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Bug 2128289 - Please port your pcre dependency to pcre2. Pcre has been deprecated
Summary: Please port your pcre dependency to pcre2. Pcre has been deprecated
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: EMBOSS
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Tom "spot" Callaway
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: 2127507
TreeView+ depends on / blocked
 
Reported: 2022-09-20 12:53 UTC by Lukas Javorsky
Modified: 2023-12-29 01:13 UTC (History)
3 users (show)

Fixed In Version: EMBOSS-6.6.0-26.fc38 EMBOSS-6.6.0-26.fc39
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2022-09-20 17:15:13 UTC
Type: ---
Embargoed:

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System ID Private Priority Status Summary Last Updated
Red Hat Bugzilla 2242051 0 unspecified CLOSED EMBOSS: incomplete pcre2 port is not working 2023-12-29 01:13:58 UTC

Description Lukas Javorsky 2022-09-20 12:53:23 UTC 
Pcre has been deprecated since Fedora 38.
Please consider porting to the new pcre2 version.

Fedora change that describes the pcre deprecation is located here: https://fedoraproject.org/wiki/PcreDeprecation
FESCo approval is located here: https://pagure.io/fesco/issue/2862

If your component has already ported to pcre2 or you don't Require/BuildRequire any pcre subpackage, feel free to close this Bugzilla.
This Bugzilla was created automatically and some issues might have occurred along the way.
Comment 1 Ben Cotton 2022-09-20 13:46:18 UTC 
Adding blocking relationship to BZ 2127507 (the Change tracker)
Comment 2 Tom "spot" Callaway 2022-09-20 17:15:13 UTC 
Ported to pcre2 in EMBOSS-6.6.0-22.fc38
Comment 3 Greg Trounson 2023-08-25 03:52:07 UTC 
With the EMBOSS-6.6.0-pcre2.patch included we get most (all?) EMBOSS programs producing a Segmentation fault (core dumped). During the build I see the following warnings:

ajreg.c:157:81: warning: passing argument 4 of 'pcre2_compile_8' from incompatible pointer type [-Wincompatible-pointer-types]
     ret->pcre = pcre2_compile((PCRE2_SPTR)rexp, PCRE2_ZERO_TERMINATED, options, &errptr, &errpos, tableptr);
                                                                                 ^~~~~~~
In file included from ajreg.h:46,
                 from ajreg.c:34:
/usr/include/pcre2.h:916:1: note: expected 'int *' but argument is of type 'const char **'
 PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ajreg.c:157:90: warning: passing argument 5 of 'pcre2_compile_8' from incompatible pointer type [-Wincompatible-pointer-types]
     ret->pcre = pcre2_compile((PCRE2_SPTR)rexp, PCRE2_ZERO_TERMINATED, options, &errptr, &errpos, tableptr);
                                                                                          ^~~~~~~
In file included from ajreg.h:46,
                 from ajreg.c:34:
/usr/include/pcre2.h:916:1: note: expected 'size_t *' {aka 'long unsigned int *'} but argument is of type 'int *'
 PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS

Would it be possible for this be looked at again? We're happy to run without the patch here for now...
Comment 4 Florian Weimer 2023-12-20 12:24:50 UTC 
The crash was also failed as bug 2242051. GCC 14 will refuse to build EMBOSS because of related type errors.
Comment 5 Fedora Update System 2023-12-20 21:54:55 UTC 
FEDORA-2023-4583e503b9 has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2023-4583e503b9
Comment 6 Fedora Update System 2023-12-20 21:54:55 UTC 
FEDORA-2023-f5e1cc77de has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-f5e1cc77de
Comment 7 Fedora Update System 2023-12-21 02:45:22 UTC 
FEDORA-2023-4583e503b9 has been pushed to the Fedora 38 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-4583e503b9`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-4583e503b9

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
Comment 8 Fedora Update System 2023-12-21 03:23:41 UTC 
FEDORA-2023-f5e1cc77de has been pushed to the Fedora 39 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-f5e1cc77de`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-f5e1cc77de

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
Comment 9 Fedora Update System 2023-12-29 01:04:58 UTC 
FEDORA-2023-4583e503b9 has been pushed to the Fedora 38 stable repository.
If problem still persists, please make note of it in this bug report.
Comment 10 Fedora Update System 2023-12-29 01:13:56 UTC 
FEDORA-2023-f5e1cc77de has been pushed to the Fedora 39 stable repository.
If problem still persists, please make note of it in this bug report.
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