Bug 210866
| Summary: | math/R: Modernize and simplify port | ||||||||||||||||||||
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| Product: | Ports & Packages | Reporter: | Joseph Mingrone <jrm> | ||||||||||||||||||
| Component: | Individual Port(s) | Assignee: | Thomas Zander <riggs> | ||||||||||||||||||
| Status: | Closed FIXED | ||||||||||||||||||||
| Severity: | Affects Only Me | CC: | jwb, rhurlin, riggs, swills, thierry | ||||||||||||||||||
| Priority: | --- | Keywords: | patch, patch-ready | ||||||||||||||||||
| Version: | Latest | ||||||||||||||||||||
| Hardware: | Any | ||||||||||||||||||||
| OS: | Any | ||||||||||||||||||||
| See Also: |
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=210983 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=210987 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=210990 |
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| Attachments: |
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Description
Joseph Mingrone
2016-07-06 05:30:24 UTC
There is a: +TCL_IMPLIES= X11 I think it should be: +TCLTK_IMPLIES= X11 Created attachment 172173 [details]
svn diff to clean up math/R
Indeed. Thanks for catching that.
TCL_IMPLIES should have been TCLTK_IMPLIES. This second, updated patch includes this fix.
Created attachment 172176 [details]
svn diff for math/R
PORTREVISION was just bumped
Created attachment 172186 [details] svn diff to clean up math/R PORTREVISION was bumped again because the update to devel/icu was reverted. While here, remove more cruft that is taken care of by autoconf now. For example, the -fPIC flag is already used when the libR library is built. New tests: portlint: OK (spurious warning about install-info) testport: OK (poudriere: 9.3-RELEASE-p36, i386, default options) [1] testport: OK (poudriere: 9.3-RELEASE-p30, amd64, default options) [2] testport: OK (poudriere: 10.3-RELEASE, i386, default options) [3] testport: OK (poudriere: 10.3-RELEASE, amd64, default options) [4] [1] http://pkg.awarnach.mathstat.dal.ca/data/9i386-default/2016-07-07_04h06m55s/logs/R-3.3.1_2.log [2] http://pkg.awarnach.mathstat.dal.ca/data/9amd64-default/2016-07-07_04h06m58s/logs/R-3.3.1_2.log [3] http://pkg.awarnach.mathstat.dal.ca/data/10i386-default/2016-07-07_04h07m01s/logs/R-3.3.1_2.log [4] http://pkg.awarnach.mathstat.dal.ca/data/10amd64-default/2016-07-07_04h06m25s/logs/R-3.3.1_2.log Thanks Joseph For future reference, build log attachments are no longer required, just the QA/testing confirmation summary as you provided in comment 4 Created attachment 172210 [details]
svn diff to clean up math/R
Append shared library versions (again). Without them, ldconfig fails to add them to the shared object cache.
With these OPTIONS:
===> The following configuration options are available for R-3.3.1_2:
DOCS=on: Build and/or install documentation
ICU=on: Unicode support via ICU
INFO=on: GNU info manuals
LDOUBLE=on: Enable long double data type
LETTER=on: US Letter paper
LIBR=on: Build dynamic (shared) R library
LTO=on: Try to produce faster code through LTO
MISSING=off: Use libmissing rather than libquadmath
NLS=on: Native Language Support
OPENMP=on: Parallel processing support via OpenMP
THREADS=on: Threading support
X11=on: X11 graphics device
====> X11-Implying Options
GHOSTSCRIPT=on: Graphics Device for Bitmap Files via Ghostscript
JPEG=on: JPEG graphics device
CAIROPANGO=on: Cairo graphics device and Pango multi-language text
PDF=on: PDF manuals (requires TeX)
PNG=on: PNG graphics device
TCLTK=on: Tcl/Tk GUI toolkit support
TIFF=on: TIFF image format support
====> Options available for the single BLAS: you have to select exactly one of them
ATLAS=off: ATLAS BLAS implementation
OPENBLAS=off: OpenBLAS BLAS implementation
NETLIB=on: Netlib BLAS implementation
RBLAS=off: Use R-bundled BLAS implementation
there is an issue during install:
===> Generating temporary packing list
mkdir /wrkdirs/usr/ports/math/R/work/stage/usr/local/lib/R
installing doc ...
