Opened 3 years ago
Closed 3 years ago
#28884 closed enhancement (fixed)
spkgconfigure for R
Reported by:  Dima Pasechnik  Owned by:  

Priority:  major  Milestone:  sage9.1 
Component:  build: configure  Keywords:  
Cc:  Thierry Monteil, François Bissey, Isuru Fernando, Emmanuel Charpentier, Erik Bray  Merged in:  
Authors:  Dima Pasechnik  Reviewers:  Emmanuel Charpentier 
Report Upstream:  N/A  Work issues:  
Branch:  1f4a7e1 (Commits, GitHub, GitLab)  Commit:  1f4a7e1c13c3cfa01de45683834be33b4e2985b7 
Dependencies:  #27870  Stopgaps: 
Description (last modified by )
a minimum working on standard distros setup.
Note that R does not have a working uninstall, so one needs to manually uninstall by
rm rf $SAGE_LOCAL/lib/R rm $SAGE_LOCAL/bin/R*
followed by
./bootstrap ./configure ./sage f rpy2 make build
and then test. (Or, of course start from make distclean
)
Change History (32)
comment:1 Changed 3 years ago by
comment:2 Changed 3 years ago by
Status:  new → needs_review 

comment:3 Changed 3 years ago by
Description:  modified (diff) 

comment:4 Changed 3 years ago by
Cc:  Thierry Monteil added 

comment:5 Changed 3 years ago by
Cc:  François Bissey Isuru Fernando added 

comment:6 Changed 3 years ago by
I guess we could check for matching versions with that kind of stuff
fbissey@moonloop ~ $ pkgconfig modversion libR 3.4.1 fbissey@moonloop ~ $ R version R version 3.4.1 (20170630)  "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64pclinuxgnu (64bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see http://www.gnu.org/licenses/.
Nice that libR comes with a .pc file.
comment:7 Changed 3 years ago by
I'll do the TODO as soon as the rest looks OK. I've done similar checks for pari...
comment:8 Changed 3 years ago by
comment:9 Changed 3 years ago by
Cc:  Emmanuel Charpentier added 

comment:10 followup: 11 Changed 3 years ago by
Dependencies:  → #27870 

comment:11 Changed 3 years ago by
comment:12 followup: 16 Changed 3 years ago by
LGTM:
 Sage R works as expected. Superficial testing is OK.
charpent@zenbookflip:/usr/local/sage9$ sage t long src/sage/interfaces/r.py Running doctests with ID 20191215105043b4fc9d4c. Git branch: t/28884/packages/rconf Using optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb Doctesting 1 file. sage t long warnlong 184.3 src/sage/interfaces/r.py [257 tests, 5.48 s]  All tests passed!  Total time for all tests: 5.7 seconds cpu time: 5.3 seconds cumulative wall time: 5.5 seconds
charpent@zenbookflip:/usr/local/sage9$ sage t long src/sage/stats/r.py Running doctests with ID 20191215105120adfb7e0b. Git branch: t/28884/packages/rconf Using optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb Doctesting 1 file. sage t long warnlong 184.3 src/sage/stats/r.py [2 tests, 0.54 s]  All tests passed!  Total time for all tests: 0.7 seconds cpu time: 0.5 seconds cumulative wall time: 0.5 seconds
make ptestalllong
underway...
comment:13 Changed 3 years ago by
Commit:  bbea1946dd5414fd529125086ca2a495e6876c12 → f66ea24ace841024370253cbcc72a3b109daadcc 

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
e5c91db  update pkgconfig to v1.5.1. See trac #28883

1720b38  a bare minumim openblas config

925266b  use openblas.pc for blas and lapack, don't require atlas is to be used

b89df80  move blas handling to build/pkgs/

6341576  create cblas.pc link, too, not only blas and lapack

f66ea24  spkgconfigure for R

comment:14 followup: 17 Changed 3 years ago by
added forgotten commit https://git.sagemath.org/sage.git/commit/?id=634157628ac3f7292e7065eae462bb6b80db7aed from #27870 to this branch (should not matter, reviewwise, I guess)
comment:15 Changed 3 years ago by
Description:  modified (diff) 

