Transcript of install and index session. 00BUILD was pre-modified to point to the database. This was done under Cygwin on a Windows XP machine. Script started on Sun Sep 11 21:07:20 2005 okane@amd3200> 00BUILD ================================================================= MARBL Copyright (c) 2005 Kevin C. O'Kane, All Rights Reserved Sun Sep 11 21:07:31 CDT 2005 Configure Line Options: default ================================================================= ============== summary ======================== checking for gcc... gcc checking for C compiler default output file name... a.exe checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... .exe checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mumpsc/memsize.h usability... yes checking mumpsc/memsize.h presence... yes checking for mumpsc/memsize.h... yes checking /home/okane/mumps_compiler/include/mumpsc/memsize.h usability... yes checking /home/okane/mumps_compiler/include/mumpsc/memsize.h presence... yes checking for /home/okane/mumps_compiler/include/mumpsc/memsize.h... yes Mumps found checking sys/cygwin.h usability... yes checking sys/cygwin.h presence... yes checking for sys/cygwin.h... yes Genbank data base: ~/genbank Home URL: http://sidhe.cs.uni.edu/marbl.html Temporary directory: /tmp =============================================== configure: creating ./config.status config.status: creating lookup1.mps config.status: creating lookup2.mps config.status: creating lookup3.mps config.status: creating lookup4.mps config.status: creating lookup5.mps config.status: creating lookup6.mps config.status: creating word.mps config.status: creating show.cgi config.status: creating fasta-query.cgi config.status: creating runperl.cgi config.status: creating cw.cgi config.status: creating Makefile config.status: creating parms.h config.status: creating rdrd.cpp config.status: creating Index Configuration complete. Makefile next begin make mumpsc lookup1.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./lookup1.mps to C++: 300 lines of Mumps; 980 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc rdrd.cpp Compiling ./rdrd.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc lookup2.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./lookup2.mps to C++: 463 lines of Mumps; 2626 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc lookup3.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./lookup3.mps to C++: 561 lines of Mumps; 3715 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc lookup4.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./lookup4.mps to C++: 332 lines of Mumps; 1217 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc lookup5.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./lookup5.mps to C++: 335 lines of Mumps; 1229 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc xperl.cpp Compiling ./xperl.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc lookup6.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./lookup6.mps to C++: 545 lines of Mumps; 3549 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc word.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./word.mps to C++: 82 lines of Mumps; 558 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc dateset.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./dateset.mps to C++: 3 lines of Mumps; 169 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc gbin.cpp Compiling ./gbin.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc iseq.cpp Compiling ./iseq.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc gbinForMedline.cpp Compiling ./gbinForMedline.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc rdrc.cpp Compiling ./rdrc.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc key.cpp Compiling ./key.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc Nrml3.cpp Compiling ./Nrml3.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc normal.cpp Compiling ./normal.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc countdoc.cpp Compiling ./countdoc.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) gcc -O3 -o countaccs.cgi countaccs.c mumpsc starttime.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./starttime.mps to C++: 30 lines of Mumps; 229 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc endtime.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./endtime.mps to C++: 34 lines of Mumps; 261 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc time.