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): grep-2.5.2-32.3 How reproducible: always 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 Actual results: No output Expected results: The last line of this file contains the pattern (see above) Additional info: 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. http://rhn.redhat.com/errata/RHBA-2009-1019.html