Red Hat Bugzilla – Bug 440258
grep-mem-exhausted.patch introduces regressions
Last modified: 2018-09-18 10:04:04 EDT
Description of problem:
grep-2.5.2-32.3 from RHEL 4.5 seems to fail on large files :
$ grep '12884102-12884161_12884190-12884243;9,5;28' /env/cns/tmp/test_file
$ tail /env/cns/tmp/test_file > /env/cns/tmp/test_file.tail
$ grep '12884102-12884161_12884190-12884243;9,5;28' /env/cns/tmp/test_file.tail
../lecures_NM_eland_result.seq-15290226 TGGGGGAGGGTTTTTTGTTTTATAAAGATGATC [...]
It appears this behaviour has been introduced by the grep-mem-exhausted.patch --
the problem disappears if we rebuild an RPM without this patch.
Version-Release number of selected component (if applicable):
Steps to Reproduce:
1. wget http://www.genoscope.cns.fr/externe/test_file (warning: 1gb)
2. grep '12884102-12884161_12884190-12884243;9,5;28' /env/cns/tmp/test_file
The last line of this file contains the pattern (see above)
Re-building without patch #9 (grep-mem-exhausted.patch) solves the problem
Please note that grep-mem-exhausted.patch was introduced to fix bug #198167.
Though the patch might actually get removed on future releases of RHEL, I decided to keep a modified version in RHEL 4 updates: when the buffer limit (200MB) is reached, grep bails out with a message "line too long".
Keep in mind that grep is a tool for processing text files; it is not suited to search arbitrary data.
Fedora rawhide clone: bug 481765
RHEL 5 clone: bug 483073
An advisory has been issued which should help the problem
described in this bug report. This report is therefore being
closed with a resolution of ERRATA. For more information
on therefore solution and/or where to find the updated files,
please follow the link below. You may reopen this bug report
if the solution does not work for you.