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./time.mps to C++: 26 lines of Mumps; 189 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) mumpsc kquery.mps Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./kquery.mps to C++: 530 lines of Mumps; 4099 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) chown: changing ownership of `genbank': No such file or directory chgrp: changing group of `genbank': No such file or directory [note on lines above - these are ok - they are peculiar to Cygwin] okane@amd3200> Index Sun Sep 11 21:13:20 2005 1126491200 build gbdata Sun Sep 11 21:13:20 2005 1126491200 gbin < /home/okane/genbank/gbvrl1.seq Sun Sep 11 21:14:05 2005 1126491245 sort --key=1,1 < words.tmp > GBwords.1 Sun Sep 11 21:14:10 2005 1126491250 gbin < /home/okane/genbank/gbvrl2.seq Sun Sep 11 21:14:45 2005 1126491285 sort --key=1,1 < words.tmp > GBwords.2 Sun Sep 11 21:14:51 2005 1126491291 gbin < /home/okane/genbank/gbvrl3.seq Sun Sep 11 21:15:27 2005 1126491327 sort --key=1,1 < words.tmp > GBwords.3 Sun Sep 11 21:15:32 2005 1126491332 gbin < /home/okane/genbank/gbvrl4.seq Sun Sep 11 21:16:07 2005 1126491367 sort --key=1,1 < words.tmp > GBwords.4 Sun Sep 11 21:16:13 2005 1126491373 gbin < /home/okane/genbank/gbvrl5.seq Sun Sep 11 21:16:26 2005 1126491386 sort --key=1,1 < words.tmp > GBwords.5 Sun Sep 11 21:16:27 2005 1126491387 iseq.cgi < offsets start time: 1126491200 end time: 1126491417 time used: 217 Compiling from Mumps source ... The Mumps Compiler 9.00 Aug 28 2005 Translating ./medline.mps to C++: 9 lines of Mumps; 214 lines of C++ generated using mpsglobal_native file system Compiling generated C++ code... Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) Compiling ./gbinForMedline.cpp using mpsglobal_native file system Info: resolving _pcre_free by linking to __imp__pcre_free (auto-import) Sun Sep 11 21:17:03 2005 1126491423 medline.cgi < medline.out > wget.codes Sun Sep 11 21:17:03 2005 1126491423 sort -u --key=1,1 < wget.codes > wget.input 7 7 707 wget.input Sun Sep 11 21:17:03 2005 1126491423 wget -q -O wget.output -i wget.input Sun Sep 11 22:27:16 2005 1126495636 mlfilter < wget.output | col -x | gbinForMedline.cgi >> words.tmp Sun Sep 11 22:27:17 2005 1126495637 sort --key=1,1 < words.tmp > GBwords.wget start time: 1126491417 end time: 1126495637 time used: 4220 Sun Sep 11 22:27:18 2005 1126495638 sort -m --key=1,1 --temporary-directory=/tmp --buffer-size=2000M GBwords.* > words.out Sun Sep 11 22:27:34 2005 1126495654 sort --temporary-directory=/tmp --buffer-size=2000M --key=2,2 --key=1,1 < words.out > words.sorted.2 Sun Sep 11 22:28:00 2005 1126495680 rdrd.cgi > words.counted.2 Sun Sep 11 22:28:31 2005 1126495711 rdrc.cgi > weighted.words Sun Sep 11 22:30:40 2005 1126495840 sort --key=1,1 --key=2,2 < weighted.words > wgted.words.sorted Sun Sep 11 22:30:47 2005 1126495847 Nrml3.cgi Sun Sep 11 22:37:48 2005 1126496268 normal.cgi > normal.out total number of elements: 1697372 number of docs 305700 6653 13306 75075 dict.lst word count start time: 1126495654 end time: 1126496756 time used: 1102 Sun Sep 11 22:45:56 2005 1126496756 Finished okane@amd3200> kquery.cgi MARBL Version 1.00. Copyright (C) 2004 Kevin C. O'Kane. MARBL comes with ABSOLUTELY NO WARRANTY; type `/w' for details. This is free software, and you are welcome to redistribute it under certain conditions; type `/c' for details. query: kinase Expanded query: kinase Pages: 567; Fields: all AF204951/AF204952/AF210454/U95206/X76296 (150) S49773 (144) U42580/U17055/U32570 (132) AY653733/AABV01000000/AABV01000001-AABV01000088/AF529888-AF529907 (114) AF170722 (72) U94848 (72) J02425 (60) K02025 (60) K02031 (60) M75136 (60) S51129 (60) X55001/X55002 (60) D10451/D01116 (48) M14493 (48) M64000 (48) M94870 (48) S56149 (48) S63520 (48) S70449 (48) S83714 (48) X52860 (48) AF198100 (42) AJ890364 (42) AY678275 (42) AY678277 (42) X01712/J02225 (42) AF438165 (36) AJ312690 (36) AY243312 (36) AY603355 (36) D00628 (36) D00629 (36) D11079 (36) J02224 (36) L07067 (36) L36721 (36) M59931 (36) M87497 (36) M96762 (36) S46714 (36) S57428 (36) S59588 (36) U25056 (36) U46577 (36) X00255/K01487 (36) X01978/J02424/K02376/M15211/V01537 (36) X16259 (36) X52655/X58790 (36) X68653 (36) X99711 (36) AJ581527 (30) AY380826 (30) D00565 (30) J04327 (30) M16617 (30) X03764 (30) X14112/D00317/D00374/D10879/S40593 (30) AB035515 (24) AB035516 (24) AB035517 (24) AF170726 (24) AF335541 (24) AJ293568 (24) AJ410493 (24) AY009089 (24) AY372243 (24) AY714813 (24) D00438 (24) D00583 (24) D00676/D00545 (24) D13956/D00561 (24) DQ008354 (24) DQ008355 (24) J05178 (24) L22858 (24) L36139 (24) M26660 (24) M29940 (24) M29941 (24) M29942 (24) M29943/M27478 (24) M36160 (24) S55844 (24) S62554 (24) S62555 (24) S83367 (24) U01142 (24) U08228 (24) U14659 (24) U14660 (24) U29944 (24) U32589 (24) U52849 (24) U59461/AF467808 (24) U61387 (24) U93872 (24) U97553 (24) X64346 (24) X67118 (24) X67119 (24) 567 found, 100 printed 1 seconds write to "fasta.out" [n]? (y/n): n Please wait - temporary file cleanup in progress ... query: exiting... okane@amd3200> exit exit Script done on Sun Sep 11 22:47:13 2005 </amp> </body> </html>