wolski@molgen.mpg.de
2004-Feb-19 19:08 UTC
[Rd] Process R segmentation with strsplit() (PR#6601)
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\"> \n<INPUT TYPE=\"radio\"
NAME=\"sort\" VALUE=\"startup\" checked>Residue
Number \n<INPUT TYPE=\"radio\" NAME=\"sort\"
VALUE=\"massup\" >Increasing Mass \n<INPUT
TYPE=\"radio\" NAME=\"sort\" VALUE=\"massdown\"
>Decreasing Mass \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 - 1 149.05 0
M </FONT> \n<FONT COLOR=#000000> 1 - 5 !
651.27 0 MVCDK
</FONT> \n<FONT COLOR=#000000> 1 - 8
1068.44 1 MVCDKCEK </FONT> \n<FONT
COLOR=#000000> 2 - 5 520.23
0 VCDK </FONT> \n<FONT COLOR=#000000> 2 - 8
937.40 1 VCDKCEK
</FONT> \n<FONT COLOR=#000000> 6 - 8
435.18 0 CEK </FONT> \n<FONT
COLOR=#000000> 6 - 9 563.27
1 CEKK </FONT> \n<FONT COLOR=#000000> 9 - 9
146.11 0 K </FONT>
\n<FONT COLOR=#000000> 9 - 12
474.32 1 KLSK </FONT> \n<FONT COLOR=#000000>
10 - 12 346.22 0
LSK </FONT> \n<FONT COLOR=#000000> 10 - 18
!
997.62 1 LSKVIVPDK </FONT>
\n<FO!
NT COLOR
=#000000> 13 - 18 669.41
0 VIVPDK </FONT> \n<FONT COLOR=#000000> 13 - 20
 \r\nf78\r\n; 983.58 1
VIVPDKWK </FONT> \n<FONT COLOR=#000000> 19 - 20
332.18 0 WK </FONT>
\n<FONT COLOR=#000000> 19 - 24
731.37 1 WKDGAR </FONT> \n<FONT
COLOR=#000000> 21 - 24 417.20
0 DGAR </FONT> \n<FONT COLOR=#000000> 21 - 32
1187.56 1 DGARNVTEGGGR
</FONT> \n<FONT COLOR=#000000> 25 - 32
788.38 0 NVTEGGGR </FONT> \n<FONT
COLOR=#000000> 25 - 33 916.47
1 NVTEGGGRK </FONT> \n<FONT COLOR=#000000> 33 - 33
146.11 0 K </FONT>!
\n<FONT COLOR=#000000> 33 - 38
744.41 1 KINENK </FONT> \n<FONT
COLOR=#000000> 34 - 38 616.32
0 INENK </FONT> \n<FONT COLOR=#000000> 34 - 42
1057.61 1 INENKLLSK
</FONT> \n<FONT COLOR=#000000> 39 - 42
459.31 0 LLSK </FONT> \n<FONT
COLOR=#000000> 39 - 43 587.40
1 LLSKK </FONT> \n<FONT COLOR=#000000> 43 - 43
146.11 0 K </FONT>
\n<FONT COLOR=#000000> 43 - 45
416.25 1 KNR </FONT> \n<FONT COLOR=#000000>
44 - 45 288.15 0
NR </FONT> \n<FONT COLOR=#000000> 44 - 55
1499.68 1 NRWSPYSTCTTK </FONT> \n<F!
ONT COLOR=#000000> 46 - 55 !
1229.54
0 WSPYSTCTTK </FONT> \n<FONT COLOR=#000000>
46 - 60 1921.82 1
WSPYSTCTTKCMICK </FONT> \n<FONT COLOR=#000000> 56 - 60
710.29 0 CMICK
</FONT> \n<FONT COLOR=#000000> 56 - 68
1630.74 1 CMICKQQVHQDGK </FONT>
\n<FONT COLOR=#000000> 61 - 68
938.46 0 QQVHQDGK </FONT> \n<FONT
COLOR=#000000> 61 - 77 2108.92
1 QQVHQDGKYCHTCAYSK </FONT> \n<FONT COLOR=#000000>
69 - 77 1188.47 0
YCHTCAYSK </FONT> \n<FONT COLOR=#000000> 69 - 85
2051.81 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!
1565.74 1
GVCAMCGKQVLDTK </FONT> \n<FONT COLOR=#000000> 86 - 91
702.39 0 QVLDTK
</FONT> \n<FONT COLOR=#000000> 86 - 94
1124.59 1 QVLDTKMYK </FONT> \n<FONT
COLOR=#000000> 92 - 94 440.21
0 MYK </FONT> \n<FONT COLOR=#000000> 92 - 98
868.41 1 MYKQSNV
</FONT> \n<FONT COLOR=#000000> 95 - 98
446.21 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]]
# aldus wolski@molgen.mpg.de :> > 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!Mmm... R crashes if you feed it a lot of junk. There must be a bug in the garbage collector. -- Peter Kleiweg