subject:"UPDATE\: math\/R"

Re: UPDATE: math/R

2022-08-03 Thread Theo Buehler

On Wed, Aug 03, 2022 at 02:09:52PM +0200, Ingo Feinerer wrote:
> Dear useRs,
> Dear Brian,
> 
> update math/R 4.1.2 -> 4.2.1
> 
> - Sync math/rstudio patch as SO_VERSION is bumped (symbols added and removed)
> 
> - There is now a (multiple) warning in the build:
> 
>   Warning message:
>   In normalizePath("~") :
> path[1]="/R-4.2.1_writes_to_HOME": No such file or directory
> 
>   The cause is likely that the _pbuild user has its home directory set
>   to /nonexistent. It tried to manually set HOME="$WRKDIR" in
>   CONFIGURE_ENV and MAKE_ENV but without success (either not picked up
>   or makes no difference).

HOME is set to PORTHOME by bsd.port.mk, so setting

PORTHOME=   ${WRKDIR}

in the Makefile fixes this.

> 
>   However, R runs fine for me and I could not identify any problems
>   later on. So I did not investigate further.
> 
> OK?

builds and packages fine, bump in rstudio is correct, so

ok tb

UPDATE: math/R

2022-08-03 Thread Ingo Feinerer

Dear useRs,
Dear Brian,

update math/R 4.1.2 -> 4.2.1

- Sync math/rstudio patch as SO_VERSION is bumped (symbols added and removed)

- There is now a (multiple) warning in the build:

  Warning message:
  In normalizePath("~") :
path[1]="/R-4.2.1_writes_to_HOME": No such file or directory

  The cause is likely that the _pbuild user has its home directory set
  to /nonexistent. It tried to manually set HOME="$WRKDIR" in
  CONFIGURE_ENV and MAKE_ENV but without success (either not picked up
  or makes no difference).

  However, R runs fine for me and I could not identify any problems
  later on. So I did not investigate further.

OK?

Best regards,
Ingo

Index: R/Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.126
diff -u -p -r1.126 Makefile
--- R/Makefile  25 Jul 2022 06:11:05 -  1.126
+++ R/Makefile  3 Aug 2022 11:49:55 -
@@ -1,9 +1,9 @@
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-4.1.2
+DISTNAME=  R-4.2.1
 
 # When bumping SO_VERSION, adjust
 # math/rstudio/patches/patch-src_cpp_core_r_util_REnvironmentPosix_cpp
-SO_VERSION=38.0
+SO_VERSION=39.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
Index: R/distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.55
diff -u -p -r1.55 distinfo
--- R/distinfo  4 Nov 2021 07:57:06 -   1.55
+++ R/distinfo  3 Aug 2022 11:49:55 -
@@ -1,2 +1,2 @@
-SHA256 (R-4.1.2.tar.gz) = IDYiXp9yB9TOCX5Ulyrs2qi0DX2ZEc0mSR+sWg+rOK8=
-SIZE (R-4.1.2.tar.gz) = 34009074
+SHA256 (R-4.2.1.tar.gz) = TVLbSG0nhI5UYT1O6XetlS7AjOF4B+G1JbEM1ENsZD8=
+SIZE (R-4.2.1.tar.gz) = 37601544
Index: R/pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.50
diff -u -p -r1.50 PLIST
--- R/pkg/PLIST 11 Mar 2022 19:36:11 -  1.50
+++ R/pkg/PLIST 3 Aug 2022 11:49:56 -
@@ -62,7 +62,6 @@ lib/R/include/R_ext/Parse.h
 lib/R/include/R_ext/Print.h
 lib/R/include/R_ext/PrtUtil.h
 lib/R/include/R_ext/QuartzDevice.h
-lib/R/include/R_ext/R-ftp-http.h
 lib/R/include/R_ext/RS.h
 lib/R/include/R_ext/RStartup.h
 lib/R/include/R_ext/Rallocators.h
@@ -82,7 +81,6 @@ lib/R/include/Rinterface.h
 lib/R/include/Rinternals.h
 lib/R/include/Rmath.h
 lib/R/include/Rversion.h
-lib/R/include/S.h
 lib/R/lib/
 @lib lib/R/lib/libR.so.${LIBR_VERSION}
 @lib lib/R/lib/libRblas.so.${LIBRblas_VERSION}
@@ -1023,10 +1021,6 @@ lib/R/library/mgcv/po/fr/
 lib/R/library/mgcv/po/fr/LC_MESSAGES/
 lib/R/library/mgcv/po/fr/LC_MESSAGES/R-mgcv.mo
 lib/R/library/mgcv/po/fr/LC_MESSAGES/mgcv.mo
-lib/R/library/mgcv/po/it/
-lib/R/library/mgcv/po/it/LC_MESSAGES/
-lib/R/library/mgcv/po/it/LC_MESSAGES/R-mgcv.mo
-lib/R/library/mgcv/po/it/LC_MESSAGES/mgcv.mo
 lib/R/library/mgcv/po/ko/
 lib/R/library/mgcv/po/ko/LC_MESSAGES/
 lib/R/library/mgcv/po/ko/LC_MESSAGES/R-mgcv.mo
@@ -1039,7 +1033,6 @@ lib/R/library/nlme/
 lib/R/library/nlme/CITATION
 lib/R/library/nlme/DESCRIPTION
 lib/R/library/nlme/INDEX
-lib/R/library/nlme/LICENCE
 lib/R/library/nlme/Meta/
 lib/R/library/nlme/Meta/Rd.rds
 lib/R/library/nlme/Meta/data.rds
@@ -1774,9 +1767,13 @@ lib/R/library/translations/lt/LC_MESSAGE
 lib/R/library/translations/lt/LC_MESSAGES/R-grDevices.mo
 lib/R/library/translations/lt/LC_MESSAGES/R-graphics.mo
 lib/R/library/translations/lt/LC_MESSAGES/R-grid.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-methods.mo
 lib/R/library/translations/lt/LC_MESSAGES/R-parallel.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-splines.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-stats.mo
 lib/R/library/translations/lt/LC_MESSAGES/R-stats4.mo
 lib/R/library/translations/lt/LC_MESSAGES/R-tcltk.mo
+lib/R/library/translations/lt/LC_MESSAGES/R-tools.mo
 lib/R/library/translations/lt/LC_MESSAGES/R-utils.mo
 lib/R/library/translations/lt/LC_MESSAGES/R.mo
 lib/R/library/translations/lt/LC_MESSAGES/RGui.mo
@@ -1788,6 +1785,7 @@ lib/R/library/translations/lt/LC_MESSAGE
 lib/R/library/translations/lt/LC_MESSAGES/splines.mo
 lib/R/library/translations/lt/LC_MESSAGES/stats.mo
 lib/R/library/translations/lt/LC_MESSAGES/tcltk.mo
+lib/R/library/translations/lt/LC_MESSAGES/tools.mo
 lib/R/library/translations/lt/LC_MESSAGES/utils.mo
 lib/R/library/translations/nn/
 lib/R/library/translations/nn/LC_MESSAGES/
@@ -1916,11 +1914,13 @@ lib/R/library/translations/zh_TW/LC_MESS
 lib/R/library/translations/zh_TW/LC_MESSAGES/R-grDevices.mo
 lib/R/library/translations/zh_TW/LC_MESSAGES/R-graphics.mo
 lib/R/library/translations/zh_TW/LC_MESSAGES/R-grid.mo
+lib/R/library/translations/zh_TW/LC_MESSAGES/R-methods.mo
 lib/R/library/translations/zh_TW/LC_MESSAGES/R-parallel.mo
 lib/R/library/translations/zh_TW/LC_MESSAGES/R-splines.mo
 lib/R/library/translations/zh_TW/LC_MESSAGES/R-stats.mo
 lib/R/library/translations/zh_

Re: UPDATE: math/R

2020-05-17 Thread Paul Irofti

On Sun, May 17, 2020 at 09:55:31AM +0200, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.6.3 -> 4.0.0
> 
> - SHARED_LIBS: increase major version number due to removals in dynamic
>   export changes in libR.so.
> 
> - Sync WANTLIB as PCRE2 is now preferred (see
>   https://stat.ethz.ch/pipermail/r-announce/2020/000653.html for details).
> 
> - Clean up MASTER_SITES as a few sites time out (for details see
>   https://cran.r-project.org/mirmon_report.html). Use the main site and the 
> new
>   cloud CDN site as backup instead.
> 
> - Update line numbers in patch.
> 
> - Recommend to use (optional) Java 11 instead of 1.8 in README.
> 
> Works for me on amd64 since a few weeks (released on 24 April).
> 
> (Note: you need to reinstall your R packages as this is a major R update.)
> 
> OK?

OK 

> 
> Best regards,
> Ingo
> 
> Index: Makefile
> ===
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.114
> diff -u -p -r1.114 Makefile
> --- Makefile  2 Mar 2020 14:07:05 -   1.114
> +++ Makefile  17 May 2020 07:33:04 -
> @@ -1,9 +1,9 @@
>  # $OpenBSD: Makefile,v 1.114 2020/03/02 14:07:05 feinerer Exp $
>  
>  COMMENT= powerful math/statistics/graphics language
> -DISTNAME=R-3.6.3
> +DISTNAME=R-4.0.0
>  
> -SO_VERSION=  36.1
> +SO_VERSION=  37.0
>  .for _lib in R Rblas Rlapack
>  SHARED_LIBS +=   ${_lib} ${SO_VERSION}
>  .endfor
> @@ -19,20 +19,12 @@ PERMIT_PACKAGE=   Yes
>  WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB} ${MODFORTRAN_WANTLIB}
>  WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
>  WANTLIB += glib-2.0 gobject-2.0 harfbuzz iconv icui18n icuuc intl jpeg lzma m
> -WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl 
> tiff z
> +WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre2-8 png readline ssl tiff z
>  
>  COMPILER =   base-clang ports-gcc base-gcc
>  
> -MASTER_SITES=https://cran.r-project.org/src/base/R-3/ \
> - http://cran.at.r-project.org/src/base/R-3/ \
> - http://cran.br.r-project.org/src/base/R-3/ \
> - http://cran.ch.r-project.org/src/base/R-3/ \
> - http://cran.dk.r-project.org/src/base/R-3/ \
> - http://cran.es.r-project.org/src/base/R-3/ \
> - http://cran.stat.ucla.edu/src/base/R-3/ \
> - http://cran.uk.r-project.org/src/base/R-3/ \
> - http://cran.us.r-project.org/src/base/R-3/ \
> - http://probability.ca/cran/src/base/R-3/
> +MASTER_SITES=https://cran.r-project.org/src/base/R-4/ \
> + https://cloud.r-project.org/src/base/R-4/
>  
>  MODULES= fortran \
>   x11/tk
> Index: distinfo
> ===
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.46
> diff -u -p -r1.46 distinfo
> --- distinfo  2 Mar 2020 14:07:05 -   1.46
> +++ distinfo  17 May 2020 07:33:04 -
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.6.3.tar.gz) = iTApkNjordU24SEl7FkdaVECLPhHWGGzaQvIvxzvqo8=
> -SIZE (R-3.6.3.tar.gz) = 33308185
> +SHA256 (R-4.0.0.tar.gz) = Br6wKRtWmXhITrDctdIzlmXsdFc3vftOhz56WnVJKUA=
> +SIZE (R-4.0.0.tar.gz) = 33173947
> Index: patches/patch-configure
> ===
> RCS file: /cvs/ports/math/R/patches/patch-configure,v
> retrieving revision 1.40
> diff -u -p -r1.40 patch-configure
> --- patches/patch-configure   18 Dec 2019 13:05:48 -  1.40
> +++ patches/patch-configure   17 May 2020 07:33:04 -
> @@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.40 2019/12
>  Index: configure
>  --- configure.orig
>  +++ configure
> -@@ -42057,8 +42057,8 @@ fi
> +@@ -45219,8 +45219,8 @@ fi
>   
>   fi
>   if test "${have_zlib}" = yes; then
> @@ -14,7 +14,7 @@ Index: configure
>   if ${r_cv_header_zlib_h+:} false; then :
> $as_echo_n "(cached) " >&6
>   else
> -@@ -42073,7 +42073,7 @@ else
> +@@ -45235,7 +45235,7 @@ else
>   #include 
>   int main() {
>   #ifdef ZLIB_VERNUM
> Index: pkg/PLIST
> ===
> RCS file: /cvs/ports/math/R/pkg/PLIST,v
> retrieving revision 1.43
> diff -u -p -r1.43 PLIST
> --- pkg/PLIST 18 Dec 2019 13:05:48 -  1.43
> +++ pkg/PLIST 17 May 2020 07:33:05 -
> @@ -415,6 +415,9 @@ lib/R/library/class/po/en@quot/LC_MESSAG
>  lib/R/library/class/po/fr/
>  lib/R/library/class/po/fr/LC_MESSAGES/
>  lib/R/library/class/po/fr/LC_MESSAGES/R-class.mo
> +lib/R/library/class/po/it/
> +lib/R/library/class/po/it

UPDATE: math/R

2020-05-17 Thread Ingo Feinerer

Dear useRs,

update math/R 3.6.3 -> 4.0.0

- SHARED_LIBS: increase major version number due to removals in dynamic
  export changes in libR.so.

- Sync WANTLIB as PCRE2 is now preferred (see
  https://stat.ethz.ch/pipermail/r-announce/2020/000653.html for details).

- Clean up MASTER_SITES as a few sites time out (for details see
  https://cran.r-project.org/mirmon_report.html). Use the main site and the new
  cloud CDN site as backup instead.

- Update line numbers in patch.

- Recommend to use (optional) Java 11 instead of 1.8 in README.

Works for me on amd64 since a few weeks (released on 24 April).

(Note: you need to reinstall your R packages as this is a major R update.)

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.114
diff -u -p -r1.114 Makefile
--- Makefile2 Mar 2020 14:07:05 -   1.114
+++ Makefile17 May 2020 07:33:04 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.114 2020/03/02 14:07:05 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.6.3
+DISTNAME=  R-4.0.0
 
-SO_VERSION=36.1
+SO_VERSION=37.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -19,20 +19,12 @@ PERMIT_PACKAGE= Yes
 WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB} ${MODFORTRAN_WANTLIB}
 WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
 WANTLIB += glib-2.0 gobject-2.0 harfbuzz iconv icui18n icuuc intl jpeg lzma m
-WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl tiff 
z
+WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre2-8 png readline ssl tiff z
 
 COMPILER = base-clang ports-gcc base-gcc
 
-MASTER_SITES=  https://cran.r-project.org/src/base/R-3/ \
-   http://cran.at.r-project.org/src/base/R-3/ \
-   http://cran.br.r-project.org/src/base/R-3/ \
-   http://cran.ch.r-project.org/src/base/R-3/ \
-   http://cran.dk.r-project.org/src/base/R-3/ \
-   http://cran.es.r-project.org/src/base/R-3/ \
-   http://cran.stat.ucla.edu/src/base/R-3/ \
-   http://cran.uk.r-project.org/src/base/R-3/ \
-   http://cran.us.r-project.org/src/base/R-3/ \
-   http://probability.ca/cran/src/base/R-3/
+MASTER_SITES=  https://cran.r-project.org/src/base/R-4/ \
+   https://cloud.r-project.org/src/base/R-4/
 
 MODULES=   fortran \
x11/tk
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.46
diff -u -p -r1.46 distinfo
--- distinfo2 Mar 2020 14:07:05 -   1.46
+++ distinfo17 May 2020 07:33:04 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.6.3.tar.gz) = iTApkNjordU24SEl7FkdaVECLPhHWGGzaQvIvxzvqo8=
-SIZE (R-3.6.3.tar.gz) = 33308185
+SHA256 (R-4.0.0.tar.gz) = Br6wKRtWmXhITrDctdIzlmXsdFc3vftOhz56WnVJKUA=
+SIZE (R-4.0.0.tar.gz) = 33173947
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.40
diff -u -p -r1.40 patch-configure
--- patches/patch-configure 18 Dec 2019 13:05:48 -  1.40
+++ patches/patch-configure 17 May 2020 07:33:04 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.40 2019/12
 Index: configure
 --- configure.orig
 +++ configure
-@@ -42057,8 +42057,8 @@ fi
+@@ -45219,8 +45219,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -42073,7 +42073,7 @@ else
+@@ -45235,7 +45235,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.43
diff -u -p -r1.43 PLIST
--- pkg/PLIST   18 Dec 2019 13:05:48 -  1.43
+++ pkg/PLIST   17 May 2020 07:33:05 -
@@ -415,6 +415,9 @@ lib/R/library/class/po/en@quot/LC_MESSAG
 lib/R/library/class/po/fr/
 lib/R/library/class/po/fr/LC_MESSAGES/
 lib/R/library/class/po/fr/LC_MESSAGES/R-class.mo
+lib/R/library/class/po/it/
+lib/R/library/class/po/it/LC_MESSAGES/
+lib/R/library/class/po/it/LC_MESSAGES/R-class.mo
 lib/R/library/class/po/ko/
 lib/R/library/class/po/ko/LC_MESSAGES/
 lib/R/library/class/po/ko/LC_MESSAGES/R-class.mo
@@ -1923,12 +1926,16 @@ share/doc/R/NEWS
 share/doc/R/NEWS.0
 share/doc/R/NEWS.1
 share/doc/R/NEWS.2
+share/doc/R/NEWS.2.rds
+share/doc/R/NEWS.3
+share/doc/R/NEWS.3.rds
 share/doc/R/NEWS.pdf
 share/doc/R/NEWS.rds
 share/doc/R/RESOURCES
 share/doc/R/THANKS
 share/doc/R/html/
 share/doc/R/html/NEWS.2.html
+share/doc/R/html/NEWS.3.html
 share/doc/R/html/NEWS.html
 share/doc/R/html/R.css
 share/doc/R/ht

Re: UPDATE: math/R

2019-12-18 Thread Brian Callahan





On 2019-12-18 02:47, Martin Reindl wrote:

On Tue, Dec 17, 2019 at 11:07:43AM -0500, Brian Callahan wrote:

Hi Ingo --

On 2019-12-17 10:52, Ingo Feinerer wrote:

On Fri, Dec 13, 2019 at 11:28:50AM +0100, Martin Reindl wrote:

On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:

update math/R 3.6.1 -> 3.6.2

[...]

Works for me on amd64.

+1 on arm64 with my Rscripts.

But does this need extra WANTLIBs?

R-3.6.2(math/R):
Missing: flang.2 from flang-8.0.1.20191107 (/usr/local/lib/R/modules/lapack.so)
Missing: flangrti.5 from flang-8.0.1.20191107 
(/usr/local/lib/R/modules/lapack.so)
Missing: pgmath.4 from libpgmath-8.0.1.20191107 
(/usr/local/lib/R/modules/lapack.so)
Extra:  c++.3 c++abi.1
WANTLIB += flang flangrti pgmath
*** Error 1 in target 'port-lib-depends-check' (ignored)

R uses flang on arm64 (changed in math/R by bcallah@ on 2019-05-08):

MODULES = fortran

.if ${MACHINE_ARCH:Maarch64}
MODFORTRAN_COMPILER = flang
.else
MODFORTRAN_COMPILER = gfortran
.endif

Fortunately, infrastructure/mk/fortran.port.mk sets MODFORTRAN_WANTLIB
according to the value of MODFORTRAN_COMPILER (either gfortran or flang).

