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Re: Bring BLAS into pkgsrc, pt. II
Attached is a draft of the changes necessary for all dependent packages
to use the new system. Following commit of the mk files, we would
simple need to remove "wip".
So far, all dependent packages have been tested on CentOS 7 with no
unexpected problems.
Should we make these changes all at once, or leave it to individual
maintainers (where there is one)?
If the former, do we need permission from each maintainer for this
change or would advance notification be sufficient?
Regards,
JB
On 2019-07-26 13:32, Jason Bacon wrote:
I just pushed some changes to address all of these issues and a few
others I noticed.
I'll begin testing dependent packages shortly.
Please review and send any additional comments ASAP. I'm hoping to
commit this in a couple weeks.
Thanks,
JB
On 2019-07-23 12:44, Roland Illig wrote:
# $NetBSD$
#
# This Makefile fragment is meant to be included by packages
# that use any BLAS implementation instead of one particular one.
In this introductory paragraph, it would be nice to describe what BLAS
actually means. A simple "that use any BLAS (Basic Linear Algebra
Subprograms) implementation" already suffices.
# Since we always ship BLAS and LAPACK together (as upstream variants
Who is "we", and how does the reader know that?
# TODO: Also set a variable to find a matching pkg-config file
# to avoid duplicating its contents in BLAS_LIBS?
There should be as few TODO lines in pkgsrc/mk as possible. (I know I'm
guilty of adding several TODOs to pkgsrc myself as well, though.)
# === Per-package variables ===
This should rather be the established "Package-settable variables", as
in many other files. Someday pkglint will parse these descriptions and
base its checks on them. Therefore it's nice if the wording is
consistent. This also benefits the human readers.
Currently, "bmake help topic=blas" only says:
No help found for blas, but it appears in:
mk/blas.buildlink3.mk
wip/mk/blas.buildlink3.mk
To change this, you can add a comment "# Keywords: blas lapack" at the
end of the introductory comment block.
.include "../../mk/bsd.prefs.mk"
This should simply be '.include "bsd.prefs.mk"', as bsd.prefs.mk will be
in the same directory as blas.buildlink3.mk.
.if(!empty(_BLAS_MATCH))
Usually we put a space between the .if and the condition. There's no
pkglint check for that yet since I am seeing this for the very first
time. Also the outer parentheses are redundant.
.if defined(_BLAS_PACKAGE)
.include "../../${_BLAS_PACKAGE}/buildlink3.mk"
.endif
This variable is closely related to the PKGPATH variable. Since the name
"PACKAGE" is highly ambiguous (it could mean one of PKGNAME,
PKGNAME_NOREV, PKGPATH, ../../PKGPATH, basename(PKGPATH)), I would
prefer this variable to be called _BLAS_PKGPATH instead.
This variable name probably originated from _MPI_PACKAGE, so I see it's
picking up existing practice. Apart from that, the word PACKAGE is not
used in variable names to identify a package, probably because of this
ambiguity.
Index: biology/mpqc/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/biology/mpqc/Makefile,v
retrieving revision 1.14
diff -u -r1.14 Makefile
--- biology/mpqc/Makefile 22 Aug 2018 09:42:59 -0000 1.14
+++ biology/mpqc/Makefile 28 Jul 2019 16:32:07 -0000
@@ -1,7 +1,7 @@
# $NetBSD: Makefile,v 1.14 2018/08/22 09:42:59 wiz Exp $
DISTNAME= mpqc-2.3.1
-PKGREVISION= 7
+PKGREVISION= 8
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=mpqc/}
EXTRACT_SUFX= .tar.bz2
@@ -39,7 +39,6 @@
.include "../../x11/tk/interpreter.mk"
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../mk/pthread.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: biology/plink/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/biology/plink/Makefile,v
retrieving revision 1.8
diff -u -r1.8 Makefile
--- biology/plink/Makefile 13 Jan 2019 22:06:42 -0000 1.8
+++ biology/plink/Makefile 28 Jul 2019 16:32:07 -0000
@@ -2,6 +2,7 @@
DISTNAME= plink-1.07-src
PKGNAME= ${DISTNAME:-src=}
+PKGREVISION= 1
CATEGORIES= biology
#MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/
