#21770 closed defect (fixed)
Package libpcre as a standard package
Reported by:  charpent  Owned by:  

Priority:  major  Milestone:  sage7.6 
Component:  packages: standard  Keywords:  rproject, days85 
Cc:  mkoeppe, dimpase  Merged in:  
Authors:  Emmanuel Charpentier  Reviewers:  JeanPierre Flori 
Report Upstream:  N/A  Work issues:  
Branch:  ef48f71 (Commits, GitHub, GitLab)  Commit:  
Dependencies:  Stopgaps: 
Description (last modified by )
Rationale : R (standard package) requires libpcre (in a nondefault configuration), but stopped to package it with version 3.3.0.
See this discussion on sagedevel, but look also here and contribute here.
Change History (36)
comment:1 Changed 6 years ago by
 Branch set to u/charpent/package_libpcre_as_a_standard_package
comment:2 Changed 6 years ago by
 Commit set to a8d77b5c25a0f20c209f04c3a5377b673683cd6e
 Description modified (diff)
comment:3 Changed 6 years ago by
 Status changed from new to needs_review
The initial packaging builds without problem and passes its own testsuite ; the resulting Sage passes ptestlong with only the usual transient error on simplicial_complex.py
(which passes standalone).
==> needs_review
.
comment:4 Changed 6 years ago by
 Status changed from needs_review to needs_work
In the light of #20692, please remove this patch block (especially given that there are no patches):
# Patch sources. for patch in ../patches/*.patch; do [ r "$patch" ]  continue # Skip nonexisting or nonreadable patches patch p1 <"$patch" if [ $? ne 0 ]; then echo >&2 "Error applying '$patch'" exit 1 fi done
comment:5 followup: ↓ 6 Changed 6 years ago by
 Commit changed from a8d77b5c25a0f20c209f04c3a5377b673683cd6e to 21ce3e75574d3a08266324b7fac41e044e0ef280
Branch pushed to git repo; I updated commit sha1. New commits:
21ce3e7  Removed patches handling.

comment:6 in reply to: ↑ 5 Changed 6 years ago by
comment:7 Changed 6 years ago by
 Status changed from needs_work to needs_review
comment:8 Changed 5 years ago by
Sage7.6.beta4 + #20523 + #21767 + #21770 (this patch) passes ptestlong witht two transient errors :
 sage t long src/sage/homology/simplicial_set_morphism.py # Bad exit: 2 sage t long src/sage/homology/simplicial_complex.py # 1 doctest failed 
Both tests pass when run standalone.
This should close the R saga (for now) by allowing the current interfaces to work with R >= 3.3.x.
Still needs_review
comment:9 Changed 5 years ago by
Merged with #20523
This ticket should be marked as invalid by someeone with the right rights...
comment:10 Changed 5 years ago by
After discussion of (potential) #20523 reviewers, I now think that this ticket should be kept, reviewed and validated. Pleas DON'T invalidate it.
comment:11 followup: ↓ 13 Changed 5 years ago by
 Status changed from needs_review to needs_work
[pcre8.39] WARNING: spkginstall is not executable, making it executable
comment:12 Changed 5 years ago by
 Commit changed from 21ce3e75574d3a08266324b7fac41e044e0ef280 to bfc26ef6badfd02ca88dcd69bd5e86684d1dce41
Branch pushed to git repo; I updated commit sha1. New commits:
bfc26ef  Wups. chmod +x spkginstall...