So I just added MODFORTRAN_WANTLIB to WANTLIB. amd64 is still happy with this
and I think it addresses your observation on arm64 (I don't have an arm64
system to test).

@martin or @bcallah: could you please confirm this?

I don't have access to my arm64 machine until Thursday; I can check then.

Alternatively, we can probably switch arm64 to
using gfortran if that makes life easier for
people. The decision to use flang for arm64
dates back to when the only fortran compiler on
arm64 was flang. But I don't think that's the
case any more. I can cook up something if that's
the direction we choose to go.

Anyhow, I'll check on Thursday if no one else
beats me to it and get back to you.

With gfortran, R needs some extra -fPIC love I think. That's probably why you
switched it to flang.

 From my point of view, it is better to set MODFORTRAN_WANTLIB for now and
stick to flang on arm64. I can confirm port-lib-depends-check is happy on
arm64 with the MODFORTRAN_WANTLIB addition.

-m


Sounds good to me.

~Brian

Re: UPDATE: math/R

2019-12-17 Thread Martin Reindl

On Tue, Dec 17, 2019 at 11:07:43AM -0500, Brian Callahan wrote:
> Hi Ingo --
> 
> On 2019-12-17 10:52, Ingo Feinerer wrote:
> > On Fri, Dec 13, 2019 at 11:28:50AM +0100, Martin Reindl wrote:
> > > On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:
> > > > update math/R 3.6.1 -> 3.6.2
> > > [...]
> > > > Works for me on amd64.
> > > +1 on arm64 with my Rscripts.
> > > 
> > > But does this need extra WANTLIBs?
> > > 
> > > R-3.6.2(math/R):
> > > Missing: flang.2 from flang-8.0.1.20191107 
> > > (/usr/local/lib/R/modules/lapack.so)
> > > Missing: flangrti.5 from flang-8.0.1.20191107 
> > > (/usr/local/lib/R/modules/lapack.so)
> > > Missing: pgmath.4 from libpgmath-8.0.1.20191107 
> > > (/usr/local/lib/R/modules/lapack.so)
> > > Extra:  c++.3 c++abi.1
> > > WANTLIB += flang flangrti pgmath
> > > *** Error 1 in target 'port-lib-depends-check' (ignored)
> > R uses flang on arm64 (changed in math/R by bcallah@ on 2019-05-08):
> > 
> > MODULES = fortran
> > 
> > .if ${MACHINE_ARCH:Maarch64}
> > MODFORTRAN_COMPILER = flang
> > .else
> > MODFORTRAN_COMPILER = gfortran
> > .endif
> > 
> > Fortunately, infrastructure/mk/fortran.port.mk sets MODFORTRAN_WANTLIB
> > according to the value of MODFORTRAN_COMPILER (either gfortran or flang).
> > 
> > So I just added MODFORTRAN_WANTLIB to WANTLIB. amd64 is still happy with 
> > this
> > and I think it addresses your observation on arm64 (I don't have an arm64
> > system to test).
> > 
> > @martin or @bcallah: could you please confirm this?
> 
> I don't have access to my arm64 machine until Thursday; I can check then.
> 
> Alternatively, we can probably switch arm64 to
> using gfortran if that makes life easier for
> people. The decision to use flang for arm64
> dates back to when the only fortran compiler on
> arm64 was flang. But I don't think that's the
> case any more. I can cook up something if that's
> the direction we choose to go.
> 
> Anyhow, I'll check on Thursday if no one else
> beats me to it and get back to you.

With gfortran, R needs some extra -fPIC love I think. That's probably why you
switched it to flang.

>From my point of view, it is better to set MODFORTRAN_WANTLIB for now and
stick to flang on arm64. I can confirm port-lib-depends-check is happy on
arm64 with the MODFORTRAN_WANTLIB addition.

-m

Re: UPDATE: math/R

2019-12-17 Thread Brian Callahan


Hi Ingo --

On 2019-12-17 10:52, Ingo Feinerer wrote:

On Fri, Dec 13, 2019 at 11:28:50AM +0100, Martin Reindl wrote:

On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:

update math/R 3.6.1 -> 3.6.2

[...]

Works for me on amd64.

+1 on arm64 with my Rscripts.

But does this need extra WANTLIBs?

R-3.6.2(math/R):
Missing: flang.2 from flang-8.0.1.20191107 (/usr/local/lib/R/modules/lapack.so)
Missing: flangrti.5 from flang-8.0.1.20191107 
(/usr/local/lib/R/modules/lapack.so)
Missing: pgmath.4 from libpgmath-8.0.1.20191107 
(/usr/local/lib/R/modules/lapack.so)
Extra:  c++.3 c++abi.1
WANTLIB += flang flangrti pgmath
*** Error 1 in target 'port-lib-depends-check' (ignored)

R uses flang on arm64 (changed in math/R by bcallah@ on 2019-05-08):

MODULES = fortran

.if ${MACHINE_ARCH:Maarch64}
MODFORTRAN_COMPILER = flang
.else
MODFORTRAN_COMPILER = gfortran
.endif

Fortunately, infrastructure/mk/fortran.port.mk sets MODFORTRAN_WANTLIB
according to the value of MODFORTRAN_COMPILER (either gfortran or flang).

So I just added MODFORTRAN_WANTLIB to WANTLIB. amd64 is still happy with this
and I think it addresses your observation on arm64 (I don't have an arm64
system to test).

@martin or @bcallah: could you please confirm this?


I don't have access to my arm64 machine until Thursday; I can check then.

Alternatively, we can probably switch arm64 to using gfortran if that 
makes life easier for people. The decision to use flang for arm64 dates 
back to when the only fortran compiler on arm64 was flang. But I don't 
think that's the case any more. I can cook up something if that's the 
direction we choose to go.


Anyhow, I'll check on Thursday if no one else beats me to it and get 
back to you.


~Brian


Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.112
diff -u -p -r1.112 Makefile
--- Makefile5 Jul 2019 19:27:30 -   1.112
+++ Makefile17 Dec 2019 15:48:33 -
@@ -1,9 +1,9 @@
  # $OpenBSD: Makefile,v 1.112 2019/07/05 19:27:30 feinerer Exp $
  
  COMMENT=	powerful math/statistics/graphics language

-DISTNAME=  R-3.6.1
+DISTNAME=  R-3.6.2
  
-SO_VERSION=	35.1

+SO_VERSION=36.0
  .for _lib in R Rblas Rlapack
  SHARED_LIBS +=${_lib} ${SO_VERSION}
  .endfor
@@ -16,7 +16,7 @@ MAINTAINER=   Ingo Feinerer   
-WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}

+WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB} ${MODFORTRAN_WANTLIB}
  WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
  WANTLIB += glib-2.0 gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
  WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl 
tiff z
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.44
diff -u -p -r1.44 distinfo
--- distinfo5 Jul 2019 19:27:30 -   1.44
+++ distinfo17 Dec 2019 15:48:33 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.6.1.tar.gz) = W6qevT5xrOzcw9ox2QQvsXTVWkKCn4MV8kVwgJeLE4k=
-SIZE (R-3.6.1.tar.gz) = 30463021
+SHA256 (R-3.6.2.tar.gz) = vWWkXN37iPNzcPvO5KyN0/GuvuvkfC+Wj9l3C6K7yVQ=
+SIZE (R-3.6.2.tar.gz) = 33311930
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.39
diff -u -p -r1.39 patch-configure
--- patches/patch-configure 5 Jul 2019 19:27:30 -   1.39
+++ patches/patch-configure 17 Dec 2019 15:48:33 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.39 2019/07
  Index: configure
  --- configure.orig
  +++ configure
-@@ -41831,8 +41831,8 @@ fi
+@@ -42057,8 +42057,8 @@ fi
   
   fi

   if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
   if ${r_cv_header_zlib_h+:} false; then :
 $as_echo_n "(cached) " >&6
   else
-@@ -41847,7 +41847,7 @@ else
+@@ -42073,7 +42073,7 @@ else
   #include 
   int main() {
   #ifdef ZLIB_VERNUM
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.42
diff -u -p -r1.42 PLIST
--- pkg/PLIST   29 Apr 2019 08:52:48 -  1.42
+++ pkg/PLIST   17 Dec 2019 15:48:33 -
@@ -114,7 +114,7 @@ lib/R/library/KernSmooth/html/
  lib/R/library/KernSmooth/html/00Index.html
  lib/R/library/KernSmooth/html/R.css
  lib/R/library/KernSmooth/libs/
-lib/R/library/KernSmooth/libs/KernSmooth.so
+@so lib/R/library/KernSmooth/libs/KernSmooth.so
  lib/R/library/KernSmooth/po/
  lib/R/library/KernSmooth/po/de/
  lib/R/library/KernSmooth/po/de/LC_MESSAGES/
@@ -163,7 +163,7 @@ lib/R/library/MASS/html/
  lib/R/library/MASS/html/00Index.html
  lib/R/library/MASS/html/R.css
  lib/R/library/MASS/libs/
-lib/R/library/MASS/libs/MASS.so
+@so lib/R/library/MASS/libs/MASS.so
  lib/R/library/MASS/po/
  lib/R/library/MASS/po/de/
  lib/R/library/MASS/po/de/LC_MESSA

Re: UPDATE: math/R

2019-12-17 Thread Ingo Feinerer

On Fri, Dec 13, 2019 at 11:28:50AM +0100, Martin Reindl wrote:
> On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:
> > update math/R 3.6.1 -> 3.6.2
> [...]
> > Works for me on amd64.
> 
> +1 on arm64 with my Rscripts.
> 
> But does this need extra WANTLIBs?
> 
> R-3.6.2(math/R):
> Missing: flang.2 from flang-8.0.1.20191107 
> (/usr/local/lib/R/modules/lapack.so)
> Missing: flangrti.5 from flang-8.0.1.20191107 
> (/usr/local/lib/R/modules/lapack.so)
> Missing: pgmath.4 from libpgmath-8.0.1.20191107 
> (/usr/local/lib/R/modules/lapack.so)
> Extra:  c++.3 c++abi.1
> WANTLIB += flang flangrti pgmath
> *** Error 1 in target 'port-lib-depends-check' (ignored)

R uses flang on arm64 (changed in math/R by bcallah@ on 2019-05-08):

MODULES = fortran

.if ${MACHINE_ARCH:Maarch64}
MODFORTRAN_COMPILER = flang
.else
MODFORTRAN_COMPILER = gfortran
.endif

Fortunately, infrastructure/mk/fortran.port.mk sets MODFORTRAN_WANTLIB
according to the value of MODFORTRAN_COMPILER (either gfortran or flang).

So I just added MODFORTRAN_WANTLIB to WANTLIB. amd64 is still happy with this
and I think it addresses your observation on arm64 (I don't have an arm64
system to test).

@martin or @bcallah: could you please confirm this?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.112
diff -u -p -r1.112 Makefile
--- Makefile5 Jul 2019 19:27:30 -   1.112
+++ Makefile17 Dec 2019 15:48:33 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.112 2019/07/05 19:27:30 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.6.1
+DISTNAME=  R-3.6.2
 
-SO_VERSION=35.1
+SO_VERSION=36.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -16,7 +16,7 @@ MAINTAINER=   Ingo Feinerer &6
  else
-@@ -41847,7 +41847,7 @@ else
+@@ -42073,7 +42073,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.42
diff -u -p -r1.42 PLIST
--- pkg/PLIST   29 Apr 2019 08:52:48 -  1.42
+++ pkg/PLIST   17 Dec 2019 15:48:33 -
@@ -114,7 +114,7 @@ lib/R/library/KernSmooth/html/
 lib/R/library/KernSmooth/html/00Index.html
 lib/R/library/KernSmooth/html/R.css
 lib/R/library/KernSmooth/libs/
-lib/R/library/KernSmooth/libs/KernSmooth.so
+@so lib/R/library/KernSmooth/libs/KernSmooth.so
 lib/R/library/KernSmooth/po/
 lib/R/library/KernSmooth/po/de/
 lib/R/library/KernSmooth/po/de/LC_MESSAGES/
@@ -163,7 +163,7 @@ lib/R/library/MASS/html/
 lib/R/library/MASS/html/00Index.html
 lib/R/library/MASS/html/R.css
 lib/R/library/MASS/libs/
-lib/R/library/MASS/libs/MASS.so
+@so lib/R/library/MASS/libs/MASS.so
 lib/R/library/MASS/po/
 lib/R/library/MASS/po/de/
 lib/R/library/MASS/po/de/LC_MESSAGES/
@@ -273,7 +273,7 @@ lib/R/library/Matrix/include/Matrix.h
 lib/R/library/Matrix/include/Matrix_stubs.c
 lib/R/library/Matrix/include/cholmod.h
 lib/R/library/Matrix/libs/
-lib/R/library/Matrix/libs/Matrix.so
+@so lib/R/library/Matrix/libs/Matrix.so
 lib/R/library/Matrix/po/
 lib/R/library/Matrix/po/de/
 lib/R/library/Matrix/po/de/LC_MESSAGES/
@@ -404,7 +404,7 @@ lib/R/library/class/html/
 lib/R/library/class/html/00Index.html
 lib/R/library/class/html/R.css
 lib/R/library/class/libs/
-lib/R/library/class/libs/class.so
+@so lib/R/library/class/libs/class.so
 lib/R/library/class/po/
 lib/R/library/class/po/de/
 lib/R/library/class/po/de/LC_MESSAGES/
@@ -453,7 +453,7 @@ lib/R/library/cluster/html/
 lib/R/library/cluster/html/00Index.html
 lib/R/library/cluster/html/R.css
 lib/R/library/cluster/libs/
-lib/R/library/cluster/libs/cluster.so
+@so lib/R/library/cluster/libs/cluster.so
 lib/R/library/cluster/po/
 lib/R/library/cluster/po/de/
 lib/R/library/cluster/po/de/LC_MESSAGES/
@@ -580,7 +580,7 @@ lib/R/library/foreign/html/
 lib/R/library/foreign/html/00Index.html
 lib/R/library/foreign/html/R.css
 lib/R/library/foreign/libs/
-lib/R/library/foreign/libs/foreign.so
+@so lib/R/library/foreign/libs/foreign.so
 lib/R/library/foreign/po/
 lib/R/library/foreign/po/de/
 lib/R/library/foreign/po/de/LC_MESSAGES/
@@ -743,8 +743,8 @@ lib/R/library/grDevices/icc/
 lib/R/library/grDevices/icc/srgb
 lib/R/library/grDevices/icc/srgb.flate
 lib/R/library/grDevices/libs/
-lib/R/library/grDevices/libs/cairo.so
-lib/R/library/grDevices/libs/grDevices.so
+@so lib/R/library/grDevices/libs/cairo.so
+@so lib/R/library/grDevices/libs/grDevices.so
 lib/R/library/graphics/
 lib/R/library/graphics/DESCRIPTION
 lib/R/library/graphics/INDEX
@@ -786,7 +786,7 @@ lib/R/library/graphics/html/
 lib/R/library/graphics/html/00Index.html
 lib/R/library/graphics/html/R.css
 lib/R/library/graphics/libs/
-lib/R/library/graphics/libs/graphics.so
+@so lib/R/library/graphics/libs/graphics.so
 l

Re: UPDATE: math/R

2019-12-13 Thread Martin Reindl

On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.6.1 -> 3.6.2
[...]
> Works for me on amd64.

+1 on arm64 with my Rscripts.

But does this need extra WANTLIBs?

R-3.6.2(math/R):
Missing: flang.2 from flang-8.0.1.20191107 (/usr/local/lib/R/modules/lapack.so)
Missing: flangrti.5 from flang-8.0.1.20191107 
(/usr/local/lib/R/modules/lapack.so)
Missing: pgmath.4 from libpgmath-8.0.1.20191107 
(/usr/local/lib/R/modules/lapack.so)
Extra:  c++.3 c++abi.1
WANTLIB += flang flangrti pgmath
*** Error 1 in target 'port-lib-depends-check' (ignored)

-m

UPDATE: math/R

2019-12-12 Thread Ingo Feinerer

Dear useRs,

update math/R 3.6.1 -> 3.6.2

- SHARED_LIBS: increase major version number due to removals in dynamic
  export changes

  $ /usr/src/lib/check_sym libR.so.35.1 libR.so.36.0
  libR.so.35.1 --> libR.so.36.0
  Dynamic export changes:
  removed:
  dummy_ii
  dummy_ii_ptr

  PLT removed:
  intpr_

- Update line numbers in patch

- Several lines in PLIST are now marked with "@so" but these files are
  no longer in the installed package. Is this expected (i.e., ignored by
  the pkg_* machinery or just coincidence)?

  All tested packages seems to work without problems; I did not notice
  any errors due to the missing .so files.

Works for me on amd64.

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.112
diff -u -p -r1.112 Makefile
--- Makefile5 Jul 2019 19:27:30 -   1.112
+++ Makefile12 Dec 2019 13:01:49 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.112 2019/07/05 19:27:30 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.6.1
+DISTNAME=  R-3.6.2
 
-SO_VERSION=35.1
+SO_VERSION=36.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.44
diff -u -p -r1.44 distinfo
--- distinfo5 Jul 2019 19:27:30 -   1.44
+++ distinfo12 Dec 2019 13:01:49 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.6.1.tar.gz) = W6qevT5xrOzcw9ox2QQvsXTVWkKCn4MV8kVwgJeLE4k=
-SIZE (R-3.6.1.tar.gz) = 30463021
+SHA256 (R-3.6.2.tar.gz) = vWWkXN37iPNzcPvO5KyN0/GuvuvkfC+Wj9l3C6K7yVQ=
+SIZE (R-3.6.2.tar.gz) = 33311930
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.39
diff -u -p -r1.39 patch-configure
--- patches/patch-configure 5 Jul 2019 19:27:30 -   1.39
+++ patches/patch-configure 12 Dec 2019 13:01:49 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.39 2019/07
 Index: configure
 --- configure.orig
 +++ configure
-@@ -41831,8 +41831,8 @@ fi
+@@ -42057,8 +42057,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -41847,7 +41847,7 @@ else
+@@ -42073,7 +42073,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.42
diff -u -p -r1.42 PLIST
--- pkg/PLIST   29 Apr 2019 08:52:48 -  1.42
+++ pkg/PLIST   12 Dec 2019 13:01:49 -
@@ -114,7 +114,7 @@ lib/R/library/KernSmooth/html/
 lib/R/library/KernSmooth/html/00Index.html
 lib/R/library/KernSmooth/html/R.css
 lib/R/library/KernSmooth/libs/
-lib/R/library/KernSmooth/libs/KernSmooth.so
+@so lib/R/library/KernSmooth/libs/KernSmooth.so
 lib/R/library/KernSmooth/po/
 lib/R/library/KernSmooth/po/de/
 lib/R/library/KernSmooth/po/de/LC_MESSAGES/
@@ -163,7 +163,7 @@ lib/R/library/MASS/html/
 lib/R/library/MASS/html/00Index.html
 lib/R/library/MASS/html/R.css
 lib/R/library/MASS/libs/
-lib/R/library/MASS/libs/MASS.so
+@so lib/R/library/MASS/libs/MASS.so
 lib/R/library/MASS/po/
 lib/R/library/MASS/po/de/
 lib/R/library/MASS/po/de/LC_MESSAGES/
@@ -273,7 +273,7 @@ lib/R/library/Matrix/include/Matrix.h
 lib/R/library/Matrix/include/Matrix_stubs.c
 lib/R/library/Matrix/include/cholmod.h
 lib/R/library/Matrix/libs/
-lib/R/library/Matrix/libs/Matrix.so
+@so lib/R/library/Matrix/libs/Matrix.so
 lib/R/library/Matrix/po/
 lib/R/library/Matrix/po/de/
 lib/R/library/Matrix/po/de/LC_MESSAGES/
@@ -404,7 +404,7 @@ lib/R/library/class/html/
 lib/R/library/class/html/00Index.html
 lib/R/library/class/html/R.css
 lib/R/library/class/libs/
-lib/R/library/class/libs/class.so
+@so lib/R/library/class/libs/class.so
 lib/R/library/class/po/
 lib/R/library/class/po/de/
 lib/R/library/class/po/de/LC_MESSAGES/
@@ -453,7 +453,7 @@ lib/R/library/cluster/html/
 lib/R/library/cluster/html/00Index.html
 lib/R/library/cluster/html/R.css
 lib/R/library/cluster/libs/
-lib/R/library/cluster/libs/cluster.so
+@so lib/R/library/cluster/libs/cluster.so
 lib/R/library/cluster/po/
 lib/R/library/cluster/po/de/
 lib/R/library/cluster/po/de/LC_MESSAGES/
@@ -580,7 +580,7 @@ lib/R/library/foreign/html/
 lib/R/library/foreign/html/00Index.html
 lib/R/library/foreign/html/R.css
 lib/R/library/foreign/libs/
-lib/R/library/foreign/libs/foreign.so
+@so lib/R/library/foreign/libs/foreign.so
 lib/R/library/foreign/po/
 lib/R/library/foreign/po/de/
 lib/R/library/foreign/po/de/LC_MESSAGES/
@@ -743,8 +743,8 @@ lib/R/library/grDevices/icc/
 lib/R/library/grDevices/icc/srgb
 lib/R/library/grDevices/icc/srgb.

