bug#51793: FAIL: tests/misc/env-signal-handler
On 12/11/2021 19:25, Andreas Schwab wrote: --- exp-err6 2021-11-11 22:58:04.360716802 + +++ err6 2021-11-11 22:58:04.752716821 + @@ -1,2 +1 @@ timeout: sending signal INT to command 'env' -timeout: sending signal KILL to command 'env' The above is for the previous command not the following. ./tests/misc/env-signal-handler.sh: line 127: 26396 Killed env timeout --verbose --kill-after=.1 --signal=INT .1 env --ignore-signal sleep 10 > /dev/null 2> err7t FAIL tests/misc/env-signal-handler.sh (exit status: 1) Could you paste a bit more context from the previous command. Specifically I'm wondering if the "Killed" message was displayed (i.e. if the SIGKILL was actually sent). I presume this is a race that you're seeing rarely. I've never seen this, and I can't see the race. What might be happening is the "sending signal KILL..." message sent to stderr, is in a buffer somewhere, which is dropped upon processing of SIGKILL. What file system, kernel, shell are you using. cheers, Pádraig
bug#51793: FAIL: tests/misc/env-signal-handler
--- exp-err6 2021-11-11 22:58:04.360716802 + +++ err6 2021-11-11 22:58:04.752716821 + @@ -1,2 +1 @@ timeout: sending signal INT to command 'env' -timeout: sending signal KILL to command 'env' ./tests/misc/env-signal-handler.sh: line 127: 26396 Killed env timeout --verbose --kill-after=.1 --signal=INT .1 env --ignore-signal sleep 10 > /dev/null 2> err7t FAIL tests/misc/env-signal-handler.sh (exit status: 1) Andreas. -- Andreas Schwab, sch...@linux-m68k.org GPG Key fingerprint = 7578 EB47 D4E5 4D69 2510 2552 DF73 E780 A9DA AEC1 "And now for something completely different."
bug#51792: coreutils - csplit - feature request
On 12/11/2021 17:05, Rodolfo Aramayo wrote:
Dear Coreutils Maintainers,
First, thank you for your work. I use coreutils daily both for my research
and teaching. It is a great set of tools.
Second, I recently needed to extract Coding Sequences information from a
GenBank file. GenBank files are used in Computational
Genomics/Bioinformatics extensively. I used csplit, and it works like a
charm.
The command I used is:
csplit -sz -n 5 --prefix=02_ 01_1
/[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]CDS[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]/
{*};
I was unable to declare: "[[:space:]]\+" as I expected for POSIX aware code.
My question is: Is csplit POSIX compatible? and if it is not, can we make
it POSIX compatible?
Well POSIX defines BRE and ERE, with csplit supporting the former.
From the code we have:
re_syntax_options =
RE_SYNTAX_POSIX_BASIC & ~RE_CONTEXT_INVALID_DUP & ~RE_NO_EMPTY_RANGES;
Generally one can replace '+' functionality from ERE, with '\{1,\}' in BRE.
So you'd be using something like:
[[:space:]]\{1,\}CDS[[:space:]]\{1,\}
We might add an option to use ERE, though there isn't a big need
for that I think for csplit use cases.
cheers,
Pádraig
bug#51792: coreutils - csplit - feature request
Dear Coreutils Maintainers,
First, thank you for your work. I use coreutils daily both for my research
and teaching. It is a great set of tools.
Second, I recently needed to extract Coding Sequences information from a
GenBank file. GenBank files are used in Computational
Genomics/Bioinformatics extensively. I used csplit, and it works like a
charm.
The command I used is:
csplit -sz -n 5 --prefix=02_ 01_1
/[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]CDS[[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]][[:space:]]/
{*};
I was unable to declare: "[[:space:]]\+" as I expected for POSIX aware code.
My question is: Is csplit POSIX compatible? and if it is not, can we make
it POSIX compatible?
Many Thanks
Rodolfo
--
Dr. Rodolfo Aramayo, PhD
Faculty of Biology and Genetics
Department of Biology, Texas A University
