/ld-2.23.so >> 7f1b927cc000-7f1b927cd000 rw-p 00000000 00:00 0 >> 7fff43890000-7fff438b1000 rw-p 00000000 00:00 0 >> [stack] >> 7fff438fe000-7fff43900000 r--p 00000000 00:00 0 >> [vvar] >> 7fff43900000-7fff43902000 r-xp 00000000 00:00 0 >> [vdso] >> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 >> [vsyscall] >> Aborted (core dumped) >> >> command "/usr/local/tpp/bin/InteractParser >> 'interact-20161103_Illumina_GulCAspN_01.pep.xml' >> '20161103_Illumina_GulCAspN_01.pep.xml' -L'7'" exited with non-zero exit >> code: 34304 >> QUIT - the job is incomplete >> >> # Error log ends >> ========== >> >> On Wednesday, November 16, 2016 at 10:55:16 AM UTC-8, Roden Luo wrote: >>> >>> Hi, >>> It takes me more than 20 hours to get this done. I do not see other >>> posts regarding the some of the problems I met. So it may be unique to >>> Ubuntu 16.04 or to my server environment. But in case someone else >>> encounters those problems, also, for seeking advice from experienced users, >>> I post it here. >>> >>> I post a detailed guidance including my debugging route here >>> <https://github.com/RodenLuo/Public_Materials/blob/master/Install_TPP_v5_on_Ubuntu_16.04.md> >>> on >>> GitHub for a better view. Below is a short description. >>> >>> 1. Follow guidance in this thread >>> <https://groups.google.com/forum/#!topic/spctools-discuss/bBQLb0PLulg>. >>> 2. Use the newest boost library to replace the old one inside TPP source >>> file and change the corresponding code in "Makefile". >>> 3. Manually install libpng-1.5.19.tar.gz in TPP source file and change >>> the corresponding code in "configure". >>> 4. Install required Perl libraries. >>> 5. Configure httpd-tpp.conf in an Apache2.4 manner. >>> 6. Change the ownership of all installed file to www-data:www-data. >>> >>> I am a novice to Linux with some experience on Perl language and shell >>> command and totally new to proteomics and TPP. This is the first time I >>> dive into the Makefile and configure file but still do not quite understand >>> what's going on there, the first time I download boost library and apache >>> stuff. Thanks to the online resources, somehow, I get this done finally. >>> But, there may be some steps being processed in an inexperienced manner. So >>> hope someone interested can have a look and give comments. (Also, there is >>> an error that has not been solved, but it seems not affecting the function >>> at all. I briefly mentioned at the end of the GitHub page. I will mention >>> in another thread soon, your suggestion will be much appreciated.) >>> >>> Thanks, >>> Roden >>> >> -- >> 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 https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