Re: UPDATE: math/R

2019-07-05 Thread Klemens Nanni

OK kn

Re: UPDATE: math/R

2019-07-05 Thread Stuart Henderson

On 2019/07/05 10:44, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.6.0 -> 3.6.1
> 
> - SHARED_LIBS: increase major version number
> 
>   check_sym reports added and removed symbols for libR:
> 
>   $ /usr/src/lib/check_sym libR.so.35.0 /usr/local/lib/R/lib/libR.so.36.0
>   libR.so.35.0 --> /usr/local/lib/R/lib/libR.so.36.0
>   Dynamic export changes:
>   added:
>   dummy_ii_ptr
> 
>   External reference changes:
>   added:
>   tilde_expand_word
> 
>   removed:
>   tilde_expand
> 
>   PLT removed:
>   dummy_ii

That is an added symbol only. The tool you are using to check this is
of wider use than just ports - the bit you are interested in here is
"dynamic export changes".

UPDATE: math/R

2019-07-05 Thread Ingo Feinerer

Dear useRs,

update math/R 3.6.0 -> 3.6.1

- SHARED_LIBS: increase major version number

  check_sym reports added and removed symbols for libR:

  $ /usr/src/lib/check_sym libR.so.35.0 /usr/local/lib/R/lib/libR.so.36.0
  libR.so.35.0 --> /usr/local/lib/R/lib/libR.so.36.0
  Dynamic export changes:
  added:
  dummy_ii_ptr

  External reference changes:
  added:
  tilde_expand_word

  removed:
  tilde_expand

  PLT removed:
  dummy_ii

- PERMIT_PACKAGE_CDROM -> PERMIT_PACKAGE

- Disable OpenMP as requested in 
https://marc.info/?l=openbsd-ports=156176148832402=2

- Regenerate patches

Works for me on amd64.

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.111
diff -u -p -r1.111 Makefile
--- Makefile17 May 2019 16:45:27 -  1.111
+++ Makefile5 Jul 2019 08:37:42 -
@@ -1,10 +1,9 @@
 # $OpenBSD: Makefile,v 1.111 2019/05/17 16:45:27 sthen Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.6.0
-REVISION=  0
+DISTNAME=  R-3.6.1
 
-SO_VERSION=35.0
+SO_VERSION=36.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -15,7 +14,7 @@ HOMEPAGE= https://www.r-project.org/
 MAINTAINER=Ingo Feinerer 
 
 # GPLv2+
-PERMIT_PACKAGE_CDROM=  Yes
+PERMIT_PACKAGE=Yes
 
 WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}
 WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
@@ -79,6 +78,7 @@ CONFIGURE_STYLE=gnu
 MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
 
 CONFIGURE_ARGS= --disable-java \
+   --disable-openmp \
--enable-BLAS-shlib \
--enable-R-shlib \
--with-tcl-config=${MODTCL_CONFIG} \
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.43
diff -u -p -r1.43 distinfo
--- distinfo29 Apr 2019 08:52:47 -  1.43
+++ distinfo5 Jul 2019 08:37:42 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.6.0.tar.gz) = NvysPkUmZhWOYkWcb8gQrcJHxxCe1xxbbDrV/Cv1dQk=
-SIZE (R-3.6.0.tar.gz) = 30449618
+SHA256 (R-3.6.1.tar.gz) = W6qevT5xrOzcw9ox2QQvsXTVWkKCn4MV8kVwgJeLE4k=
+SIZE (R-3.6.1.tar.gz) = 30463021
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.38
diff -u -p -r1.38 patch-configure
--- patches/patch-configure 29 Apr 2019 08:52:47 -  1.38
+++ patches/patch-configure 5 Jul 2019 08:37:42 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.38 2019/04
 Index: configure
 --- configure.orig
 +++ configure
-@@ -41796,8 +41796,8 @@ fi
+@@ -41831,8 +41831,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -41812,7 +41812,7 @@ else
+@@ -41847,7 +41847,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM

UPDATE: math/R to disable OpenMP

2019-06-28 Thread j

This disables OpenMP code generation in R.


Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.111
diff -u -p -r1.111 Makefile
--- Makefile17 May 2019 16:45:27 -  1.111
+++ Makefile28 Jun 2019 20:18:07 -
@@ -2,7 +2,7 @@
 
 COMMENT=   powerful math/statistics/graphics language
 DISTNAME=  R-3.6.0
-REVISION=  0
+REVISION=  1
 
 SO_VERSION=35.0
 .for _lib in R Rblas Rlapack
@@ -79,6 +79,7 @@ CONFIGURE_STYLE=gnu
 MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
 
 CONFIGURE_ARGS= --disable-java \
+   --disable-openmp \
--enable-BLAS-shlib \
--enable-R-shlib \
--with-tcl-config=${MODTCL_CONFIG} \

Re: UPDATE: math/R

2019-04-28 Thread Klemens Nanni

OK kn

UPDATE: math/R

2019-04-26 Thread Ingo Feinerer

Dear useRs,

update math/R 3.5.3 -> 3.6.0

- SHARED_LIBS: increase major version number

  check_sym reports added and removed symbols.

- CONFIGURE_ENV: Do not set F77 anymore (as we set FC)

  3.6.0 release notes mention:

  "Macro F77 is always set to the value of FC, so the latter should
  be set to user-select the Fortran compiler for both fixed-form
  and free-form Fortran.  In particular, gfortran is now the first
  choice for F77, not f95."

  and

  "Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS are
  deprecated in favour of FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS
  respectively."

- CONFIGURE_ENV: MAKEINFO -> TEXI2ANY

  3.6.0 release notes mention:

  "The configure macro MAKEINFO has been updated to TEXI2ANY."

- patch-src_modules_internet_libcurl_c was merged upstream.

- PLIST change:

  3.6.0 release notes mention:

  "The f77_f2c script has been removed: it no longer sufficed to
  compile the .f files in R."

- The `tan(1+1000i)` test still fails (see
  https://marc.info/?l=openbsd-tech=150737856618497=2).

Works for me on amd64.

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.107
diff -u -p -r1.107 Makefile
--- Makefile17 Mar 2019 07:16:32 -  1.107
+++ Makefile26 Apr 2019 15:05:02 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.107 2019/03/17 07:16:32 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.5.3
+DISTNAME=  R-3.6.0
 
-SO_VERSION=34.2
+SO_VERSION=35.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -79,14 +79,13 @@ CONFIGURE_ARGS= --disable-java \
--with-tcl-config=${MODTCL_CONFIG} \
--with-tk-config=${MODTK_CONFIG}
 
-CONFIGURE_ENV= F77="${MODFORTRAN_COMPILER}" \
-   FC="${MODFORTRAN_COMPILER}" \
+CONFIGURE_ENV= FC="${MODFORTRAN_COMPILER}" \
FFLAGS="${FFLAGS}" \
CPPFLAGS="-I${LOCALBASE}/include" \
LDFLAGS="-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib" \
LIBnn=lib \
-   MAKEINFO="${LOCALBASE}/bin/gtexi2any" \
R_DYLIB_VERSION=${SO_VERSION} \
+   TEXI2ANY="${LOCALBASE}/bin/gtexi2any" \
TEXI2DVI="${LOCALBASE}/bin/gtexi2dvi" \
rdocdir="${PREFIX}/share/doc/R"
 
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.42
diff -u -p -r1.42 distinfo
--- distinfo17 Mar 2019 07:16:32 -  1.42
+++ distinfo26 Apr 2019 15:05:02 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.5.3.tar.gz) = K/o3t71wnwA9a4oXLd+20D3dLWctYJZDlSMDn3qOZ4w=
-SIZE (R-3.5.3.tar.gz) = 30205979
+SHA256 (R-3.6.0.tar.gz) = NvysPkUmZhWOYkWcb8gQrcJHxxCe1xxbbDrV/Cv1dQk=
+SIZE (R-3.6.0.tar.gz) = 30449618
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.37
diff -u -p -r1.37 patch-configure
--- patches/patch-configure 17 Mar 2019 07:16:32 -  1.37
+++ patches/patch-configure 26 Apr 2019 15:05:02 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.37 2019/03
 Index: configure
 --- configure.orig
 +++ configure
-@@ -42293,8 +42293,8 @@ fi
+@@ -41796,8 +41796,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -42309,7 +42309,7 @@ else
+@@ -41812,7 +41812,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: patches/patch-src_modules_internet_libcurl_c
===
RCS file: patches/patch-src_modules_internet_libcurl_c
diff -N patches/patch-src_modules_internet_libcurl_c
--- patches/patch-src_modules_internet_libcurl_c21 Feb 2019 20:04:34 
-  1.1
+++ /dev/null   1 Jan 1970 00:00:00 -
@@ -1,32 +0,0 @@
-$OpenBSD: patch-src_modules_internet_libcurl_c,v 1.1 2019/02/21 20:04:34 tb 
Exp $
-
-Avoid use-after-free.  Upstream SVN commit #76143.
-
-Index: src/modules/internet/libcurl.c
 src/modules/internet/libcurl.c.orig
-+++ src/modules/internet/libcurl.c
-@@ -641,12 +641,12 @@ in_do_curlDownload(SEXP call, SEXP op, SEXP args, SEXP
- 
- n_err += curlMultiCheckerrs(mhnd);
- 
-+long status = 0L;
- for (int i = 0; i < nurls; i++) {
-   if (out[i]) {
-   fclose(out[i]);
-   double dl;
-   curl_easy_getinfo(hnd[i], CURLINFO_SIZE_DOWNLOAD, );
--  long status;
-   curl_easy_getinfo(hnd[i], CURLINFO_RESPONSE_CODE, );
-   // should we do so

UPDATE: math/R

2019-03-13 Thread Ingo Feinerer

Dear useRs,

update math/R 3.5.2 -> 3.5.3

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.106
diff -u -p -r1.106 Makefile
--- Makefile21 Feb 2019 20:04:33 -  1.106
+++ Makefile13 Mar 2019 11:46:20 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.106 2019/02/21 20:04:33 tb Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.5.2
-REVISION=  0
+DISTNAME=  R-3.5.3
 
 SO_VERSION=34.2
 .for _lib in R Rblas Rlapack
@@ -20,7 +19,7 @@ PERMIT_PACKAGE_CDROM= Yes
 WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}
 WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
 WANTLIB += glib-2.0 gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
-WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl tiff 
z
+WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png16 readline ssl 
tiff z
 
 COMPILER = base-clang ports-gcc base-gcc
 
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.41
diff -u -p -r1.41 distinfo
--- distinfo23 Dec 2018 08:03:45 -  1.41
+++ distinfo13 Mar 2019 11:46:20 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.5.2.tar.gz) = 5T2MPPIPK416nBYxtvaiKHRQb7OSA0dYs7s0HFhsW2I=
-SIZE (R-3.5.2.tar.gz) = 30186438
+SHA256 (R-3.5.3.tar.gz) = K/o3t71wnwA9a4oXLd+20D3dLWctYJZDlSMDn3qOZ4w=
+SIZE (R-3.5.3.tar.gz) = 30205979
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.36
diff -u -p -r1.36 patch-configure
--- patches/patch-configure 23 Dec 2018 08:03:45 -  1.36
+++ patches/patch-configure 13 Mar 2019 11:46:20 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.36 2018/12
 Index: configure
 --- configure.orig
 +++ configure
-@@ -39135,8 +39135,8 @@ fi
+@@ -42293,8 +42293,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -39151,7 +39151,7 @@ else
+@@ -42309,7 +42309,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM

Re: UPDATE: math/R

2018-12-27 Thread Ingo Feinerer

On Thu, Dec 27, 2018 at 02:29:11PM +, Stuart Henderson wrote:
> Maybe there will be a clue if you diff my log against yours from
> a successful build and see what's different?

The only real difference is

< checking for bison... bison
< checking version of bison... 3.2, ok
---
> checking for bison... no

Even after installing bison the build completes successfully for me.

Best regards,
Ingo

Re: UPDATE: math/R

2018-12-27 Thread Stuart Henderson

On 2018/12/27 15:02, Ingo Feinerer wrote:
> On Tue, Dec 25, 2018 at 11:52:01PM +, Stuart Henderson wrote:
> > Build failed on i386:
> > 
> > 
> > in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no 
> > definition for class "graphNEL"
> > in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no 
> > definition for class "graphNEL"
> > in method for 'coerce' with signature '"sparseMatrix","graph"': no 
> > definition for class "graph"
> > in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no 
> > definition for class "graphNEL"
> > in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no 
> > definition for class "graphNEL"
> > Creating a generic function for 'qr.R' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.Q' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.qy' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.qty' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.coef' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.resid' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.fitted' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'toeplitz' from package 'stats' in package 
> > 'Matrix'
> > ** help
> > No man pages found in package  'Matrix' 
> > Error in .get_package_metadata(dir, FALSE) : 
> >   Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
> > ERROR: installing Rd objects failed for package 'Matrix'
> > * removing '/usr/obj/ports/R-3.5.2/build-i386/library/Matrix'
> > gmake[2]: Leaving directory 
> > '/usr/obj/ports/R-3.5.2/build-i386/src/library/Recommended'
> > gmake[1]: Leaving directory 
> > '/usr/obj/ports/R-3.5.2/build-i386/src/library/Recommended'
> > ===> Exiting math/R with an error
> > gmake[2]: *** [Makefile:53: Matrix.ts] Error 1
> > gmake[1]: *** [Makefile:39: recommended-packages] Error 2
> > gmake: *** [Makefile:77: stamp-recommended] Error 2
> > *** Error 2 in math/R (/usr/ports/infrastructure/mk/bsd.port.mk:2786 
> > '/usr/obj/ports/R-3.5.2/build-i386/.build_done')
> 
> I cannot reproduce this
> (tested with a current i386 snapshot in vmm:
> $ sysctl kern.version
> kern.version=OpenBSD 6.4-current (GENERIC) #1078: Mon Dec 24 22:34:36 MST 2018
> dera...@i386.openbsd.org:/usr/src/sys/arch/i386/compile/GENERIC
> )
> 
> > ...
> > Creating a generic function for 'qr.resid' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'qr.fitted' from package 'base' in package 
> > 'Matrix'
> > Creating a generic function for 'toeplitz' from package 'stats' in package 
> > 'Matrix'
> > ** help
> > *** installing help indices
> > ** building package indices
> > Loading required package: Matrix
> > ** installing vignettes
> > ** testing if installed package can be loaded
> > * DONE (Matrix)
> 
> Maybe lacking free space or another problem when extracting the Matrix
> .tar.gz on the build machine?

There is plenty of space on the relevant partition. And unless it's doing
something weird, a failure in the Makefile command extracting the file
would normally cause make to exit with an error.

Also it says "** package 'Matrix' successfully unpacked and MD5 sums
checked" in the log :-)

Maybe there will be a clue if you diff my log against yours from
a successful build and see what's different?

Re: UPDATE: math/R

2018-12-27 Thread Ingo Feinerer

On Tue, Dec 25, 2018 at 11:52:01PM +, Stuart Henderson wrote:
> Build failed on i386:
> 
> 
> in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no 
> definition for class "graphNEL"
> in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no 
> definition for class "graphNEL"
> in method for 'coerce' with signature '"sparseMatrix","graph"': no definition 
> for class "graph"
> in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no 
> definition for class "graphNEL"
> in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no 
> definition for class "graphNEL"
> Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
> Creating a generic function for 'qr.qy' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'qr.qty' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'qr.coef' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'qr.resid' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'qr.fitted' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'toeplitz' from package 'stats' in package 
> 'Matrix'
> ** help
> No man pages found in package  'Matrix' 
> Error in .get_package_metadata(dir, FALSE) : 
>   Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
> ERROR: installing Rd objects failed for package 'Matrix'
> * removing '/usr/obj/ports/R-3.5.2/build-i386/library/Matrix'
> gmake[2]: Leaving directory 
> '/usr/obj/ports/R-3.5.2/build-i386/src/library/Recommended'
> gmake[1]: Leaving directory 
> '/usr/obj/ports/R-3.5.2/build-i386/src/library/Recommended'
> ===> Exiting math/R with an error
> gmake[2]: *** [Makefile:53: Matrix.ts] Error 1
> gmake[1]: *** [Makefile:39: recommended-packages] Error 2
> gmake: *** [Makefile:77: stamp-recommended] Error 2
> *** Error 2 in math/R (/usr/ports/infrastructure/mk/bsd.port.mk:2786 
> '/usr/obj/ports/R-3.5.2/build-i386/.build_done')

I cannot reproduce this
(tested with a current i386 snapshot in vmm:
$ sysctl kern.version
kern.version=OpenBSD 6.4-current (GENERIC) #1078: Mon Dec 24 22:34:36 MST 2018
dera...@i386.openbsd.org:/usr/src/sys/arch/i386/compile/GENERIC
)

> ...
> Creating a generic function for 'qr.resid' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'qr.fitted' from package 'base' in package 
> 'Matrix'
> Creating a generic function for 'toeplitz' from package 'stats' in package 
> 'Matrix'
> ** help
> *** installing help indices
> ** building package indices
> Loading required package: Matrix
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (Matrix)

Maybe lacking free space or another problem when extracting the Matrix
.tar.gz on the build machine?

