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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:
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
On RHEL coreutils-4.5.3-26:
bash-2.05b$ join -v 1 -o 1.2 tmp_sort /dev/null
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):
Steps to Reproduce:
1. Create a file that contains "fsh_110703_1_0351310_0351890
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.
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
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.