From wolski at molgen.mpg.de  Thu Feb 19 19:07:57 2004
From: wolski at molgen.mpg.de (wolski@molgen.mpg.de)
Date: Thu Feb 19 19:08:24 2004
Subject: [Rd] Process R segmentation with strsplit() (PR#6601)
Message-ID: <20040219180757.C1019EDF2@slim.kubism.ku.dk>

Getting a crash with R1.8.1 on windows 2000 an linux with the strsplit.
Version:
 platform = i386-pc-mingw32
 arch = i386
 os = mingw32
 system = i386, mingw32
 status = 
 major = 1
 minor = 8.1
 year = 2003
 month = 11
 day = 21
 language = R

Version:
 platform = i386-pc-mingw32
 arch = i386
 os = mingw32
 system = i386, mingw32
 status = 
 major = 1
 minor = 8.1
 year = 2003
 month = 11
 day = 21
 language = R


The code causing the crash is given below. 

Eryk.


res <- "HTTP/1.1 200 OK\r\nDate: Thu, 19 Feb 2004 17:55:04 GMT\r\nServer: Apache/1.3.26 (Win32)\r\nTransfer-Encoding: chunked\r\nContent-Type: text/html; charset=ISO-8859-1\r\n\r\nf5b\r\n\n<HTML>\n<HEAD>\n<TITLE>Mascot Search Results: Protein View</TITLE>\n</HEAD>\n\n<BODY BGCOLOR=\"#ffffff\" ALINK=\"#0000ff\" VLINK=\"#0000ff\">\n\n<H1><IMG SRC=\"../images/88x31_logo_white.gif\" WIDTH=\"88\" HEIGHT=\"31\"\nALIGN=\"TOP\" BORDER=\"0\" NATURALSIZEFLAG=\"3\"> Mascot Search Results</H1>\n\n<H3>Protein View</H3>\n<FORM METHOD=\"POST\">\n<INPUT TYPE=\"hidden\" NAME=\"file\" VALUE=\"../data/20040219/F253567.dat\">\n<INPUT TYPE=\"hidden\" NAME=\"hit\" VALUE=\"1\">\n<INPUT TYPE=\"hidden\" NAME=\"showall\" VALUE=\"true\">\n<INPUT TYPE=\"hidden\" NAME=\"protscore\" VALUE=\"0\">\n<FONT FACE='Courier New,Courier,monospace'><PRE>Match to: <B>At1g61780</B>; Score: <B>15</B>\n<B>hypothetical protein</B>\n\nNominal mass (M<SUB>r</SUB>): <B>11619</B>; Calculated pI value: <B>9.43</B>\nNCBI BLA!
 ST search of <A HREF=\"http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=Semiauto&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=(none)&EXPECT=10&FILTER=L&FORMAT_BLOCK_ON_RESPAGE=None&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GAPCOSTS=11+1&I_THRESH=0.001&LAYOUT=TwoWindows&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&QUERY=MVCDKCEKKLSKVIVPDKWKDGARNVTEGGGRKINENKLLSKKNRWSPYSTCTTKCMICKQQVHQDGKYCHTCAYSKGVCAMCGKQVLDTKMYKQSNV&SERVICE=plain&SET_DEFAULTS.x=9&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&WORD_SIZE=3&END_OF_HTTPGET=Yes\" TARGET=\"_blank\">At1g61780</A> against nr\nUnformatted <A HREF=\"../cgi/getseq.pl?GabiMips+At1g61780+seq\" TARGET=\"_blank\">sequence string</A> for pasting into other applications\n\nFixed modifications: Carbamidomethyl (C)\nVariable modifications: Oxidation (M)\nCleavage by Trypsin: cuts C-term side of KR unless next residue is P\nNumber of mass value!
 s searched: <B>6</B>\nNumber of mass values matched: <B>1</B>\!
 nSequenc
