Red Hat Bugzilla – Bug 127354
join does not produce correct output
Last modified: 2007-11-30 17:07:02 EST
From Bugzilla Helper: User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040615 Firefox/0.9 Description of problem: I have a scientific program that uses the 'join' program extensively, in some rather odd ways. In particular there is one part where it issues the following command: join -v 1 -o 1.2 data_file empty_file which is supposed to grab the second column of text in standard input. However with the version of join in coreutils-4.5.3-26, it produces an empty file with carriage returns instead of lines of text. With earlier versions of join (from textutils-2.0.21-1), or with coreutils-5.2.1 from gnu.org this bug does not exist. Sample data file: fsh_110703_1_0052990_0055770 /homes/stolcke/transfer/hub5-data/dev2004-noec-autoseg/waveforms/fsh_110703_1/fsh_110703_1_0052990_0055770.wav empty_file is just an empty file, /dev/null would suffice. On RH7.3, textutils-2.0.21-1 and RHEL 3, coreutils-5.2.1(gnu.org): bash-2.05b$ join -v 1 -o 1.2 data_file empty_file /homes/stolcke/transfer/hub5-data/dev2004-noec-autoseg/waveforms/fsh_110703_1/fsh_110703_1_0052990_0055770.wav bash-2.05b$ On RHEL coreutils-4.5.3-26: bash-2.05b$ join -v 1 -o 1.2 tmp_sort /dev/null bash-2.05b$ However if I do: bash-2.05b$ join -v 1 -o 1.3 tmp_sort /dev/null It produces the correct output. So it looks like this bug involves using whitespace space as a delimiter. Small text files of random junk with a space between the fields do not exhibit this bug though. Version-Release number of selected component (if applicable): coreutils-4.5.3-26 How reproducible: Always Steps to Reproduce: 1. Create a file that contains "fsh_110703_1_0351310_0351890 /homes/stolcke/transfer/hub5-data/dev2004-noec-autoseg/waveforms/fsh_110703_1/fsh_110703_1_0351310_0351890.wav" 2. Run join -v 1 -o 1.2 filename /dev/null Actual Results: It outputs a single carriage return. Expected Results: It should output the second column of data. With small amounts of text in the sample file this *does* work properly. Additional info:
Please attach your example data file so that I can be sure that I'm looking at the same problem here. Bugzilla has line-wrapped your comment and I can't be sure I'm looking at the same bytes.
Created attachment 101824 [details] A sample data file join -v 1 -o 1.2 data_file /dev/null produces blank lines of text.
I just noticed the produced data file has two spaces between the fields. Still, join 4.5.3 in RHEL does perform differently from join in RH 7.3 and join downloaded from gnu.org.
Okay, it is certainly the same issue I was looking at then. I have fixed this issue in our internal source repository, and the fix will be included in any future coreutils update for Red Hat Enterprise Linux 3. (Fedora Core is not affected.) Thanks for the report.
Any news on when can we expect a new version of coreutils that fixes this bug?
There is no coreutils update for Red Hat Enterprise Linux 3 currently planned.
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 the 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-2005-544.html