Best regards,
Ingo

Re: UPDATE: math/R

2018-12-25 Thread Stuart Henderson

On 2018/12/21 13:23, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.5.1 -> 3.5.2
> 
> - Bump SO_VERSION minor as check_sym
>   (/usr/src/lib/check_sym libR.so.34.1 libR.so.34.2) reports:
> 
>   No dynamic export changes
>   External reference changes:
>   added:
>   fstat
>   pthread_equal
>   pthread_kill
>   pthread_self
> 
>   I am not sure it is strictly necessary here but it does not hurt.
> 
> - Removed "curses fribidi" from WANTLIB as "make port-lib-depends-check"
>   reports them as extra. There are still
> 
>   R-3.5.2(math/R):
>   Extra:  c++.2 c++abi.0
> 
>   but I think these should not be removed?
> 
> - The `tan(1+1000i)` test still fails (see
>   https://marc.info/?l=openbsd-tech=150737856618497=2).

Build failed on i386:

in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no 
definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no 
definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition 
for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no 
definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no 
definition for class "graphNEL"
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 
'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 
'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 
'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in package 
'Matrix'
** help
No man pages found in package  'Matrix' 
Error in .get_package_metadata(dir, FALSE) : 
  Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
ERROR: installing Rd objects failed for package 'Matrix'
* removing '/usr/obj/ports/R-3.5.2/build-i386/library/Matrix'
gmake[2]: Leaving directory 
'/usr/obj/ports/R-3.5.2/build-i386/src/library/Recommended'
gmake[1]: Leaving directory 
'/usr/obj/ports/R-3.5.2/build-i386/src/library/Recommended'
===> Exiting math/R with an error
gmake[2]: *** [Makefile:53: Matrix.ts] Error 1
gmake[1]: *** [Makefile:39: recommended-packages] Error 2
gmake: *** [Makefile:77: stamp-recommended] Error 2
*** Error 2 in math/R (/usr/ports/infrastructure/mk/bsd.port.mk:2786 
'/usr/obj/ports/R-3.5.2/build-i386/.build_done')

Full log attached.

R.log.gz
Description: application/gunzip

Re: UPDATE: math/R

2018-12-21 Thread Paul Irofti

On Fri, Dec 21, 2018 at 01:23:28PM +0100, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.5.1 -> 3.5.2
> 
> - Bump SO_VERSION minor as check_sym
>   (/usr/src/lib/check_sym libR.so.34.1 libR.so.34.2) reports:
> 
>   No dynamic export changes
>   External reference changes:
>   added:
>   fstat
>   pthread_equal
>   pthread_kill
>   pthread_self
> 
>   I am not sure it is strictly necessary here but it does not hurt.
> 
> - Removed "curses fribidi" from WANTLIB as "make port-lib-depends-check"
>   reports them as extra. There are still
> 
>   R-3.5.2(math/R):
>   Extra:  c++.2 c++abi.0
> 
>   but I think these should not be removed?
> 
> - The `tan(1+1000i)` test still fails (see
>   https://marc.info/?l=openbsd-tech=150737856618497=2).
> 
> OK?

I do not have an opinion in regard to WANTLIB because I do not
understand how it works :)

Other than that, OK with me.

> 
> Best regards,
> Ingo
> 
> Index: Makefile
> ===
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.104
> diff -u -p -r1.104 Makefile
> --- Makefile  14 Nov 2018 20:48:21 -  1.104
> +++ Makefile  21 Dec 2018 12:03:22 -
> @@ -1,10 +1,9 @@
>  # $OpenBSD: Makefile,v 1.104 2018/11/14 20:48:21 sthen Exp $
>  
>  COMMENT= powerful math/statistics/graphics language
> -DISTNAME=R-3.5.1
> -REVISION=2
> +DISTNAME=R-3.5.2
>  
> -SO_VERSION=  34.1
> +SO_VERSION=  34.2
>  .for _lib in R Rblas Rlapack
>  SHARED_LIBS +=   ${_lib} ${SO_VERSION}
>  .endfor
> @@ -18,7 +17,7 @@ MAINTAINER= Ingo Feinerer   PERMIT_PACKAGE_CDROM=Yes
>  
>  WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}
> -WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl curses fribidi
> +WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
>  WANTLIB += glib-2.0 gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
>  WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl 
> tiff z
>  
> Index: distinfo
> ===
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.40
> diff -u -p -r1.40 distinfo
> --- distinfo  3 Jul 2018 21:46:50 -   1.40
> +++ distinfo  21 Dec 2018 12:03:22 -
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.5.1.tar.gz) = BGO/9e6g89k/oHH3nBjQmTh4/U8uGK5s8iwWOdEUV+0=
> -SIZE (R-3.5.1.tar.gz) = 29812849
> +SHA256 (R-3.5.2.tar.gz) = 5T2MPPIPK416nBYxtvaiKHRQb7OSA0dYs7s0HFhsW2I=
> +SIZE (R-3.5.2.tar.gz) = 30186438
> Index: patches/patch-configure
> ===
> RCS file: /cvs/ports/math/R/patches/patch-configure,v
> retrieving revision 1.35
> diff -u -p -r1.35 patch-configure
> --- patches/patch-configure   24 Apr 2018 17:13:38 -  1.35
> +++ patches/patch-configure   21 Dec 2018 12:03:22 -
> @@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.35 2018/04
>  Index: configure
>  --- configure.orig
>  +++ configure
> -@@ -38967,8 +38967,8 @@ fi
> +@@ -39135,8 +39135,8 @@ fi
>   
>   fi
>   if test "${have_zlib}" = yes; then
> @@ -14,7 +14,7 @@ Index: configure
>   if ${r_cv_header_zlib_h+:} false; then :
> $as_echo_n "(cached) " >&6
>   else
> -@@ -38983,7 +38983,7 @@ else
> +@@ -39151,7 +39151,7 @@ else
>   #include 
>   int main() {
>   #ifdef ZLIB_VERNUM
> Index: pkg/PLIST
> ===
> RCS file: /cvs/ports/math/R/pkg/PLIST,v
> retrieving revision 1.40
> diff -u -p -r1.40 PLIST
> --- pkg/PLIST 4 Sep 2018 12:46:15 -   1.40
> +++ pkg/PLIST 21 Dec 2018 12:03:22 -
> @@ -1386,6 +1386,9 @@ lib/R/library/survival/doc/adjcurve.pdf
>  lib/R/library/survival/doc/compete.R
>  lib/R/library/survival/doc/compete.Rnw
>  lib/R/library/survival/doc/compete.pdf
> +lib/R/library/survival/doc/concordance.R
> +lib/R/library/survival/doc/concordance.Rnw
> +lib/R/library/survival/doc/concordance.pdf
>  lib/R/library/survival/doc/index.html
>  lib/R/library/survival/doc/multi.R
>  lib/R/library/survival/doc/multi.Rnw

UPDATE: math/R

2018-12-21 Thread Ingo Feinerer

Dear useRs,

update math/R 3.5.1 -> 3.5.2

- Bump SO_VERSION minor as check_sym
  (/usr/src/lib/check_sym libR.so.34.1 libR.so.34.2) reports:

  No dynamic export changes
  External reference changes:
  added:
  fstat
  pthread_equal
  pthread_kill
  pthread_self

  I am not sure it is strictly necessary here but it does not hurt.

- Removed "curses fribidi" from WANTLIB as "make port-lib-depends-check"
  reports them as extra. There are still

  R-3.5.2(math/R):
  Extra:  c++.2 c++abi.0

  but I think these should not be removed?

- The `tan(1+1000i)` test still fails (see
  https://marc.info/?l=openbsd-tech=150737856618497=2).

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.104
diff -u -p -r1.104 Makefile
--- Makefile14 Nov 2018 20:48:21 -  1.104
+++ Makefile21 Dec 2018 12:03:22 -
@@ -1,10 +1,9 @@
 # $OpenBSD: Makefile,v 1.104 2018/11/14 20:48:21 sthen Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.5.1
-REVISION=  2
+DISTNAME=  R-3.5.2
 
-SO_VERSION=34.1
+SO_VERSION=34.2
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -18,7 +17,7 @@ MAINTAINER=   Ingo Feinerer &6
  else
-@@ -38983,7 +38983,7 @@ else
+@@ -39151,7 +39151,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.40
diff -u -p -r1.40 PLIST
--- pkg/PLIST   4 Sep 2018 12:46:15 -   1.40
+++ pkg/PLIST   21 Dec 2018 12:03:22 -
@@ -1386,6 +1386,9 @@ lib/R/library/survival/doc/adjcurve.pdf
 lib/R/library/survival/doc/compete.R
 lib/R/library/survival/doc/compete.Rnw
 lib/R/library/survival/doc/compete.pdf
+lib/R/library/survival/doc/concordance.R
+lib/R/library/survival/doc/concordance.Rnw
+lib/R/library/survival/doc/concordance.pdf
 lib/R/library/survival/doc/index.html
 lib/R/library/survival/doc/multi.R
 lib/R/library/survival/doc/multi.Rnw

Re: UPDATE: math/R

2018-04-24 Thread Klemens Nanni

On Mon, Apr 23, 2018 at 02:28:46PM +0200, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.4.4 -> 3.5.0
> 
> - Remove MAP_STACK patch as mmap() no longer needs to be used
>   (https://marc.info/?l=openbsd-cvs=152440172417443=2).
> - Regenerate existing configure patch
> - Add pcre2-8 to WANTLIB
> - /usr/src/lib/check_sym shows removed symbols in libR.so so
>   bump major in SHARED_LIBS
> 
> `make test` still fails for `tan(1+1000i)` (see
> https://marc.info/?l=openbsd-tech=150737856618497=2 for details).
> 
> OK?
Diff reads OK to me, it builds fine, light testing shows no errors on
amd64.

OK kn with lang added to CATEGORIES since R is an actual language and
I intuitively looked for lang/R in ports only to find it missing.

Re: UPDATE: math/R

2018-04-24 Thread Paul Irofti

OK.

UPDATE: math/R

2018-04-23 Thread Ingo Feinerer

Dear useRs,

update math/R 3.4.4 -> 3.5.0

- Remove MAP_STACK patch as mmap() no longer needs to be used
  (https://marc.info/?l=openbsd-cvs=152440172417443=2).
- Regenerate existing configure patch
- Add pcre2-8 to WANTLIB
- /usr/src/lib/check_sym shows removed symbols in libR.so so
  bump major in SHARED_LIBS

`make test` still fails for `tan(1+1000i)` (see
https://marc.info/?l=openbsd-tech=150737856618497=2 for details).

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.98
diff -u -p -r1.98 Makefile
--- Makefile17 Mar 2018 05:15:09 -  1.98
+++ Makefile23 Apr 2018 12:23:19 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.98 2018/03/17 05:15:09 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.4.4
+DISTNAME=  R-3.5.0
 
-SO_VERSION=33.0
+SO_VERSION=34.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -19,7 +19,7 @@ PERMIT_PACKAGE_CDROM= Yes
 WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}
 WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl curses glib-2.0
 WANTLIB += gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
-WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre png readline ssl tiff z
+WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl tiff 
z
 
 MASTER_SITES=  https://cran.r-project.org/src/base/R-3/ \
http://cran.at.r-project.org/src/base/R-3/ \
@@ -50,6 +50,7 @@ LIB_DEPENDS=  ${MODTK_LIB_DEPENDS} \
archivers/xz \
devel/glib2 \
devel/pango \
+   devel/pcre2 \
graphics/cairo \
graphics/jpeg \
graphics/png \
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.38
diff -u -p -r1.38 distinfo
--- distinfo17 Mar 2018 05:15:09 -  1.38
+++ distinfo23 Apr 2018 12:23:19 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.4.4.tar.gz) = s+l9L6tyVtHGVcQHWTRyW6HNfLkjckChG7Isza2WAzc=
-SIZE (R-3.4.4.tar.gz) = 30474612
+SHA256 (R-3.5.0.tar.gz) = /RclU14heX09n+qJY9mb4LpMOuytzwgbQ+JhRYtBaHA=
+SIZE (R-3.5.0.tar.gz) = 30675040
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.34
diff -u -p -r1.34 patch-configure
--- patches/patch-configure 17 Mar 2018 05:15:09 -  1.34
+++ patches/patch-configure 23 Apr 2018 12:23:19 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.34 2018/03
 Index: configure
 --- configure.orig
 +++ configure
-@@ -40313,8 +40313,8 @@ fi
+@@ -38967,8 +38967,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -40329,7 +40329,7 @@ else
+@@ -38983,7 +38983,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: patches/patch-src_main_main_c
===
RCS file: patches/patch-src_main_main_c
diff -N patches/patch-src_main_main_c
--- patches/patch-src_main_main_c   17 Mar 2018 05:15:09 -  1.10
+++ /dev/null   1 Jan 1970 00:00:00 -
@@ -1,26 +0,0 @@
-$OpenBSD: patch-src_main_main_c,v 1.10 2018/03/17 05:15:09 feinerer Exp $
-
-Allocate stack with MAP_STACK to pass stack-register checking.
-
-Index: src/main/main.c
 src/main/main.c.orig
-+++ src/main/main.c
-@@ -19,6 +19,8 @@
-  *  https://www.R-project.org/Licenses/
-  */
- 
-+#include 
-+
- #ifdef HAVE_CONFIG_H
- #include 
- #endif
-@@ -643,7 +645,8 @@ static void init_signal_handlers(void)
- {
- /*  may need to reinstall this if we do recover. */
- struct sigaction sa;
--signal_stack = malloc(SIGSTKSZ + R_USAGE);
-+signal_stack = mmap(NULL, SIGSTKSZ + R_USAGE, PROT_WRITE | PROT_READ,
-+MAP_PRIVATE | MAP_ANON | MAP_STACK, -1, 0);
- if (signal_stack != NULL) {
-   sigstk.ss_sp = signal_stack;
-   sigstk.ss_size = SIGSTKSZ + R_USAGE;
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.36
diff -u -p -r1.36 PLIST
--- pkg/PLIST   2 Jul 2017 05:18:42 -   1.36
+++ pkg/PLIST   23 Apr 2018 12:23:20 -
@@ -42,6 +42,7 @@ lib/R/etc/repositories
 lib/R/include/
 lib/R/include/R.h
 lib/R/include/R_ext/
+lib/R/include/R_ext/Altrep.h
 lib/R/include/R_ext/Applic.h
 lib/R/include/R_ext/Arith.h
 lib/R/include/R_ext/BLAS.h
@@ -473,6 +474,7 @@ lib/R/library/cluster/po/ko/LC_MESSAGES/
 lib/R/library/cluster/po/pl/
 lib/R/library/cluster/po/pl/LC_MESSAGES/
 lib/R/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
+lib/R/library/cluster/test-tools.R
 lib/R/library/codetools/
 lib/R/library/codetools/DESCRI

UPDATE: math/R

2018-03-16 Thread Ingo Feinerer

Dear useRs,

update math/R 3.4.3 -> 3.4.4

- Add a patch to pass stack-register checking when using an alternate
  signal stack. Please have a careful look at this.
- Adapt WANTLIB
- Regenerate existing patch

`make test` still fails for `tan(1+1000i)` (see
https://marc.info/?l=openbsd-tech=150737856618497=2 for details).

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.97
diff -u -p -r1.97 Makefile
--- Makefile6 Dec 2017 18:22:52 -   1.97
+++ Makefile16 Mar 2018 14:54:36 -
@@ -1,7 +1,7 @@
 # $OpenBSD: Makefile,v 1.97 2017/12/06 18:22:52 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.4.3
+DISTNAME=  R-3.4.4
 
 SO_VERSION=33.0
 .for _lib in R Rblas Rlapack
@@ -16,7 +16,7 @@ MAINTAINER=   Ingo Feinerer <feinerer@logi
 # GPLv2+
 PERMIT_PACKAGE_CDROM=  Yes
 
-WANTLIB += ${MODTK_WANTLIB}
+WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}
 WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl curses glib-2.0
 WANTLIB += gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
 WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre png readline ssl tiff z
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.37
diff -u -p -r1.37 distinfo
--- distinfo6 Dec 2017 18:22:52 -   1.37
+++ distinfo16 Mar 2018 14:54:36 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.4.3.tar.gz) = ejy4Md5bQVHh+JARPtIHUnt9SxbfnsazXglkFwAH9CY=
-SIZE (R-3.4.3.tar.gz) = 30249655
+SHA256 (R-3.4.4.tar.gz) = s+l9L6tyVtHGVcQHWTRyW6HNfLkjckChG7Isza2WAzc=
+SIZE (R-3.4.4.tar.gz) = 30474612
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.33
diff -u -p -r1.33 patch-configure
--- patches/patch-configure 6 Dec 2017 18:22:52 -   1.33
+++ patches/patch-configure 16 Mar 2018 14:54:36 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.33 2017/12
 Index: configure
 --- configure.orig
 +++ configure
-@@ -40301,8 +40301,8 @@ fi
+@@ -40313,8 +40313,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -40317,7 +40317,7 @@ else
+@@ -40329,7 +40329,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: patches/patch-src_main_main_c
===
RCS file: patches/patch-src_main_main_c
diff -N patches/patch-src_main_main_c
--- /dev/null   1 Jan 1970 00:00:00 -
+++ patches/patch-src_main_main_c   16 Mar 2018 14:54:36 -
@@ -0,0 +1,26 @@
+$OpenBSD$
+
+Allocate stack with MAP_STACK to pass stack-register checking.
+
+Index: src/main/main.c
+--- src/main/main.c.orig
 src/main/main.c
+@@ -19,6 +19,8 @@
+  *  https://www.R-project.org/Licenses/
+  */
+ 
++#include 
++
+ #ifdef HAVE_CONFIG_H
+ #include 
+ #endif
+@@ -643,7 +645,8 @@ static void init_signal_handlers(void)
+ {
+ /*  may need to reinstall this if we do recover. */
+ struct sigaction sa;
+-signal_stack = malloc(SIGSTKSZ + R_USAGE);
++signal_stack = mmap(NULL, SIGSTKSZ + R_USAGE, PROT_WRITE | PROT_READ,
++MAP_PRIVATE | MAP_ANON | MAP_STACK, -1, 0);
+ if (signal_stack != NULL) {
+   sigstk.ss_sp = signal_stack;
+   sigstk.ss_size = SIGSTKSZ + R_USAGE;

UPDATE: math/R

2017-11-30 Thread Ingo Feinerer

Dear useRs,

update math/R 3.4.2 -> 3.4.3

- WANTLIB change: ncurses -> curses
- Regenerate patch at the same time.

The problem with

R> tan(1+1000i)
[1] NaN+1i
Warning message:
In tan(1 + (0+1000i)) : NaNs produced in function "tan"

persists (and is visible with "make test") but is not unique to R
(https://marc.info/?l=openbsd-tech=150737856618497=2); so no blocker.