e Coverage: <B>8%</B>\n\nMatched peptides shown in <B><FONT COLOR=#FF0000>Bold Red</FONT></B>\n\n     <B>1</B> MVCDKCEKKL SKVIVPDKWK DGARNVTEGG GRKINENKLL SKKNRWSPYS <B>\n    51</B> TCTTKCMICK QQVHQDGKYC HTCAYSK<B><FONT COLOR=#FF0000>GVC AMCGK</FONT></B>QVLDT KMYKQSNV\n</PRE></FONT>\n<P><INPUT TYPE=\"submit\" VALUE=\"Show matched peptides only\" \n        onClick=\"this.form.showall.value='false'; return true\">\n<P><INPUT TYPE=\"submit\" VALUE=\"Sort Peptides By\">&nbsp;\n<INPUT TYPE=\"radio\" NAME=\"sort\" VALUE=\"startup\" checked>Residue Number&nbsp;\n<INPUT TYPE=\"radio\" NAME=\"sort\" VALUE=\"massup\" >Increasing Mass&nbsp;\n<INPUT TYPE=\"radio\" NAME=\"sort\" VALUE=\"massdown\" >Decreasing Mass&nbsp;\n<FONT FACE='Courier New,Courier,monospace'><PRE>\n<B> Start - End   Observed  Mr(expt) Mr(calc)   Delta   Miss Sequence</B>\n<FONT COLOR=#000000>     1 - 1            &nbsp;        &nbsp;   149.05         &nbsp;    0  M </FONT> \n<FONT COLOR=#000000>     1 - 5           !
  &nbsp;        &nbsp;   651.27         &nbsp;    0  MVCDK </FONT> \n<FONT COLOR=#000000>     1 - 8            &nbsp;        &nbsp;  1068.44         &nbsp;    1  MVCDKCEK </FONT> \n<FONT COLOR=#000000>     2 - 5            &nbsp;        &nbsp;   520.23         &nbsp;    0  VCDK </FONT> \n<FONT COLOR=#000000>     2 - 8            &nbsp;        &nbsp;   937.40         &nbsp;    1  VCDKCEK </FONT> \n<FONT COLOR=#000000>     6 - 8            &nbsp;        &nbsp;   435.18         &nbsp;    0  CEK </FONT> \n<FONT COLOR=#000000>     6 - 9            &nbsp;        &nbsp;   563.27         &nbsp;    1  CEKK </FONT> \n<FONT COLOR=#000000>     9 - 9            &nbsp;        &nbsp;   146.11         &nbsp;    0  K </FONT> \n<FONT COLOR=#000000>     9 - 12           &nbsp;        &nbsp;   474.32         &nbsp;    1  KLSK </FONT> \n<FONT COLOR=#000000>    10 - 12           &nbsp;        &nbsp;   346.22         &nbsp;    0  LSK </FONT> \n<FONT COLOR=#000000>    10 - 18           &nbsp;      !
   &nbsp;   997.62         &nbsp;    1  LSKVIVPDK </FONT> \n<FO!
 NT COLOR
=#000000>    13 - 18           &nbsp;        &nbsp;   669.41         &nbsp;    0  VIVPDK </FONT> \n<FONT COLOR=#000000>    13 - 20           &nbsp;        &nbsp\r\nf78\r\n;   983.58         &nbsp;    1  VIVPDKWK </FONT> \n<FONT COLOR=#000000>    19 - 20           &nbsp;        &nbsp;   332.18         &nbsp;    0  WK </FONT> \n<FONT COLOR=#000000>    19 - 24           &nbsp;        &nbsp;   731.37         &nbsp;    1  WKDGAR </FONT> \n<FONT COLOR=#000000>    21 - 24           &nbsp;        &nbsp;   417.20         &nbsp;    0  DGAR </FONT> \n<FONT COLOR=#000000>    21 - 32           &nbsp;        &nbsp;  1187.56         &nbsp;    1  DGARNVTEGGGR </FONT> \n<FONT COLOR=#000000>    25 - 32           &nbsp;        &nbsp;   788.38         &nbsp;    0  NVTEGGGR </FONT> \n<FONT COLOR=#000000>    25 - 33           &nbsp;        &nbsp;   916.47         &nbsp;    1  NVTEGGGRK </FONT> \n<FONT COLOR=#000000>    33 - 33           &nbsp;        &nbsp;   146.11         &nbsp;    0  K </FONT>!