comment:16 Changed 3 years ago by
Cc:  Erik Bray added 

Description:  modified (diff) 
Reviewers:  → Emmanuel Charpentier 
Status:  needs_review → positive_review 
Replying to charpent:
[ Snip... ]
make ptestalllong
underway...
ptestalllong
gets 6 transient and 3 permanent failures :
File  Result  P/T 
src/sage/plot/animate.py  7 doctests failed  T 
src/sage/modular/ssmod/ssmod.py  2 doctests failed  T 
src/sage/misc/latex.py  1 doctest failed  T 
src/sage/numerical/backends/glpk_backend.pyx  1 doctest failed  P 
src/sage/repl/load.py  1 doctest failed  T 
src/sage/tests/gap_packages.py  1 doctest failed  P 
src/sage/libs/glpk/error.pyx  1 doctest failed  P 
src/sage/combinat/designs/ext_rep.py  1 doctest failed  T 
src/sage/databases/findstat.py  1 doctest failed  T 
All of these have already been reported for previous release(s=) of Python 3based Sage 9 betas, and therefore considered not to be related to this ticket.
==> positive_review
Given the importance of this ticket (a large headache off the shoulders of active SageR users...), I recommend tests on other platforms (Mac OS X and its shenanigans, Windows and the coexistence of Windows and Cygwin libraries...).
comment:17 Changed 3 years ago by
Replying to dimpase:
added forgotten commit https://git.sagemath.org/sage.git/commit/?id=634157628ac3f7292e7065eae462bb6b80db7aed from #27870 to this branch (should not matter, reviewwise, I guess)
Aaaarghhhh...
Another check may be worthy. But maybe after tests on other platforms... Please ask as neeeded.
comment:18 followup: 19 Changed 3 years ago by
Commit:  f66ea24ace841024370253cbcc72a3b109daadcc → 3812f1ca8ecd0c15926c40d214fcb824996a5677 

Status:  positive_review → needs_review 
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:
3812f1c  list more relevant system packages to install on Debian/Fedora

comment:19 Changed 3 years ago by
Status:  needs_review → positive_review 

comment:20 Changed 3 years ago by
I think we can weaken the version requirements, it still works fine with R 3.4.4 and openblas 0.2.20.
This is what one has on Ubuntu 18.04 on 32bit machine (arando buildbot) and on Fedora 26.
comment:21 Changed 3 years ago by
Commit:  3812f1ca8ecd0c15926c40d214fcb824996a5677 → 6aba5b4cf2073b12a05b19b127f2258111b2daea 

Status:  positive_review → needs_review 
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:
6aba5b4  lower versions of R and openblas

comment:22 Changed 3 years ago by
Milestone:  sage9.1 → sage9.0 

Status:  needs_review → positive_review 
setting it back to positive review, as it does only change version numbers
comment:23 Changed 3 years ago by
It works on MacOS 10.13.6 with Homebrew's R and openblas packages.
It doesn't work with R installed with standalone isntaller from R Project,
probably as there is some kind of library/compiler incompatibility  they don't build R with Xcode compiler, they use their "own"; more precisely, OpenMPenabled
clang 8, see https://cran.rproject.org/bin/macosx/tools.
Somehow I see an error message while building rpy2, attempting to use fopenmp
switch with Xcode's clang.
comment:24 Changed 3 years ago by
Branch:  u/dimpase/packages/rconf → 6aba5b4cf2073b12a05b19b127f2258111b2daea 

Resolution:  → fixed 
Status:  positive_review → closed 
comment:25 Changed 3 years ago by
Commit:  6aba5b4cf2073b12a05b19b127f2258111b2daea 

Resolution:  fixed 
Status:  closed → new 
More stuff that has #28883 merged in
comment:26 Changed 3 years ago by
Status:  new → needs_review 

comment:27 Changed 3 years ago by
Status:  needs_review → positive_review 

comment:28 Changed 3 years ago by
Branch:  6aba5b4cf2073b12a05b19b127f2258111b2daea → u/dimpase/packages/rconf 

Commit:  → 6aba5b4cf2073b12a05b19b127f2258111b2daea 
New commits:
e5c91db  update pkgconfig to v1.5.1. See trac #28883

1720b38  a bare minumim openblas config

925266b  use openblas.pc for blas and lapack, don't require atlas is to be used

b89df80  move blas handling to build/pkgs/

6341576  create cblas.pc link, too, not only blas and lapack

f66ea24  spkgconfigure for R

3812f1c  list more relevant system packages to install on Debian/Fedora

6aba5b4  lower versions of R and openblas

comment:29 Changed 3 years ago by
Commit:  6aba5b4cf2073b12a05b19b127f2258111b2daea → 1f4a7e1c13c3cfa01de45683834be33b4e2985b7 

Status:  positive_review → needs_review 
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. This was a forced push. New commits:
f74f554  update pkgconfig to v1.5.1. See trac #28883

fb8f4e5  allow absent zlib.pc

b3a8891  a bare minumim openblas config

c031c9e  use openblas.pc for blas and lapack, don't require atlas is to be used

b49f79e  move blas handling to build/pkgs/

81bf522  create cblas.pc link, too, not only blas and lapack

6df5985  spkgconfigure for R

0bad8b4  list more relevant system packages to install on Debian/Fedora

1f4a7e1  lower versions of R and openblas

comment:30 Changed 3 years ago by
Status:  needs_review → positive_review 

routine rebase over updated #27870
comment:31 Changed 3 years ago by
Milestone:  sage9.0 → sage9.1 

comment:32 Changed 3 years ago by
Branch:  u/dimpase/packages/rconf → 1f4a7e1c13c3cfa01de45683834be33b4e2985b7 

Resolution:  → fixed 
Status:  positive_review → closed 
TODO: check that versions of R and libR match