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.96
diff -u -p -r1.96 Makefile
--- Makefile9 Oct 2017 12:55:30 -   1.96
+++ Makefile30 Nov 2017 11:41:45 -
@@ -1,7 +1,7 @@
 # $OpenBSD: Makefile,v 1.96 2017/10/09 12:55:30 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.4.2
+DISTNAME=  R-3.4.3
 
 SO_VERSION=33.0
 .for _lib in R Rblas Rlapack
@@ -17,8 +17,8 @@ MAINTAINER=   Ingo Feinerer <feinerer@logi
 PERMIT_PACKAGE_CDROM=  Yes
 
 WANTLIB += ${MODTK_WANTLIB}
-WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl glib-2.0
-WANTLIB += gobject-2.0 iconv icui18n icuuc intl jpeg lzma m ncurses
+WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl curses glib-2.0
+WANTLIB += gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
 WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre png readline ssl tiff z
 
 MASTER_SITES=  https://cran.r-project.org/src/base/R-3/ \
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.36
diff -u -p -r1.36 distinfo
--- distinfo9 Oct 2017 12:55:30 -   1.36
+++ distinfo30 Nov 2017 11:41:45 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.4.2.tar.gz) = lx4wwkNs9kX1hVKQUQXXV4i9lzO928t8T7/0wabYDGQ=
-SIZE (R-3.4.2.tar.gz) = 30255544
+SHA256 (R-3.4.3.tar.gz) = ejy4Md5bQVHh+JARPtIHUnt9SxbfnsazXglkFwAH9CY=
+SIZE (R-3.4.3.tar.gz) = 30249655
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.32
diff -u -p -r1.32 patch-configure
--- patches/patch-configure 9 Oct 2017 12:55:30 -   1.32
+++ patches/patch-configure 30 Nov 2017 11:41:45 -
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.32 2017/10
 Index: configure
 --- configure.orig
 +++ configure
-@@ -40291,8 +40291,8 @@ fi
+@@ -40301,8 +40301,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -40307,7 +40307,7 @@ else
+@@ -40317,7 +40317,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM

Re: UPDATE: math/R

2017-10-06 Thread Ingo Feinerer

On Thu, Oct 05, 2017 at 12:24:08PM +0200, Rafael Sadowski wrote:
> On Thu Oct 05, 2017 at 06:42:32AM +, Ingo Feinerer wrote:
> > update math/R 3.4.1 -> 3.4.2
> > OK?
> 
> I ran into:
> 
> ===>  Regression tests for R-3.4.2
> ...
> gmake[3]: Entering directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
> running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/complex.R' 
> ...gmake[3]: *** [/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/Makefile.common:100: 
> complex.Rout] Error 1

The problem is on -current:

> (z <- tan(1+1000i))
[1] NaN+1i

At first glance it seems like a regression in OpenBSD:

3.4.2/amd64/-current:
3.4.1/amd64/-current:
3.4.0/amd64/-current:
3.3.3/amd64/-current:

> (z <- tan(1+1000i))
[1] NaN+1i
Warning message:
In tan(1 + (0+1000i)) : NaNs produced in function "tan"

3.3.3/i386/6.1 (kindly tested by ratchov@):

> (z <- tan(1+1000i))
[1] 0+1i

I investigated libm commits
(http://cvsweb.openbsd.org/cgi-bin/cvsweb/src/lib/libm/) but found
nothing obvious (for me).

Any ideas?

Best regards,
Ingo

Re: UPDATE: math/R

2017-10-05 Thread Rafael Sadowski

On Thu Oct 05, 2017 at 06:42:32AM +, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.4.1 -> 3.4.2
> 
> The only visible package change is the trimming of README. Since we have
> clang now the section on using "modern compilers" is obsolete (as it was
> primarly targeted at amd64 and i386).
> 
> Regenerate patch at the same time.
> 
> OK?
> 
> Best regards,
> Ingo
> 

I ran into:

===>  Regression tests for R-3.4.2
gmake[1]: Entering directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
gmake[2]: Entering directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
gmake[3]: Entering directory 
'/usr/ports/pobj/R-3.4.2/build-amd64/tests/Examples'
Testing examples for package 'base'
  comparing 'base-Ex.Rout' to 'base-Ex.Rout.prev' ... NOTE
  6674c6674
  < 60
  ---
  > 5
  7254c7254
  < R_SESSION_TMPDIR: /tmp/RtmpjpkdMP
  ---
  > R_SESSION_TMPDIR: /tmp/RtmpBcomxX
Testing examples for package 'tools'
  comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
Testing examples for package 'utils'
  comparing 'utils-Ex.Rout' to 'utils-Ex.Rout.prev' ... OK
Testing examples for package 'grDevices'
  comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK
Testing examples for package 'graphics'
  comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK
Testing examples for package 'stats'
  comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... OK
Testing examples for package 'datasets'
  comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK
Testing examples for package 'methods'
  comparing 'methods-Ex.Rout' to 'methods-Ex.Rout.prev' ... OK
Testing examples for package 'grid'
  comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK
Testing examples for package 'splines'
  comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK
Testing examples for package 'stats4'
  comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK
Testing examples for package 'tcltk'
  comparing 'tcltk-Ex.Rout' to 'tcltk-Ex.Rout.prev' ... OK
Testing examples for package 'compiler'
  comparing 'compiler-Ex.Rout' to 'compiler-Ex.Rout.prev' ... OK
Testing examples for package 'parallel'
  comparing 'parallel-Ex.Rout' to 'parallel-Ex.Rout.prev' ... OK
gmake[3]: Leaving directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests/Examples'
gmake[2]: Leaving directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
gmake[2]: Entering directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
running strict specific tests
gmake[3]: Entering directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/eval-etc.R' ... OK
  comparing 'eval-etc.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/eval-etc.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/simple-true.R' ... OK
  comparing 'simple-true.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/simple-true.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/arith-true.R' ... OK
  comparing 'arith-true.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/arith-true.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/arith.R' ... OK
  comparing 'arith.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/arith.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/lm-tests.R' ... OK
  comparing 'lm-tests.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/lm-tests.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/ok-errors.R' ... OK
  comparing 'ok-errors.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/ok-errors.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/method-dispatch.R' ... OK
  comparing 'method-dispatch.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/method-dispatch.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/any-all.R' ... OK
  comparing 'any-all.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/any-all.Rout.save' ... OK
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/d-p-q-r-tests.R' ... OK
  comparing 'd-p-q-r-tests.Rout' to 
'/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/d-p-q-r-tests.Rout.save' ... OK
gmake[3]: Leaving directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
running sloppy specific tests
gmake[3]: Entering directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
running code in '/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/complex.R' ...gmake[3]: 
*** [/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/Makefile.common:100: complex.Rout] 
Error 1
gmake[3]: Leaving directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
gmake[2]: *** [/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/Makefile.common:189: 
test-Specific] Error 2
gmake[2]: Leaving directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
gmake[1]: *** [/usr/ports/pobj/R-3.4.2/R-3.4.2/tests/Makefile.common:165: 
test-all-basics] Error 1
gmake[1]: Leaving directory '/usr/ports/pobj/R-3.4.2/build-amd64/tests'
gmake: *** [Makefile:239: check] Error 2
*** Error 2 in . (/usr

UPDATE: math/R

2017-10-05 Thread Ingo Feinerer

Dear useRs,

update math/R 3.4.1 -> 3.4.2

The only visible package change is the trimming of README. Since we have
clang now the section on using "modern compilers" is obsolete (as it was
primarly targeted at amd64 and i386).

Regenerate patch at the same time.

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.95
diff -u -p -r1.95 Makefile
--- Makefile24 Aug 2017 09:45:23 -  1.95
+++ Makefile5 Oct 2017 06:37:37 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.95 2017/08/24 09:45:23 sthen Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.4.1
-REVISION=  0
+DISTNAME=  R-3.4.2
 
 SO_VERSION=33.0
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.35
diff -u -p -r1.35 distinfo
--- distinfo2 Jul 2017 05:18:42 -   1.35
+++ distinfo5 Oct 2017 06:37:37 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.4.1.tar.gz) = ArETXRXqlpo1gsrrlVlKBegwpt6821uF7S1YNqaj/Hg=
-SIZE (R-3.4.1.tar.gz) = 30200109
+SHA256 (R-3.4.2.tar.gz) = lx4wwkNs9kX1hVKQUQXXV4i9lzO928t8T7/0wabYDGQ=
+SIZE (R-3.4.2.tar.gz) = 30255544
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.31
diff -u -p -r1.31 patch-configure
--- patches/patch-configure 26 Apr 2017 17:29:58 -  1.31
+++ patches/patch-configure 5 Oct 2017 06:37:37 -
@@ -1,8 +1,9 @@
 $OpenBSD: patch-configure,v 1.31 2017/04/26 17:29:58 feinerer Exp $
 
 configure.orig Wed Apr 19 22:38:22 2017
-+++ configure  Sat Apr 22 18:00:09 2017
-@@ -40238,8 +40238,8 @@ fi
+Index: configure
+--- configure.orig
 configure
+@@ -40291,8 +40291,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -13,7 +14,7 @@ $OpenBSD: patch-configure,v 1.31 2017/04
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -40254,7 +40254,7 @@ else
+@@ -40307,7 +40307,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: pkg/README
===
RCS file: /cvs/ports/math/R/pkg/README,v
retrieving revision 1.7
diff -u -p -r1.7 README
--- pkg/README  26 Apr 2017 17:29:58 -  1.7
+++ pkg/README  5 Oct 2017 06:37:37 -
@@ -16,16 +16,3 @@ Running:
 
 as root, will update both ${TRUEPREFIX}/lib/R/etc/Makeconf and
 ${TRUEPREFIX}/lib/R/etc/ldpaths with the right settings.
-
-Customizing package compilation
-===
-Make variables to be used by R packages compiling code at installation time
-can be customized via ~/.R/Makevars
-(https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Customizing-package-compilation).
-E.g., for using recent compilers (packages g++ and gcc) add
-
-CC=egcc -std=gnu99
-CXX=eg++
-CXX11=eg++
-CXX11STD=-std=c++11
-CXX11PICFLAGS=-fpic

Re: UPDATE: math/R

2017-07-01 Thread Ingo Feinerer

On Sun, Jul 02, 2017 at 12:34:25AM +0300, Paul Irofti wrote:
> What are the new .sav files? Are they supposed to be there? If the answer is 
> yes, OK.

They are included in the official package
(https://cran.r-project.org/src/contrib/foreign_0.8-69.tar.gz), so they
are supposed to be there.

Thanks for the review.

Re: UPDATE: math/R

2017-07-01 Thread Paul Irofti

What are the new .sav files? Are they supposed to be there? If the answer is 
yes, OK.

De la: Ingo Feinerer
Trimis: sâmbătă, 1 iulie 2017 20:33
Către: ports@openbsd.org
Subiect: UPDATE: math/R

Dear useRs,

update math/R 3.4.0 -> 3.4.1

OK?

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.93
diff -u -p -r1.93 Makefile
--- Makefile4 May 2017 11:13:52 -   1.93
+++ Makefile1 Jul 2017 17:30:12 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.93 2017/05/04 11:13:52 edd Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.4.0
-REVISION = 0
+DISTNAME=  R-3.4.1
 
 SO_VERSION=33.0
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.34
diff -u -p -r1.34 distinfo
--- distinfo26 Apr 2017 17:29:58 -  1.34
+++ distinfo1 Jul 2017 17:30:12 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.4.0.tar.gz) = KI6e1CRXxHcgeAQzs9XDwgmDBIt4kpHManuqEflCi5E=
-SIZE (R-3.4.0.tar.gz) = 30175855
+SHA256 (R-3.4.1.tar.gz) = ArETXRXqlpo1gsrrlVlKBegwpt6821uF7S1YNqaj/Hg=
+SIZE (R-3.4.1.tar.gz) = 30200109
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.35
diff -u -p -r1.35 PLIST
--- pkg/PLIST   4 May 2017 11:13:52 -   1.35
+++ pkg/PLIST   1 Jul 2017 17:30:13 -
@@ -566,7 +566,9 @@ lib/R/library/foreign/R/foreign.rdx
 lib/R/library/foreign/files/
 lib/R/library/foreign/files/HillRace.SYD
 lib/R/library/foreign/files/Iris.syd
+lib/R/library/foreign/files/electric.sav
 lib/R/library/foreign/files/sids.dbf
+lib/R/library/foreign/files/testdata.sav
 lib/R/library/foreign/help/
 lib/R/library/foreign/help/AnIndex
 lib/R/library/foreign/help/aliases.rds

UPDATE: math/R

2017-07-01 Thread Ingo Feinerer

Dear useRs,

update math/R 3.4.0 -> 3.4.1

OK?

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.93
diff -u -p -r1.93 Makefile
--- Makefile4 May 2017 11:13:52 -   1.93
+++ Makefile1 Jul 2017 17:30:12 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.93 2017/05/04 11:13:52 edd Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.4.0
-REVISION = 0
+DISTNAME=  R-3.4.1
 
 SO_VERSION=33.0
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.34
diff -u -p -r1.34 distinfo
--- distinfo26 Apr 2017 17:29:58 -  1.34
+++ distinfo1 Jul 2017 17:30:12 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.4.0.tar.gz) = KI6e1CRXxHcgeAQzs9XDwgmDBIt4kpHManuqEflCi5E=
-SIZE (R-3.4.0.tar.gz) = 30175855
+SHA256 (R-3.4.1.tar.gz) = ArETXRXqlpo1gsrrlVlKBegwpt6821uF7S1YNqaj/Hg=
+SIZE (R-3.4.1.tar.gz) = 30200109
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.35
diff -u -p -r1.35 PLIST
--- pkg/PLIST   4 May 2017 11:13:52 -   1.35
+++ pkg/PLIST   1 Jul 2017 17:30:13 -
@@ -566,7 +566,9 @@ lib/R/library/foreign/R/foreign.rdx
 lib/R/library/foreign/files/
 lib/R/library/foreign/files/HillRace.SYD
 lib/R/library/foreign/files/Iris.syd
+lib/R/library/foreign/files/electric.sav
 lib/R/library/foreign/files/sids.dbf
+lib/R/library/foreign/files/testdata.sav
 lib/R/library/foreign/help/
 lib/R/library/foreign/help/AnIndex
 lib/R/library/foreign/help/aliases.rds

UPDATE: math/R

2017-04-22 Thread Ingo Feinerer

Dear useRs,

update math/R 3.3.3 -> 3.4.0
(Changes listed at https://cran.r-project.org/doc/manuals/r-release/NEWS.html)

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.91
diff -u -p -r1.91 Makefile
--- Makefile9 Mar 2017 10:10:41 -   1.91
+++ Makefile22 Apr 2017 17:38:55 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.91 2017/03/09 10:10:41 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.3.3
+DISTNAME=  R-3.4.0
 
-SO_VERSION=32.0
+SO_VERSION=33.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.33
diff -u -p -r1.33 distinfo
--- distinfo9 Mar 2017 05:18:44 -   1.33
+++ distinfo22 Apr 2017 17:38:55 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.3.3.tar.gz) = WrdoBTonUIRhj7ZptPuq3MORWJmKh+hGUyOClZC8/Gw=
-SIZE (R-3.3.3.tar.gz) = 29804326
+SHA256 (R-3.4.0.tar.gz) = KI6e1CRXxHcgeAQzs9XDwgmDBIt4kpHManuqEflCi5E=
+SIZE (R-3.4.0.tar.gz) = 30175855
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.30
diff -u -p -r1.30 patch-configure
--- patches/patch-configure 9 Mar 2017 05:18:44 -   1.30
+++ patches/patch-configure 22 Apr 2017 17:38:55 -
@@ -1,8 +1,8 @@
 $OpenBSD: patch-configure,v 1.30 2017/03/09 05:18:44 feinerer Exp $
 
 configure.orig Tue Mar  7 13:02:27 2017
-+++ configure  Tue Mar  7 13:03:01 2017
-@@ -35492,8 +35492,8 @@ fi
+--- configure.orig Wed Apr 19 22:38:22 2017
 configure  Sat Apr 22 18:00:09 2017
+@@ -40238,8 +40238,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -13,7 +13,7 @@ $OpenBSD: patch-configure,v 1.30 2017/03
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -35508,7 +35508,7 @@ else
+@@ -40254,7 +40254,7 @@ else
  #include 
  int main() {
  #ifdef ZLIB_VERNUM
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.33
diff -u -p -r1.33 PLIST
--- pkg/PLIST   9 Mar 2017 05:18:44 -   1.33
+++ pkg/PLIST   22 Apr 2017 17:38:55 -
@@ -94,6 +94,7 @@ lib/R/library/KernSmooth/DESCRIPTION
 lib/R/library/KernSmooth/INDEX
 lib/R/library/KernSmooth/Meta/
 lib/R/library/KernSmooth/Meta/Rd.rds
+lib/R/library/KernSmooth/Meta/features.rds
 lib/R/library/KernSmooth/Meta/hsearch.rds
 lib/R/library/KernSmooth/Meta/links.rds
 lib/R/library/KernSmooth/Meta/nsInfo.rds
@@ -137,6 +138,7 @@ lib/R/library/MASS/INDEX
 lib/R/library/MASS/Meta/
 lib/R/library/MASS/Meta/Rd.rds
 lib/R/library/MASS/Meta/data.rds
+lib/R/library/MASS/Meta/features.rds
 lib/R/library/MASS/Meta/hsearch.rds
 lib/R/library/MASS/Meta/links.rds
 lib/R/library/MASS/Meta/nsInfo.rds
@@ -204,6 +206,7 @@ lib/R/library/Matrix/LICENCE
 lib/R/library/Matrix/Meta/
 lib/R/library/Matrix/Meta/Rd.rds
 lib/R/library/Matrix/Meta/data.rds
+lib/R/library/Matrix/Meta/features.rds
 lib/R/library/Matrix/Meta/hsearch.rds
 lib/R/library/Matrix/Meta/links.rds
 lib/R/library/Matrix/Meta/nsInfo.rds
@@ -301,6 +304,7 @@ lib/R/library/base/INDEX
 lib/R/library/base/Meta/
 lib/R/library/base/Meta/Rd.rds
 lib/R/library/base/Meta/demo.rds
+lib/R/library/base/Meta/features.rds
 lib/R/library/base/Meta/hsearch.rds
 lib/R/library/base/Meta/links.rds
 lib/R/library/base/Meta/package.rds
@@ -330,6 +334,7 @@ lib/R/library/boot/INDEX
 lib/R/library/boot/Meta/
 lib/R/library/boot/Meta/Rd.rds
 lib/R/library/boot/Meta/data.rds
+lib/R/library/boot/Meta/features.rds
 lib/R/library/boot/Meta/hsearch.rds
 lib/R/library/boot/Meta/links.rds
 lib/R/library/boot/Meta/nsInfo.rds
@@ -378,6 +383,7 @@ lib/R/library/class/DESCRIPTION
 lib/R/library/class/INDEX
 lib/R/library/class/Meta/
 lib/R/library/class/Meta/Rd.rds
+lib/R/library/class/Meta/features.rds
 lib/R/library/class/Meta/hsearch.rds
 lib/R/library/class/Meta/links.rds
 lib/R/library/class/Meta/nsInfo.rds
@@ -422,6 +428,7 @@ lib/R/library/cluster/INDEX
 lib/R/library/cluster/Meta/
 lib/R/library/cluster/Meta/Rd.rds
 lib/R/library/cluster/Meta/data.rds
+lib/R/library/cluster/Meta/features.rds
 lib/R/library/cluster/Meta/hsearch.rds
 lib/R/library/cluster/Meta/links.rds
 lib/R/library/cluster/Meta/nsInfo.rds
@@ -471,6 +478,7 @@ lib/R/library/codetools/DESCRIPTION
 lib/R/library/codetools/INDEX
 lib/R/library/codetools/Meta/
 lib/R/library/codetools/Meta/Rd.rds
+lib/R/library/codetools/Meta/features.rds
 lib/R/library/codetools/Meta/hsearch.rds
 lib/R/library/codetools/Meta/links.rds
 lib/R/library/codetools/Meta/nsInfo.rds
@@ -494,6 +502,7 @@ lib/R/library/compiler/DESCRIPTION
 lib/R/library/compiler/INDEX
 lib/R/library/compiler/Meta/
 lib/

Re: UPDATE: math/R

2017-03-09 Thread Stuart Henderson

On 2017/03/08 21:32, Ingo Feinerer wrote:
> On Wed, Mar 08, 2017 at 05:08:19PM +, Stuart Henderson wrote:
> > On 2017/03/08 16:34, Ingo Feinerer wrote:
> > > update math/R 3.3.2 -> 3.3.3
> > > 
> > > - The zlib configure version test logic changed so adapt.
> > > - Several R packages (e.g. RCpp) profit from a C++11 compiler, so
> > >   mention CXX1X et al. in the README.
> > > - make package reports
> > >   LIB_DEPENDS devel/libidn not needed for math/R ?
> > >   I am not sure if this is true or not (or what triggered the change).
> > 
> > What does "make port-lib-depends-check" say?
> 
> It produces no output.
> 

Ok - just remove devel/libidn from LIB_DEPENDS then. It was probably added
mistakenly as LIB_DEPENDS before (curl used it but only a WANTLIB would have
been needed - and curl stopped using it).