comment:13 in reply to: ↑ 11 Changed 5 years ago by
 Status changed from needs_work to needs_review
Replying to jdemeyer:
[pcre8.39] WARNING: spkginstall is not executable, making it executable
Done. needs_review
comment:14 Changed 5 years ago by
 Cc mkoeppe added
 Milestone changed from sage7.5 to sage7.6
I wonder if pcre
also pops up in polymake
related tickets (which do need a lot of perl
)...
comment:15 Changed 5 years ago by
 Description modified (diff)
Updated the address of the original tarball (patchbots seem to be unable to use an FTP address...).
comment:16 followup: ↓ 17 Changed 5 years ago by
 Status changed from needs_review to needs_work
I would suggest to make the package optional for now and only make it standard when really needed.
comment:17 in reply to: ↑ 16 ; followup: ↓ 19 Changed 5 years ago by
Replying to jdemeyer:
I would suggest to make the package optional for now and only make it standard when really needed.
We've already been there (see previous saga...) :
 R is a standard package
 R depends on PCRE starting 3.3.x
 A standard package cannot depend on an optional package
Therefore pcre has to be standard. QED.
comment:18 Changed 5 years ago by
 Status changed from needs_work to needs_review
And, yes, it needs_review
.
comment:19 in reply to: ↑ 17 ; followup: ↓ 20 Changed 5 years ago by
Replying to charpent:
 R version 3.2.4revised is a standard package
 R version 3.3.x depends on PCRE
 A standard package cannot depend on an optional package
I stand by my proposal: make it standard when really needed.
comment:20 in reply to: ↑ 19 ; followup: ↓ 21 Changed 5 years ago by
Replying to jdemeyer:
Replying to charpent:
 R version 3.2.4revised is a standard package
And is about 1 year late on current R. Having an uptodate R version is a sine qua non to get help on Rhelp, and to be able to install recent versions of the >10 000 R packages. Which are a not inconsiderable resource to those lowly lifeforms called applied statisticians...
 R version 3.3.x depends on PCRE
 A standard package cannot depend on an optional package
I stand by my proposal: make it standard when really needed.
IMHO it *is* really needed. But it happens that I need R for my everyday work. Do you ?
comment:21 in reply to: ↑ 20 ; followup: ↓ 22 Changed 5 years ago by
Replying to charpent:
Replying to jdemeyer:
Replying to charpent:
 R version 3.2.4revised is a standard package
And is about 1 year late on current R. Having an uptodate R version is a sine qua non to get help on Rhelp, and to be able to install recent versions of the >10 000 R packages. Which are a not inconsiderable resource to those lowly lifeforms called applied statisticians...
That may be all true, but I don't see how that matters here.
 R version 3.3.x depends on PCRE
 A standard package cannot depend on an optional package
I stand by my proposal: make it standard when really needed.
IMHO it *is* really needed.
...when we upgrade to R3.3.0, which is not the case yet.
comment:22 in reply to: ↑ 21 ; followup: ↓ 23 Changed 5 years ago by
Replying to jdemeyer:
Replying to charpent:
Replying to jdemeyer:
Replying to charpent:
 R version 3.2.4revised is a standard package
And is about 1 year late on current R. Having an uptodate R version is a sine qua non to get help on Rhelp, and to be able to install recent versions of the >10 000 R packages. Which are a not inconsiderable resource to those lowly lifeforms called applied statisticians...
That may be all true, but I don't see how that matters here.
 R version 3.3.x depends on PCRE
 A standard package cannot depend on an optional package
I stand by my proposal: make it standard when really needed.
IMHO it *is* really needed.
...when we upgrade to R3.3.0, which is not the case yet.
#20523 is waiting on this ticket for review (and has been for a looong time : it has been delayed by the openssl brouhaha).
comment:23 in reply to: ↑ 22 ; followup: ↓ 24 Changed 5 years ago by
comment:24 in reply to: ↑ 23 ; followup: ↓ 25 Changed 5 years ago by
comment:25 in reply to: ↑ 24 ; followup: ↓ 26 Changed 5 years ago by
Replying to charpent:
I can't see the point... Care to explain ?
I don't see the point of having a standard package which is not used by anything in Sage.
comment:26 in reply to: ↑ 25 Changed 5 years ago by
Replying to jdemeyer:
Replying to charpent:
I can't see the point... Care to explain ?
I don't see the point of having a standard package which is not used by anything in Sage.
OK. If I follow you :
 PCRE is not used by anything in Sage
 PCRE is used by R
Therefore, by modus tollens:
 R is not in Sage.
We should submit this interesting conclusion to sagedevel
: the discussion would probably be lively and entertaining (for questionable values of "entertaining"...).
comment:27 Changed 5 years ago by
 Cc dimpase added
comment:28 followup: ↓ 29 Changed 5 years ago by
@emmanuel: can you update to 8.40 pls?
comment:29 in reply to: ↑ 28 Changed 5 years ago by
comment:30 Changed 5 years ago by
 Commit changed from bfc26ef6badfd02ca88dcd69bd5e86684d1dce41 to ef48f715189d6629f776b7a87334fc4da2e6219f
Branch pushed to git repo; I updated commit sha1. New commits:
ef48f71  Upgraded to pcre 8.40

comment:31 Changed 5 years ago by
 Description modified (diff)
Upgrade as requested. Therefore, tarball modified accordingly.
New commits:
ef48f71  Upgraded to pcre 8.40

comment:32 Changed 5 years ago by
 Passes its own testsuite.
 (#21567 + #21770 + #20523 remerged with the two previous ones) passes ptestlong with two failures :
 sage t long src/sage/homology/simplicial_complex.py # 1 doctest failed sage t long src/sage/rings/polynomial/multi_polynomial_ideal.py # 1 doctest failed 
The first one is transient (passes when ran standalone) ; the second one is a welldocumented, ticketed and not yet fixed difference on the expression of the expected result.
==> needs_review
for good.
comment:33 Changed 5 years ago by
 Reviewers set to JeanPierre Flori
 Status changed from needs_review to positive_review
Looks ok.
comment:34 Changed 5 years ago by
 Keywords days85 added
comment:35 Changed 5 years ago by
 Branch changed from u/charpent/package_libpcre_as_a_standard_package to ef48f715189d6629f776b7a87334fc4da2e6219f
 Resolution set to fixed
 Status changed from positive_review to closed
comment:36 Changed 5 years ago by
 Commit ef48f715189d6629f776b7a87334fc4da2e6219f deleted
Is the enablejit
flag really required? It already caused problems on Cygwin and it is breaking on Solaris too (#24628).
New commits:
Initial packaging of pcre : unconditionnal installation.