EXTRACT_SUFX= .zip
@@ -36,7 +37,6 @@
.include "../../devel/libf2c/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../mk/dlopen.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: lang/lush/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/lang/lush/Makefile,v
retrieving revision 1.11
diff -u -r1.11 Makefile
--- lang/lush/Makefile 25 Apr 2015 14:23:26 -0000 1.11
+++ lang/lush/Makefile 28 Jul 2019 16:32:12 -0000
@@ -1,7 +1,7 @@
# $NetBSD: Makefile,v 1.11 2015/04/25 14:23:26 tnn Exp $
DISTNAME= lush-1.2.1
-PKGREVISION= 3
+PKGREVISION= 4
CATEGORIES= lang
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=lush/}
@@ -21,8 +21,7 @@
${RM} ${DESTDIR}${PREFIX}/share/lush/lsh/libc/*.lsh.orig
.include "../../math/gsl/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../devel/SDL/buildlink3.mk"
# rl_getc, rl_basic_quote_characters, rl_insert_close
.include "../../devel/readline/buildlink3.mk"
Index: math/R/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/R/Makefile,v
retrieving revision 1.200
diff -u -r1.200 Makefile
--- math/R/Makefile 20 Jul 2019 22:46:31 -0000 1.200
+++ math/R/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,7 +1,7 @@
# $NetBSD: Makefile,v 1.200 2019/07/20 22:46:31 wiz Exp $
DISTNAME= R-3.6.0
-PKGREVISION= 2
+PKGREVISION= 3
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-3/}
@@ -178,8 +178,7 @@
.include "../../graphics/png/buildlink3.mk"
.include "../../graphics/tiff/buildlink3.mk"
.if !exists(/System/Library/Frameworks/Accelerate.framework)
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.endif
.include "../../www/curl/buildlink3.mk"
.include "../../x11/tk/buildlink3.mk"
Index: math/R/buildlink3.mk
===================================================================
RCS file: /cvsroot/pkgsrc/math/R/buildlink3.mk,v
retrieving revision 1.13
diff -u -r1.13 buildlink3.mk
--- math/R/buildlink3.mk 7 Mar 2018 23:16:03 -0000 1.13
+++ math/R/buildlink3.mk 28 Jul 2019 16:32:13 -0000
@@ -14,9 +14,6 @@
.include "../../archivers/xz/buildlink3.mk"
.include "../../devel/gettext-lib/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
-.if !exists(/System/Library/Frameworks/Accelerate.framework)
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
-.endif
+.include "../../wip/mk/blas.buildlink3.mk"
BUILDLINK_TREE+= -R
Index: math/R-RandomFields/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/R-RandomFields/Makefile,v
retrieving revision 1.3
diff -u -r1.3 Makefile
--- math/R-RandomFields/Makefile 28 Jul 2018 14:40:46 -0000 1.3
+++ math/R-RandomFields/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,5 +1,6 @@
# $NetBSD: Makefile,v 1.3 2018/07/28 14:40:46 brook Exp $
+PKGREVISION= 1
CATEGORIES= math
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
@@ -13,5 +14,5 @@
USE_LANGUAGES+= c c++ fortran
.include "../../math/R/Makefile.extension"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/R-gstat/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/R-gstat/Makefile,v
retrieving revision 1.10
diff -u -r1.10 Makefile
--- math/R-gstat/Makefile 28 Jul 2018 14:40:48 -0000 1.10
+++ math/R-gstat/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,5 +1,6 @@
# $NetBSD: Makefile,v 1.10 2018/07/28 14:40:48 brook Exp $
+PKGREVISION= 1
CATEGORIES= math
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
@@ -15,5 +16,5 @@
DEPENDS+= R-FNN>=0:../../math/R-FNN
.include "../../math/R/Makefile.extension"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/R-quantreg/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/R-quantreg/Makefile,v
retrieving revision 1.5
diff -u -r1.5 Makefile
--- math/R-quantreg/Makefile 28 Jul 2018 14:40:50 -0000 1.5
+++ math/R-quantreg/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,6 +1,7 @@
# $NetBSD: Makefile,v 1.5 2018/07/28 14:40:50 brook Exp $
#
+PKGREVISION= 1
CATEGORIES= math
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
@@ -16,7 +17,6 @@
DEPENDS+= R-SparseM>=0:../../math/R-SparseM \
R-MatrixModels>=0:../../math/R-MatrixModels
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/R/Makefile.extension"
.include "../../mk/bsd.pkg.mk"