Re: UPDATE: math/R

2017-03-09 Thread Stuart Henderson

On 2017/03/08 19:12, Zé Loff wrote:
> - Some packages need W^X (e.g. rJava and V8) to run.  If you end up
>   needing those packages I *think* R needs to be flagged as WX_NEEDED,
>   since they run "inside" R.  Not sure if its worth it to flag R only
>   because of optional packages, though.

We do that for Python already, purely because of a few modules that most
people won't be running (webkit in that case), so it probably makes sense
for R too.

> - If you install those packages on a user library instead of on the
>   system-wide library, you'll need to mount /home (or wherever your
>   library is) as wxallowed.
> 
> - At compile time, some packages run tests with W^X code in them.  This
>   means "configure" will fail, since it detects that binaries can't be
>   run (for instance it asks if we're cross-compiling).  Since packages
>   are unpacked and compiled in /tmp, this means that at least during
>   compilation /tmp also needs to be mounted as wxallowed.
> 
> As I told you before, I don't know what the correct approach here would
> be, but I believe at least a pkg-readme or a install-message would help.

Would it make sense to provide ports for these with things patched so that
they work with just the usual requirement that WRKOBJDIR is on a wxallowed
filesystem?

Re: UPDATE: math/R

2017-03-08 Thread Ingo Feinerer

On Wed, Mar 08, 2017 at 05:08:19PM +, Stuart Henderson wrote:
> On 2017/03/08 16:34, Ingo Feinerer wrote:
> > update math/R 3.3.2 -> 3.3.3
> > 
> > - The zlib configure version test logic changed so adapt.
> > - Several R packages (e.g. RCpp) profit from a C++11 compiler, so
> >   mention CXX1X et al. in the README.
> > - make package reports
> >   LIB_DEPENDS devel/libidn not needed for math/R ?
> >   I am not sure if this is true or not (or what triggered the change).
> 
> What does "make port-lib-depends-check" say?

It produces no output.

Re: UPDATE: math/R

2017-03-08 Thread Zé Loff


On Wed, Mar 08, 2017 at 04:34:47PM +0100, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.3.2 -> 3.3.3
> 
> - The zlib configure version test logic changed so adapt.
> - Several R packages (e.g. RCpp) profit from a C++11 compiler, so
>   mention CXX1X et al. in the README.
> - make package reports
>   LIB_DEPENDS devel/libidn not needed for math/R ?
>   I am not sure if this is true or not (or what triggered the change).
> 
> OK?
> 
> Best regards,
> Ingo

Hi Ingo (and list)

As I mentioned in our private conversation, I've been having some issues
with some R packages and W^X.  I've been meaning to look at it more
systematically and do a nice write-up for ports@ but haven't had the
time yet.  However, this seemed like a good time to bring the issue to
the list.

What I noticed so far is:

- Some packages need W^X (e.g. rJava and V8) to run.  If you end up
  needing those packages I *think* R needs to be flagged as WX_NEEDED,
  since they run "inside" R.  Not sure if its worth it to flag R only
  because of optional packages, though.

- If you install those packages on a user library instead of on the
  system-wide library, you'll need to mount /home (or wherever your
  library is) as wxallowed.

- At compile time, some packages run tests with W^X code in them.  This
  means "configure" will fail, since it detects that binaries can't be
  run (for instance it asks if we're cross-compiling).  Since packages
  are unpacked and compiled in /tmp, this means that at least during
  compilation /tmp also needs to be mounted as wxallowed.

As I told you before, I don't know what the correct approach here would
be, but I believe at least a pkg-readme or a install-message would help.

Let me know if I can help and sorry for the messy reporting.

Cheers
Zé


> Index: Makefile
> ===
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.89
> diff -u -p -r1.89 Makefile
> --- Makefile  4 Nov 2016 11:35:19 -  1.89
> +++ Makefile  8 Mar 2017 15:28:29 -
> @@ -1,8 +1,7 @@
>  # $OpenBSD: Makefile,v 1.89 2016/11/04 11:35:19 sthen Exp $
>  
>  COMMENT=  powerful math/statistics/graphics language
> -DISTNAME=  R-3.3.2
> -REVISION=  0
> +DISTNAME=  R-3.3.3
>  
>  SO_VERSION=  32.0
>  .for _lib in R Rblas Rlapack
> Index: distinfo
> ===
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.32
> diff -u -p -r1.32 distinfo
> --- distinfo  1 Nov 2016 16:55:13 -  1.32
> +++ distinfo  8 Mar 2017 15:28:29 -
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.3.2.tar.gz) = 0pStIen1dPtIKOuzqUuMs09PMEpBaHqZS+AN1BpOUUw=
> -SIZE (R-3.3.2.tar.gz) = 29440670
> +SHA256 (R-3.3.3.tar.gz) = WrdoBTonUIRhj7ZptPuq3MORWJmKh+hGUyOClZC8/Gw=
> +SIZE (R-3.3.3.tar.gz) = 29804326
> Index: patches/patch-configure
> ===
> RCS file: /cvs/ports/math/R/patches/patch-configure,v
> retrieving revision 1.29
> diff -u -p -r1.29 patch-configure
> --- patches/patch-configure  1 Nov 2016 16:55:13 -  1.29
> +++ patches/patch-configure  8 Mar 2017 15:28:29 -
> @@ -1,7 +1,7 @@
>  $OpenBSD: patch-configure,v 1.29 2016/11/01 16:55:13 feinerer Exp $
>  
>  configure.orig  Mon Oct 24 13:34:26 2016
> -+++ configure  Tue Nov  1 09:06:08 2016
> +--- configure.orig  Tue Mar  7 13:02:27 2017
>  configure  Tue Mar  7 13:03:01 2017
>  @@ -35492,8 +35492,8 @@ fi
>   
>   fi
> @@ -13,12 +13,12 @@ $OpenBSD: patch-configure,v 1.29 2016/11
>   if ${r_cv_header_zlib_h+:} false; then :
> $as_echo_n "(cached) " >&6
>   else
> -@@ -35510,7 +35510,7 @@ int main() {
> - #ifdef ZLIB_VERSION
> - /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
> -version on the master site zlib.net */
> --  exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
> -+  exit(strncmp(ZLIB_VERSION, "1.2.3", 5) < 0);
> - #else
> -   exit(1);
> - #endif
> +@@ -35508,7 +35508,7 @@ else
> + #include 
> + int main() {
> + #ifdef ZLIB_VERNUM
> +-  if (ZLIB_VERNUM < 0x1250) {
> ++  if (ZLIB_VERNUM < 0x1230) {
> + exit(1);
> +   }
> +   exit(0);
> Index: pkg/PLIST
> ===
> RCS file: /cvs/ports/math/R/pkg/PLIST,v
> retrieving revision 1.32
> diff -u -p -r1.32 PLIST
> --- pkg/PLIST  1 Nov 2016 16:55:13 -  1.32
> +++ pkg/PLIST  8 Mar 2017 15:28:30 -
> @@ -1358,6 +1358,9 @@ lib/R/library/survival/doc/compete.R
>  lib/R/library/survival/doc/compete.Rnw
>  lib/R/library/survival/doc/compete.pdf
>  lib/R/library/survival/doc/index.html
> +lib/R/library/

Re: UPDATE: math/R

2017-03-08 Thread Stuart Henderson

On 2017/03/08 16:34, Ingo Feinerer wrote:
> Dear useRs,
> 
> update math/R 3.3.2 -> 3.3.3
> 
> - The zlib configure version test logic changed so adapt.
> - Several R packages (e.g. RCpp) profit from a C++11 compiler, so
>   mention CXX1X et al. in the README.
> - make package reports
>   LIB_DEPENDS devel/libidn not needed for math/R ?
>   I am not sure if this is true or not (or what triggered the change).

What does "make port-lib-depends-check" say?

Re: UPDATE: math/R

2017-03-08 Thread paul

OK

De la: Ingo Feinerer
Trimis: miercuri, 8 martie 2017 17:36
Către: ports@openbsd.org
Cc: dco...@openbsd.org
Subiect: UPDATE: math/R

Dear useRs,

update math/R 3.3.2 -> 3.3.3

- The zlib configure version test logic changed so adapt.
- Several R packages (e.g. RCpp) profit from a C++11 compiler, so
  mention CXX1X et al. in the README.
- make package reports
  LIB_DEPENDS devel/libidn not needed for math/R ?
  I am not sure if this is true or not (or what triggered the change).

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.89
diff -u -p -r1.89 Makefile
--- Makefile4 Nov 2016 11:35:19 -   1.89
+++ Makefile8 Mar 2017 15:28:29 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.89 2016/11/04 11:35:19 sthen Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.3.2
-REVISION=  0
+DISTNAME=  R-3.3.3
 
 SO_VERSION=32.0
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.32
diff -u -p -r1.32 distinfo
--- distinfo1 Nov 2016 16:55:13 -   1.32
+++ distinfo8 Mar 2017 15:28:29 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.3.2.tar.gz) = 0pStIen1dPtIKOuzqUuMs09PMEpBaHqZS+AN1BpOUUw=
-SIZE (R-3.3.2.tar.gz) = 29440670
+SHA256 (R-3.3.3.tar.gz) = WrdoBTonUIRhj7ZptPuq3MORWJmKh+hGUyOClZC8/Gw=
+SIZE (R-3.3.3.tar.gz) = 29804326
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.29
diff -u -p -r1.29 patch-configure
--- patches/patch-configure 1 Nov 2016 16:55:13 -   1.29
+++ patches/patch-configure 8 Mar 2017 15:28:29 -
@@ -1,7 +1,7 @@
 $OpenBSD: patch-configure,v 1.29 2016/11/01 16:55:13 feinerer Exp $
 
 configure.orig Mon Oct 24 13:34:26 2016
-+++ configure  Tue Nov  1 09:06:08 2016
+--- configure.orig Tue Mar  7 13:02:27 2017
 configure  Tue Mar  7 13:03:01 2017
 @@ -35492,8 +35492,8 @@ fi
  
  fi
@@ -13,12 +13,12 @@ $OpenBSD: patch-configure,v 1.29 2016/11
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -35510,7 +35510,7 @@ int main() {
- #ifdef ZLIB_VERSION
- /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
-version on the master site zlib.net */
--  exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
-+  exit(strncmp(ZLIB_VERSION, "1.2.3", 5) < 0);
- #else
-   exit(1);
- #endif
+@@ -35508,7 +35508,7 @@ else
+ #include 
+ int main() {
+ #ifdef ZLIB_VERNUM
+-  if (ZLIB_VERNUM < 0x1250) {
++  if (ZLIB_VERNUM < 0x1230) {
+ exit(1);
+   }
+   exit(0);
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.32
diff -u -p -r1.32 PLIST
--- pkg/PLIST   1 Nov 2016 16:55:13 -   1.32
+++ pkg/PLIST   8 Mar 2017 15:28:30 -
@@ -1358,6 +1358,9 @@ lib/R/library/survival/doc/compete.R
 lib/R/library/survival/doc/compete.Rnw
 lib/R/library/survival/doc/compete.pdf
 lib/R/library/survival/doc/index.html
+lib/R/library/survival/doc/multi.R
+lib/R/library/survival/doc/multi.Rnw
+lib/R/library/survival/doc/multi.pdf
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 lib/R/library/survival/doc/splines.pdf
Index: pkg/README
===
RCS file: /cvs/ports/math/R/pkg/README,v
retrieving revision 1.5
diff -u -p -r1.5 README
--- pkg/README  19 Aug 2016 07:02:47 -  1.5
+++ pkg/README  8 Mar 2017 15:28:30 -
@@ -26,3 +26,5 @@ E.g., for using recent compilers (packag
 
 CC=egcc -std=gnu99
 CXX=eg++
+CXX1X=eg++ -std=c++11
+CXX1XPICFLAGS=-fpic

UPDATE: math/R

2017-03-08 Thread Ingo Feinerer

Dear useRs,

update math/R 3.3.2 -> 3.3.3

- The zlib configure version test logic changed so adapt.
- Several R packages (e.g. RCpp) profit from a C++11 compiler, so
  mention CXX1X et al. in the README.
- make package reports
  LIB_DEPENDS devel/libidn not needed for math/R ?
  I am not sure if this is true or not (or what triggered the change).

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.89
diff -u -p -r1.89 Makefile
--- Makefile4 Nov 2016 11:35:19 -   1.89
+++ Makefile8 Mar 2017 15:28:29 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.89 2016/11/04 11:35:19 sthen Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.3.2
-REVISION=  0
+DISTNAME=  R-3.3.3
 
 SO_VERSION=32.0
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.32
diff -u -p -r1.32 distinfo
--- distinfo1 Nov 2016 16:55:13 -   1.32
+++ distinfo8 Mar 2017 15:28:29 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.3.2.tar.gz) = 0pStIen1dPtIKOuzqUuMs09PMEpBaHqZS+AN1BpOUUw=
-SIZE (R-3.3.2.tar.gz) = 29440670
+SHA256 (R-3.3.3.tar.gz) = WrdoBTonUIRhj7ZptPuq3MORWJmKh+hGUyOClZC8/Gw=
+SIZE (R-3.3.3.tar.gz) = 29804326
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.29
diff -u -p -r1.29 patch-configure
--- patches/patch-configure 1 Nov 2016 16:55:13 -   1.29
+++ patches/patch-configure 8 Mar 2017 15:28:29 -
@@ -1,7 +1,7 @@
 $OpenBSD: patch-configure,v 1.29 2016/11/01 16:55:13 feinerer Exp $
 
 configure.orig Mon Oct 24 13:34:26 2016
-+++ configure  Tue Nov  1 09:06:08 2016
+--- configure.orig Tue Mar  7 13:02:27 2017
 configure  Tue Mar  7 13:03:01 2017
 @@ -35492,8 +35492,8 @@ fi
  
  fi
@@ -13,12 +13,12 @@ $OpenBSD: patch-configure,v 1.29 2016/11
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -35510,7 +35510,7 @@ int main() {
- #ifdef ZLIB_VERSION
- /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
-version on the master site zlib.net */
--  exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
-+  exit(strncmp(ZLIB_VERSION, "1.2.3", 5) < 0);
- #else
-   exit(1);
- #endif
+@@ -35508,7 +35508,7 @@ else
+ #include 
+ int main() {
+ #ifdef ZLIB_VERNUM
+-  if (ZLIB_VERNUM < 0x1250) {
++  if (ZLIB_VERNUM < 0x1230) {
+ exit(1);
+   }
+   exit(0);
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.32
diff -u -p -r1.32 PLIST
--- pkg/PLIST   1 Nov 2016 16:55:13 -   1.32
+++ pkg/PLIST   8 Mar 2017 15:28:30 -
@@ -1358,6 +1358,9 @@ lib/R/library/survival/doc/compete.R
 lib/R/library/survival/doc/compete.Rnw
 lib/R/library/survival/doc/compete.pdf
 lib/R/library/survival/doc/index.html
+lib/R/library/survival/doc/multi.R
+lib/R/library/survival/doc/multi.Rnw
+lib/R/library/survival/doc/multi.pdf
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 lib/R/library/survival/doc/splines.pdf
Index: pkg/README
===
RCS file: /cvs/ports/math/R/pkg/README,v
retrieving revision 1.5
diff -u -p -r1.5 README
--- pkg/README  19 Aug 2016 07:02:47 -  1.5
+++ pkg/README  8 Mar 2017 15:28:30 -
@@ -26,3 +26,5 @@ E.g., for using recent compilers (packag
 
 CC=egcc -std=gnu99
 CXX=eg++
+CXX1X=eg++ -std=c++11
+CXX1XPICFLAGS=-fpic

Re: UPDATE: math/R

2016-11-01 Thread Stuart Henderson

On 2016/11/01 09:53, Ingo Feinerer wrote:
> - remove two FTP mirrors (there are plenty of HTTP)

Personally I don't mind either way for math/R, but just in case this prompts
someone to go and kill a whole bunch of them: some ports have ftp:// URLs
on purpose (though lower in the MASTER_SITES list) in order that "make
peek-ftp" works.

Re: UPDATE: math/R

2016-11-01 Thread David Coppa

On Tue, Nov 1, 2016 at 9:53 AM, Ingo Feinerer <feine...@logic.at> wrote:
> Dear useRs,
>
> update math/R 3.3.1 -> 3.3.2
>
> - remove two FTP mirrors (there are plenty of HTTP)
> - add print/texinfo to RUN_DEPENDS as 'R CMD build' needs it
> - regen patch
>
> Works for me on amd64.
>
> OK?

