regex remembers failure, refuses to match later

[p5pRT]

Migrated from rt.perl.org#24517 (status was 'resolved')

Searchable as RT24517$

[p5pRT]

From [email protected]

Created by [email protected]

I've been working with someone on CLPM, trying to develop a program
that creates regexes for matching DNA-like strings. I have found a
problem in the regex engine that prevents a string from matching even
though it is a valid match​:

  "GGAAACCAAA" =~ m{
  ^
  ( [ACGU]{1,3} ) (?{ print "1=[$1] $'\n" })
  ( [ACGU]{1,3} ) (?{ print " 2=[$2] $'\n" })
  ( [ACGU]{1,3} ) (?{ print " 3=[$3] ($3) $'\n" })
  ( \3 ) (?{ print " 4=[$4] ($2) $'\n" })
  ( \2 ) (?{ print " 5=[$5] $'\n" })
  $
  }x and print "OK!";

It SHOULD match like so​:

  $1 should be 'GG'
  $2 should be 'AAA'
  $3 should be 'C'
  $4 should be 'C'
  $5 should be 'AAA'

However, the output from the program shows that it doesn't try to
match 'C' when it should​:

1=[GGA] AACCAAA
  2=[AAC] CAAA
  3=[CAA] (CAA) A
  3=[CA] (CA) AA
  3=[C] (C) AAA
  2=[AA]CCAAA
  3=[C] (C) CAAA
  4=[C] (AA) AAA
  5=[AA] A
  2=[A] ACCAAA
  3=[AC] (AC) CAAA
  3=[A] (A) CCAAA
1=[GG] AAACCAAA
  2=[AAA] CCAAA
  3=[CCA] (CCA) AA
  3=[CC] (CC) AAA
<<< HERE >>>
  2=[AA] ACCAAA
  3=[AC] (AC) CAAA
  3=[A] (A) CCAAA
<<< snipped >>>

Where I've marked with "<<< HERE >>>", it should be trying

  3=[C] (C) CAAA
  4=[C] (AAA) AAA
  5=[AAA]

whereupon it should print "OK!". It never tries this; I think this
is because earlier in the regex, when it was here, it failed, so it
doesn't even bother. But now it has different values for $2 and $3,
so it *should* try. I'm not sure I have the ability to fix this one.

Perl Info

Flags:
    category=core
    severity=medium

Site configuration information for perl v5.8.0:

Configured by Debian Project at Fri Jun  6 00:10:15 EST 2003.

Summary of my perl5 (revision 5.0 version 8 subversion 0) configuration:
  Platform:
    osname=linux, osvers=2.4.20-xfs+ti1211, archname=i386-linux-thread-multi
    uname='linux kosh 2.4.20-xfs+ti1211 #1 sat nov 30 19:19:08 est 2002 i686 gnulinux '
    config_args='-Dusethreads -Duselargefiles -Dccflags=-DDEBIAN -Dcccdlflags=-fPIC -Darchname=i386-linux -Dprefix=/usr -Dprivlib=/usr/share/perl/5.8.0 -Darchlib=/usr/lib/perl/5.8.0 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/perl5 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.8.0 -Dsitearch=/usr/local/lib/perl/5.8.0 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Uusesfio -Uusenm -Duseshrplib -Dlibperl=libperl.so.5.8.0 -Dd_dosuid -des'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=undef use64bitall=undef uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O3',
    cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing'
    ccversion='', gccversion='3.3 (Debian)', gccosandvers=''
    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
    ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
    alignbytes=4, prototype=define
  Linker and Libraries:
    ld='cc', ldflags =' -L/usr/local/lib'
    libpth=/usr/local/lib /lib /usr/lib
    libs=-lgdbm -ldb -ldl -lm -lpthread -lc -lcrypt
    perllibs=-ldl -lm -lpthread -lc -lcrypt
    libc=/lib/libc-2.3.1.so, so=so, useshrplib=true, libperl=libperl.so.5.8.0
    gnulibc_version='2.3.1'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-rdynamic'
    cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'

Locally applied patches:
    


@INC for perl v5.8.0:
    /etc/perl
    /usr/local/lib/perl/5.8.0
    /usr/local/share/perl/5.8.0
    /usr/lib/perl5
    /usr/share/perl5
    /usr/lib/perl/5.8.0
    /usr/share/perl/5.8.0
    /usr/local/lib/site_perl
    .