mkdir /wrkdirs/usr/ports/math/R/work/stage/usr/local/share/doc/R
install: NEWS.rds: No such file or directory
*** Error code 71
Stop.
make[2]: stopped in /wrkdirs/usr/ports/math/R/work/R-3.3.1/doc
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/math/R/work/R-3.3.1
*** Error code 1
Stop.
make: stopped in /usr/ports/math/R
Could you take a look? Thanks!
Created attachment 172280 [details]
svn diff to fix latest issue
Thanks for catching that. It's fixed in this new patch.
(In reply to Joseph Mingrone from comment #8) Thanks, looks good now! In the initial submission, you stated that you were waiting for feedback from maintainers of dependent ports. Did you receive replies? If chances are high that this change causes breakage of many ports, we can request an exp-run. From the plist changes, personally I would expect not much trouble. Hi Joseph,
Many, many thanks for your work on renewing the port, really appreciated!
I think it is also necessary to add 'USES=objc' to the ports Makefile. Otherwise we get a mixture of lang/gcc and gcc from base:
# make configure [[without USES=objc]]
[-snip----------------------------------------------------]
R is now configured for amd64-portbld-freebsd11.0
Source directory: .
Installation directory: /usr/local
C compiler: gcc48 -std=gnu99 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing
Fortran 77 compiler: gfortran48 -O -Wl,-rpath=/usr/local/lib/gcc48
C++ compiler: g++48 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -DLIBICONV_PLUG -Wl,-rpath=/usr/local/lib/gcc48
C++11 compiler: g++48 -std=c++11 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -DLIBICONV_PLUG -Wl,-rpath=/usr/local/lib/gcc48
Fortran 90/95 compiler: gfortran48 -Wl,-rpath=/usr/local/lib/gcc48
Obj-C compiler: gcc -g -O2 -fobjc-exceptions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
# make configure [[with USES=objc]]
[-snip----------------------------------------------------]
R is now configured for amd64-portbld-freebsd11.0
Source directory: .
Installation directory: /usr/local
C compiler: gcc48 -std=gnu99 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing
Fortran 77 compiler: gfortran48 -O -Wl,-rpath=/usr/local/lib/gcc48
C++ compiler: g++48 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -DLIBICONV_PLUG -Wl,-rpath=/usr/local/lib/gcc48
C++11 compiler: g++48 -std=c++11 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -DLIBICONV_PLUG -Wl,-rpath=/usr/local/lib/gcc48
Fortran 90/95 compiler: gfortran48 -Wl,-rpath=/usr/local/lib/gcc48
Obj-C compiler: gcc48 -O2 -pipe -fno-builtin-erfcl -fno-builtin-powl -fno-builtin-sinhl -fno-builtin-tgammal -DLIBICONV_PLUG -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wno-import -DLIBICONV_PLUG -I/usr/local/include -fobjc-exceptions
And, is 'MAKE_JOBS_UNSAFE=yes' really needed? For me, it also builds fine without.
Thomas, The maintainer-feedback flag shoudn't have been set. I am the maintainer. The only breakage I expect is with math/libR and math/libRmath, both of which are already broken. The math/libRmath port is already marked BROKEN. Can you mark math/libR BROKEN as well? No other ports depend on either math/libR or math/libRmath, so I feel the fallout will be minimal. I plan to "unenslave" both in the near future. Thanks, Joseph Created attachment 172288 [details]
svn diff
Hi Rainer,
Thanks for your feedback.
I don't see any objective-c code in the source tree, other than OS X specific parts. Are you (or anyone else) confident USES=objc is necessary?