Looks good portswise, and works as expected.

ok dcoppa@

Ciao!
David

> Index: Makefile
> ===
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.87
> diff -u -p -r1.87 Makefile
> --- Makefile2 Sep 2016 13:02:24 -   1.87
> +++ Makefile1 Nov 2016 08:44:32 -
> @@ -1,8 +1,7 @@
>  # $OpenBSD: Makefile,v 1.87 2016/09/02 13:02:24 dcoppa Exp $
>
>  COMMENT=   powerful math/statistics/graphics language
> -DISTNAME=  R-3.3.1
> -REVISION=  1
> +DISTNAME=  R-3.3.2
>
>  SO_VERSION=32.0
>  .for _lib in R Rblas Rlapack
> @@ -23,8 +22,6 @@ WANTLIB += lzma m ncurses nghttp2 pango-
>  WANTLIB += png readline ssl tiff z ${MODTK_WANTLIB}
>
>  MASTER_SITES=  https://cran.r-project.org/src/base/R-3/ \
> -   ftp://cran.r-project.org/pub/R/src/base/R-3/ \
> -   ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
> http://cran.at.r-project.org/src/base/R-3/ \
> http://cran.br.r-project.org/src/base/R-3/ \
> http://cran.ch.r-project.org/src/base/R-3/ \
> @@ -67,6 +64,7 @@ RUN_DEPENDS=  ${MODFORTRAN_BUILD_DEPENDS}
> archivers/zip \
> devel/gmake \
> devel/xdg-utils \
> +   print/texinfo \
> print/texlive/base>=2014p1
>
>  CONFIGURE_STYLE=gnu
> Index: distinfo
> ===
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.31
> diff -u -p -r1.31 distinfo
> --- distinfo21 Jun 2016 18:21:52 -  1.31
> +++ distinfo1 Nov 2016 08:44:32 -
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.3.1.tar.gz) = PcWa5YMfU4D4PBabrCEDrQUu/g7OxP+nS95NhaD9qeI=
> -SIZE (R-3.3.1.tar.gz) = 29848329
> +SHA256 (R-3.3.2.tar.gz) = 0pStIen1dPtIKOuzqUuMs09PMEpBaHqZS+AN1BpOUUw=
> +SIZE (R-3.3.2.tar.gz) = 29440670
> Index: patches/patch-configure
> ===
> RCS file: /cvs/ports/math/R/patches/patch-configure,v
> retrieving revision 1.28
> diff -u -p -r1.28 patch-configure
> --- patches/patch-configure 6 May 2016 08:52:28 -   1.28
> +++ patches/patch-configure 1 Nov 2016 08:44:32 -
> @@ -1,8 +1,8 @@
>  $OpenBSD: patch-configure,v 1.28 2016/05/06 08:52:28 feinerer Exp $
>
>  configure.orig Tue May  3 12:17:51 2016
> -+++ configure  Tue May  3 12:19:33 2016
> -@@ -35481,8 +35481,8 @@ fi
> +--- configure.orig Mon Oct 24 13:34:26 2016
>  configure  Tue Nov  1 09:06:08 2016
> +@@ -35492,8 +35492,8 @@ fi
>
>   fi
>   if test "${have_zlib}" = yes; then
> @@ -13,7 +13,7 @@ $OpenBSD: patch-configure,v 1.28 2016/05
>   if ${r_cv_header_zlib_h+:} false; then :
> $as_echo_n "(cached) " >&6
>   else
> -@@ -35499,7 +35499,7 @@ int main() {
> +@@ -35510,7 +35510,7 @@ int main() {
>   #ifdef ZLIB_VERSION
>   /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
>  version on the master site zlib.net */
> Index: pkg/PLIST
> ===
> RCS file: /cvs/ports/math/R/pkg/PLIST,v
> retrieving revision 1.31
> diff -u -p -r1.31 PLIST
> --- pkg/PLIST   21 Jun 2016 18:21:52 -  1.31
> +++ pkg/PLIST   1 Nov 2016 08:44:33 -
> @@ -1910,14 +1910,12 @@ share/doc/R/manual/images/fig12.png
>  share/doc/R/manual/images/hist.png
>  share/doc/R/manual/images/ice.png
>  share/doc/pkg-readmes/${FULLPKGNAME}
> -share/texmf-local/
>  share/texmf-local/bibtex/
>  share/texmf-local/bibtex/bib/
>  share/texmf-local/bibtex/bib/RJournal.bib
>  share/texmf-local/bibtex/bib/Rnews.bib
>  share/texmf-local/bibtex/bst/
>  share/texmf-local/bibtex/bst/jss.bst
> -share/texmf-local/tex/
>  share/texmf-local/tex/latex/
>  share/texmf-local/tex/latex/Rd.sty
>  share/texmf-local/tex/latex/Sweave.sty
>



-- 
"If you try a few times and give up, you'll never get there. But if
you keep at it... There's a lot of problems in the world which can
really be solved by applying two or three times the persistence that
other people will."
-- Stewart Nelson

UPDATE: math/R

2016-11-01 Thread Ingo Feinerer

Dear useRs,

update math/R 3.3.1 -> 3.3.2

- remove two FTP mirrors (there are plenty of HTTP)
- add print/texinfo to RUN_DEPENDS as 'R CMD build' needs it
- regen patch

Works for me on amd64.

OK?

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.87
diff -u -p -r1.87 Makefile
--- Makefile2 Sep 2016 13:02:24 -   1.87
+++ Makefile1 Nov 2016 08:44:32 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.87 2016/09/02 13:02:24 dcoppa Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.3.1
-REVISION=  1
+DISTNAME=  R-3.3.2
 
 SO_VERSION=32.0
 .for _lib in R Rblas Rlapack
@@ -23,8 +22,6 @@ WANTLIB += lzma m ncurses nghttp2 pango-
 WANTLIB += png readline ssl tiff z ${MODTK_WANTLIB}
 
 MASTER_SITES=  https://cran.r-project.org/src/base/R-3/ \
-   ftp://cran.r-project.org/pub/R/src/base/R-3/ \
-   ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://cran.at.r-project.org/src/base/R-3/ \
http://cran.br.r-project.org/src/base/R-3/ \
http://cran.ch.r-project.org/src/base/R-3/ \
@@ -67,6 +64,7 @@ RUN_DEPENDS=  ${MODFORTRAN_BUILD_DEPENDS}
archivers/zip \
devel/gmake \
devel/xdg-utils \
+   print/texinfo \
print/texlive/base>=2014p1
 
 CONFIGURE_STYLE=gnu
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.31
diff -u -p -r1.31 distinfo
--- distinfo21 Jun 2016 18:21:52 -  1.31
+++ distinfo1 Nov 2016 08:44:32 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.3.1.tar.gz) = PcWa5YMfU4D4PBabrCEDrQUu/g7OxP+nS95NhaD9qeI=
-SIZE (R-3.3.1.tar.gz) = 29848329
+SHA256 (R-3.3.2.tar.gz) = 0pStIen1dPtIKOuzqUuMs09PMEpBaHqZS+AN1BpOUUw=
+SIZE (R-3.3.2.tar.gz) = 29440670
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.28
diff -u -p -r1.28 patch-configure
--- patches/patch-configure 6 May 2016 08:52:28 -   1.28
+++ patches/patch-configure 1 Nov 2016 08:44:32 -
@@ -1,8 +1,8 @@
 $OpenBSD: patch-configure,v 1.28 2016/05/06 08:52:28 feinerer Exp $
 
 configure.orig Tue May  3 12:17:51 2016
-+++ configure  Tue May  3 12:19:33 2016
-@@ -35481,8 +35481,8 @@ fi
+--- configure.orig Mon Oct 24 13:34:26 2016
 configure  Tue Nov  1 09:06:08 2016
+@@ -35492,8 +35492,8 @@ fi
  
  fi
  if test "${have_zlib}" = yes; then
@@ -13,7 +13,7 @@ $OpenBSD: patch-configure,v 1.28 2016/05
  if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
  else
-@@ -35499,7 +35499,7 @@ int main() {
+@@ -35510,7 +35510,7 @@ int main() {
  #ifdef ZLIB_VERSION
  /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
 version on the master site zlib.net */
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.31
diff -u -p -r1.31 PLIST
--- pkg/PLIST   21 Jun 2016 18:21:52 -  1.31
+++ pkg/PLIST   1 Nov 2016 08:44:33 -
@@ -1910,14 +1910,12 @@ share/doc/R/manual/images/fig12.png
 share/doc/R/manual/images/hist.png
 share/doc/R/manual/images/ice.png
 share/doc/pkg-readmes/${FULLPKGNAME}
-share/texmf-local/
 share/texmf-local/bibtex/
 share/texmf-local/bibtex/bib/
 share/texmf-local/bibtex/bib/RJournal.bib
 share/texmf-local/bibtex/bib/Rnews.bib
 share/texmf-local/bibtex/bst/
 share/texmf-local/bibtex/bst/jss.bst
-share/texmf-local/tex/
 share/texmf-local/tex/latex/
 share/texmf-local/tex/latex/Rd.sty
 share/texmf-local/tex/latex/Sweave.sty

Re: UPDATE: math/R

2016-06-21 Thread David Coppa

On Tue, Jun 21, 2016 at 5:18 PM, Ingo Feinerer <feine...@logic.at> wrote:
> Dear useRs,
>
> update math/R 3.3.0 -> 3.3.1
>
> OK?

Ok with me.

Ciao!
David

UPDATE: math/R

2016-06-21 Thread Ingo Feinerer

Dear useRs,

update math/R 3.3.0 -> 3.3.1

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.83
diff -u -p -r1.83 Makefile
--- Makefile6 May 2016 08:52:28 -   1.83
+++ Makefile21 Jun 2016 15:15:38 -
@@ -1,7 +1,7 @@
 # $OpenBSD: Makefile,v 1.83 2016/05/06 08:52:28 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.3.0
+DISTNAME=  R-3.3.1
 
 SO_VERSION=32.0
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.30
diff -u -p -r1.30 distinfo
--- distinfo6 May 2016 08:52:28 -   1.30
+++ distinfo21 Jun 2016 15:15:38 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.3.0.tar.gz) = klaxVLGlmT2ES+57GVXNScma1yzvA8zjzRvcoTEDEeQ=
-SIZE (R-3.3.0.tar.gz) = 29820067
+SHA256 (R-3.3.1.tar.gz) = PcWa5YMfU4D4PBabrCEDrQUu/g7OxP+nS95NhaD9qeI=
+SIZE (R-3.3.1.tar.gz) = 29848329
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.30
diff -u -p -r1.30 PLIST
--- pkg/PLIST   6 May 2016 08:52:28 -   1.30
+++ pkg/PLIST   21 Jun 2016 15:15:39 -
@@ -974,6 +974,7 @@ lib/R/library/nlme/
 lib/R/library/nlme/CITATION
 lib/R/library/nlme/DESCRIPTION
 lib/R/library/nlme/INDEX
+lib/R/library/nlme/LICENCE
 lib/R/library/nlme/Meta/
 lib/R/library/nlme/Meta/Rd.rds
 lib/R/library/nlme/Meta/data.rds
@@ -1034,6 +1035,7 @@ lib/R/library/nlme/scripts/ch04.R
 lib/R/library/nlme/scripts/ch05.R
 lib/R/library/nlme/scripts/ch06.R
 lib/R/library/nlme/scripts/ch08.R
+lib/R/library/nlme/scripts/runme.R
 lib/R/library/nlme/scripts/sims.rda
 lib/R/library/nnet/
 lib/R/library/nnet/CITATION

Re: UPDATE: math/R

2016-05-05 Thread Paul Irofti

On Tue, May 03, 2016 at 08:04:10PM +0200, Ingo Feinerer wrote:
> On Tue, May 03, 2016 at 07:58:10PM +0300, Paul Irofti wrote:
> > > there is one new patch as configure looks for system zlib >= 1.2.5 (and
> > > we only have 1.2.3 in base).
> > 
> > Why is it looking for 1.2.5 specifically?
> 
> I do not know. So far R works fine for me with zlib from base.

Go ahead then.

Re: UPDATE: math/R

2016-05-03 Thread Ingo Feinerer

On Tue, May 03, 2016 at 07:58:10PM +0300, Paul Irofti wrote:
> > there is one new patch as configure looks for system zlib >= 1.2.5 (and
> > we only have 1.2.3 in base).
> 
> Why is it looking for 1.2.5 specifically?

I do not know. So far R works fine for me with zlib from base.

Best regards,
Ingo

Re: UPDATE: math/R

2016-05-03 Thread Paul Irofti

> there is one new patch as configure looks for system zlib >= 1.2.5 (and
> we only have 1.2.3 in base).

Why is it looking for 1.2.5 specifically?

UPDATE: math/R

2016-05-03 Thread Ingo Feinerer

Dear useRs,

update math/R 3.2.5 -> 3.3.0:

Gets rid of two patches with are now incorporated upstream. However,
there is one new patch as configure looks for system zlib >= 1.2.5 (and
we only have 1.2.3 in base).

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.82
diff -u -p -r1.82 Makefile
--- Makefile16 Apr 2016 10:04:36 -  1.82
+++ Makefile3 May 2016 15:37:42 -
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.82 2016/04/16 10:04:36 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.2.5
+DISTNAME=  R-3.3.0
 
-SO_VERSION=31.2
+SO_VERSION=32.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.29
diff -u -p -r1.29 distinfo
--- distinfo16 Apr 2016 10:04:36 -  1.29
+++ distinfo3 May 2016 15:37:42 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.2.5.tar.gz) = YHRWctzl3cIBgG+ln21OC6ZVTY7XjQ+fDXmmKZePgLU=
-SIZE (R-3.2.5.tar.gz) = 29876312
+SHA256 (R-3.3.0.tar.gz) = klaxVLGlmT2ES+57GVXNScma1yzvA8zjzRvcoTEDEeQ=
+SIZE (R-3.3.0.tar.gz) = 29820067
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.27
diff -u -p -r1.27 patch-configure
--- patches/patch-configure 14 Dec 2015 16:49:02 -  1.27
+++ patches/patch-configure 3 May 2016 15:37:42 -
@@ -1,29 +1,24 @@
 $OpenBSD: patch-configure,v 1.27 2015/12/14 16:49:02 feinerer Exp $
 
-Unbreak build on powerpc (relocation truncated to fit: R_PPC_GOT16...)
-
 configure.orig Thu Dec 10 15:45:13 2015
-+++ configure  Thu Dec 10 15:47:05 2015
-@@ -26576,6 +26576,22 @@ $as_echo "$as_me: WARNING: Use of flat namespace is re
-   main_ldflags="${wl}-export-dynamic"
-   shlib_ldflags="-shared -fPIC"
- fi
-+case "${host_cpu}" in
-+  powerpc*)
-+  ## GCC -fpic limits to 2**16 on OpenBSD powerpc.
-+  ## Error message without -fPIC:
-+  ##   relocation truncated to fit: R_PPC_GOT16...
-+if test "${GCC}" = yes; then
-+  cpicflags="-fPIC"
-+fi
-+if test "${G77}" = yes; then
-+  fpicflags="-fPIC"
-+fi
-+if test "${GXX}" = yes; then
-+  cxxpicflags="-fPIC"
-+fi
-+;;
-+esac
- ;;
-   osf*)
- cpicflags=
+--- configure.orig Tue May  3 12:17:51 2016
 configure  Tue May  3 12:19:33 2016
+@@ -35481,8 +35481,8 @@ fi
+ 
+ fi
+ if test "${have_zlib}" = yes; then
+-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib version >= 1.2.5" 
>&5
+-$as_echo_n "checking if zlib version >= 1.2.5... " >&6; }
++  { $as_echo "$as_me:${as_lineno-$LINENO}: checking if zlib version >= 1.2.3" 
>&5
++$as_echo_n "checking if zlib version >= 1.2.3... " >&6; }
+ if ${r_cv_header_zlib_h+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+@@ -35499,7 +35499,7 @@ int main() {
+ #ifdef ZLIB_VERSION
+ /* Work around Debian bug: it uses 1.2.3.4 even though there was no such
+version on the master site zlib.net */
+-  exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
++  exit(strncmp(ZLIB_VERSION, "1.2.3", 5) < 0);
+ #else
+   exit(1);
+ #endif
Index: patches/patch-src_library_tools_R_news_R
===
RCS file: patches/patch-src_library_tools_R_news_R
diff -N patches/patch-src_library_tools_R_news_R
--- patches/patch-src_library_tools_R_news_R1 Mar 2016 17:57:06 -   
1.1
+++ /dev/null   1 Jan 1970 00:00:00 -
@@ -1,14 +0,0 @@
-$OpenBSD: patch-src_library_tools_R_news_R,v 1.1 2016/03/01 17:57:06 feinerer 
Exp $
 src/library/tools/R/news.R.origTue Mar  1 18:28:22 2016
-+++ src/library/tools/R/news.R Tue Mar  1 18:29:09 2016
-@@ -372,7 +372,9 @@ function(f, pdf_file)
- close(out)
- od <- setwd(dirname(f3))
- on.exit(setwd(od))
--texi2pdf("NEWS.tex", quiet = TRUE)
-+## avoid broken texi2pdf scripts: this is simple LaTeX
-+## and emulation suffices
-+texi2pdf("NEWS.tex", quiet = TRUE, texi2dvi = "emulation")
- setwd(od); on.exit()
- invisible(file.copy(file.path(dirname(f3), "NEWS.pdf"),
- pdf_file, overwrite = TRUE))
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.29
diff -u -p -r1.29 PLIST
--- pkg/PLIST   19 Mar 2016 11:42:57 -  1.29
+++ pkg/PLIST   3 May 2016 15:37:

UPDATE: math/R

2016-04-16 Thread Ingo Feinerer

Dear useRs,

update math/R 3.2.4 -> 3.2.5:

- "This is a rebadging of the quick-fix release 3.2.4-revised."
  (https://www.r-project.org/)
- Get rid of the devel/gettext module.

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.81
diff -u -p -r1.81 Makefile
--- Makefile19 Mar 2016 11:42:57 -  1.81
+++ Makefile16 Apr 2016 07:53:00 -
@@ -1,7 +1,7 @@
 # $OpenBSD: Makefile,v 1.81 2016/03/19 11:42:57 feinerer Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.2.4
+DISTNAME=  R-3.2.5
 
 SO_VERSION=31.2
 .for _lib in R Rblas Rlapack
@@ -16,12 +16,10 @@ MAINTAINER= Ingo Feinerer <feinerer@logi
 # GPLv2+
 PERMIT_PACKAGE_CDROM=  Yes
 
-WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
-   cairo readline glib-2.0 \
-   gobject-2.0 icui18n icuuc idn jpeg lzma m \
-   ncurses nghttp2 pango-1.0 pangocairo-1.0 \
-   pcre png pthread ssl tiff z \
-   ${MODTK_WANTLIB}
+WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
+WANTLIB += glib-2.0 gobject-2.0 iconv icui18n icuuc idn intl jpeg
+WANTLIB += lzma m ncurses nghttp2 pango-1.0 pangocairo-1.0 pcre
+WANTLIB += png readline ssl tiff z ${MODTK_WANTLIB}
 
 MASTER_SITES=  https://cran.r-project.org/src/base/R-3/ \
ftp://cran.r-project.org/pub/R/src/base/R-3/ \
@@ -37,7 +35,6 @@ MASTER_SITES= https://cran.r-project.org
http://probability.ca/cran/src/base/R-3/
 
 MODULES=   gcc4 \
-   devel/gettext \
x11/tk
 
 MODGCC4_ARCHS= *
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.28
diff -u -p -r1.28 distinfo
--- distinfo19 Mar 2016 11:42:57 -  1.28
+++ distinfo16 Apr 2016 07:53:00 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.2.4.tar.gz) = uv1AX+nC/ju+R6incwrRIPA7ffn7D2FnT8oZzwYd01A=
-SIZE (R-3.2.4.tar.gz) = 29879523
+SHA256 (R-3.2.5.tar.gz) = YHRWctzl3cIBgG+ln21OC6ZVTY7XjQ+fDXmmKZePgLU=
+SIZE (R-3.2.5.tar.gz) = 29876312

Re: UPDATE: math/R

2016-03-21 Thread David Coppa

On Sat, Mar 19, 2016 at 12:21 PM, Ingo Feinerer <feine...@logic.at> wrote:
> Update math/R 3.2.3 -> 3.2.4
>
> OK?

Yes, ok with me.