Environment for perl v5.8.0:
    HOME=/home/japhy
    LANG=C
    LANGUAGE (unset)
    LD_LIBRARY_PATH (unset)
    LOGDIR (unset)
    PATH=/usr/local/bin:/usr/bin:/usr/ucb:/usr/sbin:/usr/openwin/bin:/bin:/usr/local/netscape:/usr/ccs/bin:/home/japhy/bin:.
    PERL_BADLANG (unset)
    SHELL=/bin/tcsh

[p5pRT]

From @Abigail

On Tue, Nov 18, 2003 at 08​:47​:40PM -0000, japhy@​perlmonk.org (via RT) wrote​:

# New Ticket Created by japhy@​perlmonk.org
# Please include the string​: [perl #24517]
# in the subject line of all future correspondence about this issue.
# <URL​: http​://rt.perl.org/rt2/Ticket/Display.html?id=24517 >

This is a bug report for perl from japhy@​perlmonk.org,
generated with the help of perlbug 1.34 running under perl v5.8.0.

-----------------------------------------------------------------
[Please enter your report here]

I've been working with someone on CLPM, trying to develop a program
that creates regexes for matching DNA-like strings. I have found a
problem in the regex engine that prevents a string from matching even
though it is a valid match​:

"GGAAACCAAA" =~ m{
^
( [ACGU]{1,3} ) (?{ print "1=[$1] $'\n" })
( [ACGU]{1,3} ) (?{ print " 2=[$2] $'\n" })
( [ACGU]{1,3} ) (?{ print " 3=[$3] ($3) $'\n" })
( \3 ) (?{ print " 4=[$4] ($2) $'\n" })
( \2 ) (?{ print " 5=[$5] $'\n" })
$
}x and print "OK!";

It SHOULD match like so​:

$1 should be 'GG'
$2 should be 'AAA'
$3 should be 'C'
$4 should be 'C'
$5 should be 'AAA'

However, the output from the program shows that it doesn't try to
match 'C' when it should​:

[ SNIP ]

whereupon it should print "OK!". It never tries this; I think this
is because earlier in the regex, when it was here, it failed, so it
doesn't even bother. But now it has different values for $2 and $3,
so it *should* try. I'm not sure I have the ability to fix this one.

In 5.8.1 and 5.8.2 it prints​:

1=[GGA] AACCAAA
  2=[AAC] CAAA
  3=[CAA] (CAA) A
  3=[CA] (CA) AA
  3=[C] (C) AAA
  2=[AA] CCAAA
  3=[CCA] (CCA) AA
  3=[CC] (CC) AAA
  3=[C] (C) CAAA
  4=[C] (AA) AAA
  5=[AA] A
  2=[A] ACCAAA
  3=[ACC] (ACC) AAA
  3=[AC] (AC) CAAA
  3=[A] (A) CCAAA
1=[GG] AAACCAAA
  2=[AAA] CCAAA
  3=[CCA] (CCA) AA
  3=[CC] (CC) AAA
  3=[C] (C) CAAA
  4=[C] (AAA) AAA
  5=[AAA]
OK!

So, I'd say the bug has already been fixed.

Abigail

[p5pRT]

From [email protected]

On Nov 19, via RT and UNEXPECTED_DATA_AFTERabigail@​abigail.nlsaid​:

On Tue, Nov 18, 2003 at 08​:47​:40PM -0000, japhy@​perlmonk.org (via RT) wrote​:

# New Ticket Created by japhy@​perlmonk.org
# Please include the string​: [perl #24517]
# in the subject line of all future correspondence about this issue.
# <URL​: http​://rt.perl.org/rt2/Ticket/Display.html?id=24517 >

whereupon it should print "OK!". It never tries this; I think this
is because earlier in the regex, when it was here, it failed, so it
doesn't even bother. But now it has different values for $2 and $3,
so it *should* try. I'm not sure I have the ability to fix this one.

In 5.8.1 and 5.8.2 it prints​:
[snip]
So, I'd say the bug has already been fixed.

Excellent.

--
Jeff "japhy" Pinyan japhy@​pobox.com http​://www.pobox.com/~japhy/
RPI Acacia brother #734 http​://www.perlmonks.org/ http​://www.cpan.org/
<stu> what does y/// stand for? <tenderpuss> why, yansliterate of course.
[ I'm looking for programming work. If you like my work, let me know. ]

[p5pRT]

@rgs - Status changed from 'new' to 'resolved'