I've removed MAKE_JOBS=unsafe. Without it, the build was breaking, but something must have changed in the meantime. I've tested with various options in different versions and the build is successful without out it. Thanks.
(In reply to Joseph Mingrone from comment #12) To be honest, I am not sure, if 'USES=objc' really improves linkage of libs. I do not remember, but once I heard about some R packages, using Objective-C, linked against the R libs. I think, 'USES=objc' is a step in the right direction ;) On the other hand, there is something else, at least on CURRENT, which brings in base compiler (here clang, libc++ and libcxxrt). So I get a compiler mixture linked in: #ldd /usr/local/lib/R/lib/libR.so.1 libR.so.1: libRblas.so => /usr/local/lib/R/lib/libRblas.so (0x415d8000) libmissing.so.2 => /usr/local/lib/libmissing.so.2 (0x41806000) libm.so.5 => /lib/libm.so.5 (0x41a09000) libgfortran.so.3 => /usr/local/lib/gcc48/libgfortran.so.3 (0x41c33000) libquadmath.so.0 => /usr/local/lib/gcc48/libquadmath.so.0 (0x41f4a000) libintl.so.8 => /usr/local/lib/libintl.so.8 (0x42185000) libreadline.so.6 => /usr/local/lib/libreadline.so.6 (0x4238f000) libpcre.so.1 => /usr/local/lib/libpcre.so.1 (0x425db000) liblzma.so.5 => /usr/lib/liblzma.so.5 (0x42853000) libbz2.so.4 => /usr/lib/libbz2.so.4 (0x42a7c000) libz.so.6 => /lib/libz.so.6 (0x42c91000) libicuuc.so.55 => /usr/local/lib/libicuuc.so.55 (0x42ea8000) libicui18n.so.55 => /usr/local/lib/libicui18n.so.55 (0x43400000) libgomp.so.1 => /usr/local/lib/gcc48/libgomp.so.1 (0x438a3000) libthr.so.3 => /lib/libthr.so.3 (0x43ab1000) libc.so.7 => /lib/libc.so.7 (0x40823000) libmpc.so.3 => /usr/local/lib/libmpc.so.3 (0x43cd8000) libgcc_s.so.1 => /usr/local/lib/gcc48/libgcc_s.so.1 (0x43eee000) libncurses.so.8 => /lib/libncurses.so.8 (0x44104000) libicudata.so.55 => /usr/local/lib/libicudata.so.55 (0x44400000) libc++.so.1 => /usr/lib/libc++.so.1 (0x45f20000) libcxxrt.so.1 => /lib/libcxxrt.so.1 (0x461df000) libmpfr.so.4 => /usr/local/lib/libmpfr.so.4 (0x463fd000) libgmp.so.10 => /usr/local/lib/libgmp.so.10 (0x46663000) Created attachment 172290 [details]
another svn diff
Added USES=objc:compiler after conversations with bapt and rhurlin (Rainer) on IRC.
P.S. In my last comment I should have written 'MAKE_JOBS_UNSAFE=yes' and not 'MAKE_JOBS=unsafe'.
A commit references this bug: Author: riggs Date: Sat Jul 9 19:28:22 UTC 2016 New revision: 418289 URL: https://svnweb.freebsd.org/changeset/ports/418289 Log: Modernize and simplify port PR: 210866 Submitted by: jrm@ftfl.ca (maintainer) Reviewed by: rhurlin@gwdg.de, bapt, riggs Changes: head/math/R/Makefile head/math/R/pkg-plist A commit references this bug: Author: riggs Date: Sat Jul 9 19:32:32 UTC 2016 New revision: 418290 URL: https://svnweb.freebsd.org/changeset/ports/418290 Log: Mark broken while restructuring the master port is ongoing PR: 210866 Reported by: jrm@ftfl.ca (maintainer) Changes: head/math/libR/Makefile |