  \n<FONT COLOR=#000000>    33 - 38           &nbsp;        &nbsp;   744.41         &nbsp;    1  KINENK </FONT> \n<FONT COLOR=#000000>    34 - 38           &nbsp;        &nbsp;   616.32         &nbsp;    0  INENK </FONT> \n<FONT COLOR=#000000>    34 - 42           &nbsp;        &nbsp;  1057.61         &nbsp;    1  INENKLLSK </FONT> \n<FONT COLOR=#000000>    39 - 42           &nbsp;        &nbsp;   459.31         &nbsp;    0  LLSK </FONT> \n<FONT COLOR=#000000>    39 - 43           &nbsp;        &nbsp;   587.40         &nbsp;    1  LLSKK </FONT> \n<FONT COLOR=#000000>    43 - 43           &nbsp;        &nbsp;   146.11         &nbsp;    0  K </FONT> \n<FONT COLOR=#000000>    43 - 45           &nbsp;        &nbsp;   416.25         &nbsp;    1  KNR </FONT> \n<FONT COLOR=#000000>    44 - 45           &nbsp;        &nbsp;   288.15         &nbsp;    0  NR </FONT> \n<FONT COLOR=#000000>    44 - 55           &nbsp;        &nbsp;  1499.68         &nbsp;    1  NRWSPYSTCTTK </FONT> \n<F!
 ONT COLOR=#000000>    46 - 55           &nbsp;        &nbsp;  !
 1229.54 
        &nbsp;    0  WSPYSTCTTK </FONT> \n<FONT COLOR=#000000>    46 - 60           &nbsp;        &nbsp;  1921.82         &nbsp;    1  WSPYSTCTTKCMICK </FONT> \n<FONT COLOR=#000000>    56 - 60           &nbsp;        &nbsp;   710.29         &nbsp;    0  CMICK </FONT> \n<FONT COLOR=#000000>    56 - 68           &nbsp;        &nbsp;  1630.74         &nbsp;    1  CMICKQQVHQDGK </FONT> \n<FONT COLOR=#000000>    61 - 68           &nbsp;        &nbsp;   938.46         &nbsp;    0  QQVHQDGK </FONT> \n<FONT COLOR=#000000>    61 - 77           &nbsp;        &nbsp;  2108.92         &nbsp;    1  QQVHQDGKYCHTCAYSK </FONT> \n<FONT COLOR=#000000>    69 - 77           &nbsp;        &nbsp;  1188.47         &nbsp;    0  YCHTCAYSK </FONT> \n<FONT COLOR=#000000>    69 - 85           &nbsp;        &nbsp;  2051.81         &nbsp;    1  YCHTCAYSKGVCAMCGK </FONT> \n<B><FONT COLOR=#FF0000>    78 - 85      882.30   881.29   881.36    -0.06     0  GVCAMCGK </FONT></B> \n<FONT COLOR=#000000>    78 - 91!
            &nbsp;        &nbsp;  1565.74         &nbsp;    1  GVCAMCGKQVLDTK </FONT> \n<FONT COLOR=#000000>    86 - 91           &nbsp;        &nbsp;   702.39         &nbsp;    0  QVLDTK </FONT> \n<FONT COLOR=#000000>    86 - 94           &nbsp;        &nbsp;  1124.59         &nbsp;    1  QVLDTKMYK </FONT> \n<FONT COLOR=#000000>    92 - 94           &nbsp;        &nbsp;   440.21         &nbsp;    0  MYK </FONT> \n<FONT COLOR=#000000>    92 - 98           &nbsp;        &nbsp;   868.41         &nbsp;    1  MYKQSNV </FONT> \n<FONT COLOR=#000000>    95 - 98           &nbsp;        &nbsp;   446.21         &nbsp;    0  QSNV </FONT> \n\n<B>No match to:</B> 742.10, 758.09, 816.95, 832.89, 864.11\n<P><IMG SRC=\"mass_error.pl?file=../data/20040219/F253567.dat&px=&units=ppm&hit=1\" WIDTH=450 HEIGHT=150 ALT=\"Error Distribution\">\n</FORM><HR>\nNo source defined for full-text report\n</PRE></FONT>\n<P><TABL"



rget<- gsub("\r\n[0-9a-z]+\r\n","",res,perl=T)
rtmp <- strsplit(rget,"\n")[[1]]


[Rd] Process R segmentation with strsplit() (PR#6601)
wolski@molgen.mpg.de