Index: math/R-wle/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/R-wle/Makefile,v
retrieving revision 1.13
diff -u -r1.13 Makefile
--- math/R-wle/Makefile 28 Jul 2018 14:40:51 -0000 1.13
+++ math/R-wle/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,5 +1,6 @@
# $NetBSD: Makefile,v 1.13 2018/07/28 14:40:51 brook Exp $
+PKGREVISION= 1
CATEGORIES= math
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
@@ -16,5 +17,5 @@
.include "../../devel/gettext-lib/buildlink3.mk"
.include "../../math/R/Makefile.extension"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/harminv/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/harminv/Makefile,v
retrieving revision 1.3
diff -u -r1.3 Makefile
--- math/harminv/Makefile 28 Jan 2018 16:24:14 -0000 1.3
+++ math/harminv/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,7 +1,7 @@
# $NetBSD: Makefile,v 1.3 2018/01/28 16:24:14 wiz Exp $
DISTNAME= harminv-1.3.1
-PKGREVISION= 1
+PKGREVISION= 2
CATEGORIES= math
MASTER_SITES= http://ab-initio.mit.edu/harminv/
@@ -19,7 +19,6 @@
TEST_TARGET= check
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/mpcomplex/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/ipopt/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/ipopt/Makefile,v
retrieving revision 1.2
diff -u -r1.2 Makefile
--- math/ipopt/Makefile 18 Jul 2018 00:06:21 -0000 1.2
+++ math/ipopt/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,6 +1,7 @@
# $NetBSD: Makefile,v 1.2 2018/07/18 00:06:21 joerg Exp $
DISTNAME= Ipopt-3.11.5
+PKGREVISION= 1
CATEGORIES= math
MASTER_SITES= http://www.coin-or.org/download/source/Ipopt/
EXTRACT_SUFX= .tgz
@@ -16,6 +17,5 @@
TEST_TARGET= test
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/ipopt/buildlink3.mk
===================================================================
RCS file: /cvsroot/pkgsrc/math/ipopt/buildlink3.mk,v
retrieving revision 1.1.1.1
diff -u -r1.1.1.1 buildlink3.mk
--- math/ipopt/buildlink3.mk 14 Nov 2013 15:04:12 -0000 1.1.1.1
+++ math/ipopt/buildlink3.mk 28 Jul 2019 16:32:13 -0000
@@ -8,8 +8,7 @@
BUILDLINK_API_DEPENDS.Ipopt+= Ipopt>=3.11.5
BUILDLINK_PKGSRCDIR.Ipopt?= ../../math/ipopt
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.endif # IPOPT_BUILDLINK3_MK
BUILDLINK_TREE+= -Ipopt
Index: math/itpp/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/itpp/Makefile,v
retrieving revision 1.5
diff -u -r1.5 Makefile
--- math/itpp/Makefile 16 Aug 2017 20:21:11 -0000 1.5
+++ math/itpp/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,6 +1,7 @@
# $NetBSD: Makefile,v 1.5 2017/08/16 20:21:11 wiz Exp $
DISTNAME= itpp-4.0.7
+PKGREVISION= 1
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=itpp/}
@@ -15,8 +16,7 @@
USE_LANGUAGES+= c c++ fortran77
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/fftw/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/octave/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/octave/Makefile,v
retrieving revision 1.191
diff -u -r1.191 Makefile
--- math/octave/Makefile 21 Jul 2019 22:25:20 -0000 1.191
+++ math/octave/Makefile 28 Jul 2019 16:32:13 -0000
@@ -1,7 +1,7 @@
# $NetBSD: Makefile,v 1.191 2019/07/21 22:25:20 wiz Exp $
DISTNAME= octave-5.1.0
-PKGREVISION= 5
+PKGREVISION= 6
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_GNU:=octave/}
@@ -108,10 +108,9 @@
.include "../../devel/zlib/buildlink3.mk"
.include "../../graphics/hicolor-icon-theme/buildlink3.mk"
.include "../../math/arpack/buildlink3.mk"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/fftw/buildlink3.mk"
.include "../../math/fftwf/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
.include "../../www/curl/buildlink3.mk"
.if ${OPSYS} != "Darwin"
.include "../../x11/libX11/buildlink3.mk"
Index: math/octave/buildlink3.mk
===================================================================
RCS file: /cvsroot/pkgsrc/math/octave/buildlink3.mk,v
retrieving revision 1.19
diff -u -r1.19 buildlink3.mk
--- math/octave/buildlink3.mk 31 Dec 2016 09:26:31 -0000 1.19
+++ math/octave/buildlink3.mk 28 Jul 2019 16:32:13 -0000
@@ -22,9 +22,8 @@
.include "../../devel/readline/buildlink3.mk"
