#13443 closed enhancement (fixed)
Some clean up of R spkg
Reported by: | jdemeyer | Owned by: | tbd |
---|---|---|---|
Priority: | major | Milestone: | sage-5.4 |
Component: | packages: standard | Keywords: | r-project spkg |
Cc: | kcrisman | Merged in: | sage-5.4.beta2 |
Authors: | Jeroen Demeyer | Reviewers: | Karl-Dieter Crisman, John Palmieri |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #13348, #9906 | Stopgaps: |
Description (last modified by )
Clean up the R spkg, also proof-of-concept for #13348.
spkg: http://boxen.math.washington.edu/home/jdemeyer/spkg/r-2.14.0.p6.spkg
r-2.14.0.p6 (Jeroen Demeyer, 10 September 2012)
Attachments (1)
Change History (14)
comment:1 Changed 9 years ago by
- Description modified (diff)
- Keywords r-project spkg added
comment:2 Changed 9 years ago by
- Cc kcrisman added
Changed 9 years ago by
comment:3 Changed 9 years ago by
- Description modified (diff)
- Status changed from new to needs_review
comment:4 follow-ups: ↓ 5 ↓ 6 ↓ 7 Changed 9 years ago by
Okay, the diff looks okay to this somewhat untrained eye. A few questions that are doubtless not that important.
- I still get a lot of "make -jN disabled setting jobserver mode" and the like - but it seems like it's obeying the j. ?
- I don't see the extra C flags that #13348 supposedly adds.
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fvisibility=hidden -c pcre_xclass.c -o pcre_xclass.o
but probably I don't understand this.
I had trouble on sage.math. It installs, but:
installing translations: mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/en/LC_MESSAGES en mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/en_GB/LC_MESSAGES en_GB mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/es/LC_MESSAGES es mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/fr/LC_MESSAGES fr mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/de/LC_MESSAGES de mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/it/LC_MESSAGES it mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/ja/LC_MESSAGES ja mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/ko/LC_MESSAGES ko mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/nn/LC_MESSAGES nn mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/pt_BR/LC_MESSAGES pt_BR mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/ru/LC_MESSAGES ru mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/tr/LC_MESSAGES tr mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/zh_CN/LC_MESSAGES zh_CN mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/zh_TW/LC_MESSAGES zh_TW mkdir -p -- /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/local/lib/R/share/locale/en@quot/LC_MESSAGES en@quot make[1]: Leaving directory `/scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/spkg/build/r-2.14.0.p6/src/po' real 9m10.329s user 13m9.990s sys 1m7.740s Successfully installed r-2.14.0.p6 cat: /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/VERSION.txt: No such file or directory Deleting temporary build directory /scratch/kcrisman/sage-5.4.beta1-sage.math.washington.edu-x86_64-Linux/spkg/build/r-2.14.0.p6 Making Python scripts relocatable... Finished installing r-2.14.0.p6.spkg
What is up with that cat
error message?
comment:5 in reply to: ↑ 4 Changed 9 years ago by
comment:6 in reply to: ↑ 4 Changed 9 years ago by
Replying to kcrisman:
- I still get a lot of "make -jN disabled setting jobserver mode" and the like - but it seems like it's obeying the j. ?
I guess you mean
warning: -jN forced in submake: disabling jobserver mode.
Anyway, that's really a bug in the Sage documentation:
MAKE="make -j8" make
is not the correct way to do things, one should use MAKEFLAGS
instead (similar to the difference between CC
and CFLAGS
). There is a work-around for this "mistake" when compiling using spkg/install
(e.g. when issuing make
from SAGE_ROOT
), but not when installing using ./sage -i
.
In any case, it has nothing to do with this specific package.
comment:7 in reply to: ↑ 4 Changed 9 years ago by
Replying to kcrisman:
- I don't see the extra C flags that #13348 supposedly adds.
gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fvisibility=hidden -c pcre_xclass.c -o pcre_xclass.o
but probably I don't understand this.
Exactly, these are implicit options. It's similar to a hypothetical -I/usr/include
option.
The compiler always looks for include files in /usr/include
, so you never need to add -I/usr/include
. With #13348, $SAGE_ROOT/local/include
becomes an automatic directory for includes, just like /usr/include
already is.
comment:8 Changed 9 years ago by
- Reviewers set to Karl-Dieter Crisman
Thanks for clarifying these things. It all seems to work on Linux and (new) Mac, relevant tests and SAGE_CHECK
pass. I also tried some R stuff and it seems to be working.
I'm still a little uncomfortable giving final positive review just because of the big changes in the spkg-install, but it certainly all looks ok. Maybe someone else can just make sure they like the syntax; R itself seems to be fine, and it looks like all relevant flags are still passed in the right ways.
comment:9 Changed 9 years ago by
- Status changed from needs_review to positive_review
The changes to spkg-install look fine to me.
comment:10 Changed 9 years ago by
- Reviewers changed from Karl-Dieter Crisman to Karl-Dieter Crisman, John Palmieri
Thanks.
comment:11 Changed 9 years ago by
- Merged in set to sage-5.4.beta2
- Resolution set to fixed
- Status changed from positive_review to closed
comment:12 follow-up: ↓ 13 Changed 8 years ago by
This again breaks linking against Sage's libreadline
; R's configure
doesn't support specifying a (non-standard) location for readline, only [--with-readline=]yes
(default) and no
, where everything but no
is interpreted as yes
.
comment:13 in reply to: ↑ 12 Changed 8 years ago by
Replying to leif:
This again breaks linking against Sage's
libreadline
; R'sconfigure
doesn't support specifying a (non-standard) location for readline, only[--with-readline=]yes
(default) andno
, where everything butno
is interpreted asyes
.
See #14709 for the general problem, and #14706 where R is supposed to get upgraded (which alone doesn't fix the issue; we'd have to revert the changes to R's spkg-install
, or patch R's configure
accordingly).
Diff for the R spkg. For reference / review only.