.include "../../devel/ncurses/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/fftw/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
.endif # OCTAVE_BUILDLINK3_MK
BUILDLINK_TREE+= -octave
Index: math/py-numpy/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/py-numpy/Makefile,v
retrieving revision 1.61
diff -u -r1.61 Makefile
--- math/py-numpy/Makefile 14 Jun 2019 14:33:07 -0000 1.61
+++ math/py-numpy/Makefile 28 Jul 2019 16:32:13 -0000
@@ -2,6 +2,7 @@
DISTNAME= numpy-1.16.4
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION= 1
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=n/numpy/}
EXTRACT_SUFX= .zip
@@ -53,7 +54,6 @@
.include "../../lang/python/egg.mk"
.if ${OPSYS} != "Darwin"
# blas and lapack are not needed; numpy will use Accelerate.framework
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.endif
.include "../../mk/bsd.pkg.mk"
Index: math/py-numpy/buildlink3.mk
===================================================================
RCS file: /cvsroot/pkgsrc/math/py-numpy/buildlink3.mk,v
retrieving revision 1.4
diff -u -r1.4 buildlink3.mk
--- math/py-numpy/buildlink3.mk 28 Feb 2014 09:43:10 -0000 1.4
+++ math/py-numpy/buildlink3.mk 28 Jul 2019 16:32:13 -0000
@@ -12,10 +12,7 @@
.include "../../mk/bsd.fast.prefs.mk"
-.if ${OPSYS} != "Darwin"
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
-.endif
+.include "../../wip/mk/blas.buildlink3.mk"
.endif # PY_NUMPY_BUILDLINK3_MK
BUILDLINK_TREE+= -py-numpy
Index: math/py-scikit-learn/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/py-scikit-learn/Makefile,v
retrieving revision 1.8
diff -u -r1.8 Makefile
--- math/py-scikit-learn/Makefile 17 Jun 2019 15:01:45 -0000 1.8
+++ math/py-scikit-learn/Makefile 28 Jul 2019 16:32:13 -0000
@@ -2,6 +2,7 @@
DISTNAME= scikit-learn-0.21.2
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION= 1
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scikit-learn/}
@@ -23,10 +24,8 @@
.include "../../devel/py-cython/buildlink3.mk"
.include "../../lang/python/egg.mk"
-.if !exists(/System/Library/Frameworks/Accelerate.framework)
-.include "../../math/blas/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
-.endif
+# Select Darwin Accelerate framework via blas.bl3
+.include "../../wip/mk/blas.buildlink3.mk"
BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.11.0
.include "../../math/py-numpy/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/py-scipy/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/py-scipy/Makefile,v
retrieving revision 1.38
diff -u -r1.38 Makefile
--- math/py-scipy/Makefile 14 Jun 2019 14:53:29 -0000 1.38
+++ math/py-scipy/Makefile 28 Jul 2019 16:32:13 -0000
@@ -2,6 +2,7 @@
DISTNAME= scipy-1.3.0
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION= 1
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scipy/}
@@ -61,9 +62,8 @@
.include "../../lang/python/application.mk"
.include "../../lang/python/distutils.mk"
.include "../../devel/py-cython/buildlink3.mk"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/fftw/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.8.2
.include "../../math/py-numpy/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
Index: math/py-scipy12/Makefile
===================================================================
RCS file: /cvsroot/pkgsrc/math/py-scipy12/Makefile,v
retrieving revision 1.1
diff -u -r1.1 Makefile
--- math/py-scipy12/Makefile 15 Jun 2019 17:51:13 -0000 1.1
+++ math/py-scipy12/Makefile 28 Jul 2019 16:32:13 -0000
@@ -2,6 +2,7 @@
DISTNAME= scipy-1.2.2
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
+PKGREVISION= 1
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scipy/}
@@ -59,9 +60,8 @@
.include "../../lang/python/application.mk"
.include "../../lang/python/distutils.mk"
.include "../../devel/py-cython/buildlink3.mk"
-.include "../../math/blas/buildlink3.mk"
+.include "../../wip/mk/blas.buildlink3.mk"
.include "../../math/fftw/buildlink3.mk"
-.include "../../math/lapack/buildlink3.mk"
BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.8.2
.include "../../math/py-numpy/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
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