> Best regards,
> Ingo

Ciao!
David

> Index: Makefile
> ===
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.80
> diff -u -p -r1.80 Makefile
> --- Makefile18 Mar 2016 23:12:18 -  1.80
> +++ Makefile19 Mar 2016 11:18:49 -
> @@ -1,8 +1,7 @@
>  # $OpenBSD: Makefile,v 1.80 2016/03/18 23:12:18 naddy Exp $
>
>  COMMENT=   powerful math/statistics/graphics language
> -DISTNAME=  R-3.2.3
> -REVISION=  0
> +DISTNAME=  R-3.2.4
>
>  SO_VERSION=31.2
>  .for _lib in R Rblas Rlapack
> Index: distinfo
> ===
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.27
> diff -u -p -r1.27 distinfo
> --- distinfo14 Dec 2015 16:49:02 -  1.27
> +++ distinfo19 Mar 2016 11:18:49 -
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.2.3.tar.gz) = uTt9h4E4J5I0Fg8AfLm3+BuKcsASoVVm6exTlc/ZtsE=
> -SIZE (R-3.2.3.tar.gz) = 29816176
> +SHA256 (R-3.2.4.tar.gz) = uv1AX+nC/ju+R6incwrRIPA7ffn7D2FnT8oZzwYd01A=
> +SIZE (R-3.2.4.tar.gz) = 29879523
> Index: pkg/PLIST
> ===
> RCS file: /cvs/ports/math/R/pkg/PLIST,v
> retrieving revision 1.28
> diff -u -p -r1.28 PLIST
> --- pkg/PLIST   28 Sep 2015 07:32:19 -  1.28
> +++ pkg/PLIST   19 Mar 2016 11:18:49 -
> @@ -200,6 +200,7 @@ lib/R/library/Matrix/Copyrights
>  lib/R/library/Matrix/DESCRIPTION
>  lib/R/library/Matrix/Doxyfile
>  lib/R/library/Matrix/INDEX
> +lib/R/library/Matrix/LICENCE
>  lib/R/library/Matrix/Meta/
>  lib/R/library/Matrix/Meta/Rd.rds
>  lib/R/library/Matrix/Meta/data.rds
>



-- 
"If you try a few times and give up, you'll never get there. But if
you keep at it... There's a lot of problems in the world which can
really be solved by applying two or three times the persistence that
other people will."
-- Stewart Nelson

UPDATE: math/R

2016-03-19 Thread Ingo Feinerer

Update math/R 3.2.3 -> 3.2.4

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.80
diff -u -p -r1.80 Makefile
--- Makefile18 Mar 2016 23:12:18 -  1.80
+++ Makefile19 Mar 2016 11:18:49 -
@@ -1,8 +1,7 @@
 # $OpenBSD: Makefile,v 1.80 2016/03/18 23:12:18 naddy Exp $
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.2.3
-REVISION=  0
+DISTNAME=  R-3.2.4
 
 SO_VERSION=31.2
 .for _lib in R Rblas Rlapack
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.27
diff -u -p -r1.27 distinfo
--- distinfo14 Dec 2015 16:49:02 -  1.27
+++ distinfo19 Mar 2016 11:18:49 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.2.3.tar.gz) = uTt9h4E4J5I0Fg8AfLm3+BuKcsASoVVm6exTlc/ZtsE=
-SIZE (R-3.2.3.tar.gz) = 29816176
+SHA256 (R-3.2.4.tar.gz) = uv1AX+nC/ju+R6incwrRIPA7ffn7D2FnT8oZzwYd01A=
+SIZE (R-3.2.4.tar.gz) = 29879523
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.28
diff -u -p -r1.28 PLIST
--- pkg/PLIST   28 Sep 2015 07:32:19 -  1.28
+++ pkg/PLIST   19 Mar 2016 11:18:49 -
@@ -200,6 +200,7 @@ lib/R/library/Matrix/Copyrights
 lib/R/library/Matrix/DESCRIPTION
 lib/R/library/Matrix/Doxyfile
 lib/R/library/Matrix/INDEX
+lib/R/library/Matrix/LICENCE
 lib/R/library/Matrix/Meta/
 lib/R/library/Matrix/Meta/Rd.rds
 lib/R/library/Matrix/Meta/data.rds

Re: UPDATE: math/R

2015-12-14 Thread David Coppa

On Thu, Dec 10, 2015 at 4:21 PM, Ingo Feinerer <feine...@logic.at> wrote:
> Dear useRs,
>
> Update math/R 3.2.2 -> 3.2.3:
>
> - Use new --disable-java which eliminates the need for patch-Makefile_in
> - Use new R_DYLIB_VERSION variable which allows us to get rid of
>   MAKE_FLAGS and patch-src_scripts_javareconf_in. However we now need to
>   have all SHARED_LIBS in sync (consequently bumping libR).
> - External libintl handling is now fixed upstream
>   (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16464), so zap
>   patch-src_main_Makefile_in and corresponding parts in patch-configure
> - Use upstream tests in patch-configure to unbreak build on powerpc*
>   (already in R-devel)
> - Fix typo and sync with recommended upstream settings for egcc in
>   pkg/README
> - make port-lib-depends-check tells me that WANTLIB no longer should
>   include "fontconfig freetype pangoft2-1.0"
>
> OK?

Finally managed to test this update.

All looks good: ok dcoppa@.

> Best regards,
> Ingo

Ciao!
David

> Index: Makefile
> ===
> RCS file: /cvs/ports/math/R/Makefile,v
> retrieving revision 1.76
> diff -u -p -r1.76 Makefile
> --- Makefile30 Oct 2015 12:47:40 -  1.76
> +++ Makefile10 Dec 2015 14:52:24 -
> @@ -3,12 +3,12 @@
>  SHARED_ONLY=   Yes
>
>  COMMENT=   powerful math/statistics/graphics language
> -DISTNAME=  R-3.2.2
> -REVISION=  1
> +DISTNAME=  R-3.2.3
>
> -SHARED_LIBS=   R   3.1
> -SHARED_LIBS+=  Rlapack 31.2# 31.2
> -SHARED_LIBS+=  Rblas   31.2# 31.2
> +SO_VERSION=31.2
> +.for _lib in R Rblas Rlapack
> +SHARED_LIBS += ${_lib} ${SO_VERSION}
> +.endfor
>
>  CATEGORIES=math
>  HOMEPAGE=  http://www.r-project.org/
> @@ -19,10 +19,10 @@ MAINTAINER= Ingo Feinerer <feinerer@logi
>  PERMIT_PACKAGE_CDROM=  Yes
>
>  WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
> -   cairo readline fontconfig freetype glib-2.0 \
> +   cairo readline glib-2.0 \
> gobject-2.0 icui18n icuuc idn jpeg lzma m \
> ncurses nghttp2 pango-1.0 pangocairo-1.0 \
> -   pangoft2-1.0 pcre png pthread ssl tiff z \
> +   pcre png pthread ssl tiff z \
> ${MODTK_WANTLIB}
>
>  MASTER_SITES=  http://cran.r-project.org/src/base/R-3/ \
> @@ -79,6 +79,7 @@ CONFIGURE_STYLE=gnu
>  MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
>
>  CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
> +   --disable-java \
> --enable-BLAS-shlib \
> --enable-R-shlib \
> --with-tcl-config=${MODTCL_CONFIG} \
> @@ -89,12 +90,9 @@ CONFIGURE_ENV=   FFLAGS="${FFLAGS}" \
> LDFLAGS="-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib" \
> LIBnn=lib \
> MAKEINFO="${LOCALBASE}/bin/gtexi2any" \
> +   R_DYLIB_VERSION=${SO_VERSION} \
> TEXI2DVI="${LOCALBASE}/bin/gtexi2dvi" \
> rdocdir="${PREFIX}/share/doc/R"
> -
> -MAKE_FLAGS=DYLIB_EXT=".so.${LIBR_VERSION}" \
> -   Rblas_la="libRblas.so.${LIBRblas_VERSION}" \
> -   Rlapack_la="libRlapack.so.$(LIBRlapack_VERSION)"
>
>  SEPARATE_BUILD=Yes
>
> Index: distinfo
> ===
> RCS file: /cvs/ports/math/R/distinfo,v
> retrieving revision 1.26
> diff -u -p -r1.26 distinfo
> --- distinfo17 Aug 2015 15:33:04 -  1.26
> +++ distinfo10 Dec 2015 14:52:24 -
> @@ -1,2 +1,2 @@
> -SHA256 (R-3.2.2.tar.gz) = nJFS50E0tosPOhxwg3ZK3By1b9gza+wAP9DKVQzSRh0=
> -SIZE (R-3.2.2.tar.gz) = 29772864
> +SHA256 (R-3.2.3.tar.gz) = uTt9h4E4J5I0Fg8AfLm3+BuKcsASoVVm6exTlc/ZtsE=
> +SIZE (R-3.2.3.tar.gz) = 29816176
> Index: patches/patch-Makefile_in
> ===
> RCS file: patches/patch-Makefile_in
> diff -N patches/patch-Makefile_in
> --- patches/patch-Makefile_in   23 Jun 2015 15:14:52 -  1.8
> +++ /dev/null   1 Jan 1970 00:00:00 -
> @@ -1,13 +0,0 @@
> -$OpenBSD: patch-Makefile_in,v 1.8 2015/06/23 15:14:52 feinerer Exp $
> -
>  Makefile.in.orig   Thu Mar 19 02:02:06 2015
> -+++ Makefile.inSat May  2 11:47:48 2015
> -@@ -82,8 +82,6 @@ vignettes: stamp-recommended
> - ## This needs packages built, hence 'R' dependence on 'javaconf'
> - ## javareconf gets remade often.
> - stamp-java : etc/javaconf $(srcdir)/src/scripts/javareconf.in
> --  @$(ECHO) "configuring Java ..."
> --

Re: UPDATE: math/R

2015-12-10 Thread Rafael Sadowski

On Thu Dec 10, 2015 at 04:21:50PM +0100, Ingo Feinerer wrote:
> Dear useRs,
> 
> Update math/R 3.2.2 -> 3.2.3:
> 
>  
>  CATEGORIES=  math
>  HOMEPAGE=http://www.r-project.org/

HTTPS is available for R: https://www.r-project.org/

Best regards, Rafael

UPDATE: math/R

2015-12-10 Thread Ingo Feinerer

Dear useRs,

Update math/R 3.2.2 -> 3.2.3:

- Use new --disable-java which eliminates the need for patch-Makefile_in
- Use new R_DYLIB_VERSION variable which allows us to get rid of
  MAKE_FLAGS and patch-src_scripts_javareconf_in. However we now need to
  have all SHARED_LIBS in sync (consequently bumping libR).
- External libintl handling is now fixed upstream
  (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16464), so zap
  patch-src_main_Makefile_in and corresponding parts in patch-configure
- Use upstream tests in patch-configure to unbreak build on powerpc*
  (already in R-devel)
- Fix typo and sync with recommended upstream settings for egcc in
  pkg/README
- make port-lib-depends-check tells me that WANTLIB no longer should
  include "fontconfig freetype pangoft2-1.0"

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.76
diff -u -p -r1.76 Makefile
--- Makefile30 Oct 2015 12:47:40 -  1.76
+++ Makefile10 Dec 2015 14:52:24 -
@@ -3,12 +3,12 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.2.2
-REVISION=  1
+DISTNAME=  R-3.2.3
 
-SHARED_LIBS=   R   3.1
-SHARED_LIBS+=  Rlapack 31.2# 31.2
-SHARED_LIBS+=  Rblas   31.2# 31.2
+SO_VERSION=31.2
+.for _lib in R Rblas Rlapack
+SHARED_LIBS += ${_lib} ${SO_VERSION}
+.endfor
 
 CATEGORIES=math
 HOMEPAGE=  http://www.r-project.org/
@@ -19,10 +19,10 @@ MAINTAINER= Ingo Feinerer <feinerer@logi
 PERMIT_PACKAGE_CDROM=  Yes
 
 WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
-   cairo readline fontconfig freetype glib-2.0 \
+   cairo readline glib-2.0 \
gobject-2.0 icui18n icuuc idn jpeg lzma m \
ncurses nghttp2 pango-1.0 pangocairo-1.0 \
-   pangoft2-1.0 pcre png pthread ssl tiff z \
+   pcre png pthread ssl tiff z \
${MODTK_WANTLIB}
 
 MASTER_SITES=  http://cran.r-project.org/src/base/R-3/ \
@@ -79,6 +79,7 @@ CONFIGURE_STYLE=gnu
 MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
 
 CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
+   --disable-java \
--enable-BLAS-shlib \
--enable-R-shlib \
--with-tcl-config=${MODTCL_CONFIG} \
@@ -89,12 +90,9 @@ CONFIGURE_ENV=   FFLAGS="${FFLAGS}" \
LDFLAGS="-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib" \
LIBnn=lib \
MAKEINFO="${LOCALBASE}/bin/gtexi2any" \
+   R_DYLIB_VERSION=${SO_VERSION} \
TEXI2DVI="${LOCALBASE}/bin/gtexi2dvi" \
rdocdir="${PREFIX}/share/doc/R"
-
-MAKE_FLAGS=DYLIB_EXT=".so.${LIBR_VERSION}" \
-   Rblas_la="libRblas.so.${LIBRblas_VERSION}" \
-   Rlapack_la="libRlapack.so.$(LIBRlapack_VERSION)"
 
 SEPARATE_BUILD=Yes
 
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.26
diff -u -p -r1.26 distinfo
--- distinfo17 Aug 2015 15:33:04 -  1.26
+++ distinfo10 Dec 2015 14:52:24 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.2.2.tar.gz) = nJFS50E0tosPOhxwg3ZK3By1b9gza+wAP9DKVQzSRh0=
-SIZE (R-3.2.2.tar.gz) = 29772864
+SHA256 (R-3.2.3.tar.gz) = uTt9h4E4J5I0Fg8AfLm3+BuKcsASoVVm6exTlc/ZtsE=
+SIZE (R-3.2.3.tar.gz) = 29816176
Index: patches/patch-Makefile_in
===
RCS file: patches/patch-Makefile_in
diff -N patches/patch-Makefile_in
--- patches/patch-Makefile_in   23 Jun 2015 15:14:52 -  1.8
+++ /dev/null   1 Jan 1970 00:00:00 -
@@ -1,13 +0,0 @@
-$OpenBSD: patch-Makefile_in,v 1.8 2015/06/23 15:14:52 feinerer Exp $
-
 Makefile.in.orig   Thu Mar 19 02:02:06 2015
-+++ Makefile.inSat May  2 11:47:48 2015
-@@ -82,8 +82,6 @@ vignettes: stamp-recommended
- ## This needs packages built, hence 'R' dependence on 'javaconf'
- ## javareconf gets remade often.
- stamp-java : etc/javaconf $(srcdir)/src/scripts/javareconf.in
--  @$(ECHO) "configuring Java ..."
--  @-bin/R CMD javareconf
-   @touch stamp-java
- 
- javaconf: R
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.26
diff -u -p -r1.26 patch-configure
--- patches/patch-configure 28 Sep 2015 07:32:19 -  1.26
+++ patches/patch-configure 10 Dec 2015 14:52:24 -
@@ -2,64 +2,28 @@ $OpenBSD: patch-configure,v 1.26 2015/09
 
 Unbreak build on powerpc (relocation truncated to fit: R_PPC_GOT16...)
 
-Fix linking with external libintl
-(https://marc.info/?l=openbsd-ports=143526271406832=2)
-
 configure.orig Thu Aug 13 11:21:16 2015
-+++ configu

Re: UPDATE: math/R

2015-08-15 Thread Ingo Feinerer

On Sat, Aug 15, 2015 at 10:00:13AM +0200, Antoine Jacoutot wrote:
  - Add @comment no checksum in pkg/PLIST for lib/R/etc/Makeconf and
lib/R/etc/ldpaths as they are modified by R CMD javareconf (which we
describe in pkg/README); otherwise pkg_delete fails/complains.
 
 Doesn't this mean they'll get overwritten at each pkg update?

Yes. I think this is fine as these lib/R/etc/* files are generated by
configure and are not typical configuration files to be edited by the
user (at least this is my impression). Moreover I am not confident that
these files could be directly used whenever there is an R update (what I
would expect from normal configuration files).

The only reason to bother is if someone wants Java support. They need to
ensure that they run R CMD javareconf when needed (which might mean
after each pkg update).

Manual configuration should go IMHO into ~/.R/Makevars (as outlined in
pkg/README).

 Wouldn't it make more sense to make them @sample instead?

If my above argument makes sense, then no.

Best regards,
Ingo

Re: UPDATE: math/R

2015-08-15 Thread Antoine Jacoutot

On Sat, Aug 15, 2015 at 10:37:52AM +0200, Ingo Feinerer wrote:
 On Sat, Aug 15, 2015 at 10:00:13AM +0200, Antoine Jacoutot wrote:
   - Add @comment no checksum in pkg/PLIST for lib/R/etc/Makeconf and
 lib/R/etc/ldpaths as they are modified by R CMD javareconf (which we
 describe in pkg/README); otherwise pkg_delete fails/complains.
  
  Doesn't this mean they'll get overwritten at each pkg update?
 
 Yes. I think this is fine as these lib/R/etc/* files are generated by
 configure and are not typical configuration files to be edited by the
 user (at least this is my impression). Moreover I am not confident that
 these files could be directly used whenever there is an R update (what I
 would expect from normal configuration files).
 
 The only reason to bother is if someone wants Java support. They need to
 ensure that they run R CMD javareconf when needed (which might mean
 after each pkg update).
 
 Manual configuration should go IMHO into ~/.R/Makevars (as outlined in
 pkg/README).
 
  Wouldn't it make more sense to make them @sample instead?
 
 If my above argument makes sense, then no.

Oki. That much more clear now, thanks :-)
The diff reads fine to me fwiw.

-- 
Antoine

Re: UPDATE: math/R

2015-06-25 Thread Christian Weisgerber

On 2015-06-22, Ingo Feinerer feine...@logic.at wrote:

 Update math/R 3.2.0 - 3.2.1:

 - Avoid LIBINTL-LTLIBINTL patches (works fine for me in various locales)

From configure:

checking how to link with libintl... /usr/local/lib/libintl.a 
/usr/local/lib/libiconv.a -lc -Wl,-rpath,/usr/local/lib

From build:

... -L../../lib -lRblas -R/usr/local/lib/R/lib -lgfortran -lm -lquadmath  
/usr/local/lib/libintl.a /usr/local/lib/libiconv.a -lc 
-Wl,-rpath,/usr/local/lib -lreadline -lncurses  -lpcre -llzma -lbz2 -lm -liconv 
-licuuc -licui18n

So you're now linking statically with libintl.a libiconv.a.  That's
exactly what the LIBINTL-LTLIBINTL patches fixed.

-- 
Christian naddy Weisgerber  na...@mips.inka.de

Re: UPDATE: math/R

2015-06-25 Thread David Coppa

On Thu, Jun 25, 2015 at 9:57 PM, Christian Weisgerber
na...@mips.inka.de wrote:
 On 2015-06-22, Ingo Feinerer feine...@logic.at wrote:

 Update math/R 3.2.0 - 3.2.1:

 - Avoid LIBINTL-LTLIBINTL patches (works fine for me in various locales)

 From configure:

 checking how to link with libintl... /usr/local/lib/libintl.a 
 /usr/local/lib/libiconv.a -lc -Wl,-rpath,/usr/local/lib

 From build:

 ... -L../../lib -lRblas -R/usr/local/lib/R/lib -lgfortran -lm -lquadmath  
 /usr/local/lib/libintl.a /usr/local/lib/libiconv.a -lc 
 -Wl,-rpath,/usr/local/lib -lreadline -lncurses  -lpcre -llzma -lbz2 -lm 
 -liconv -licuuc -licui18n

 So you're now linking statically with libintl.a libiconv.a.  That's
 exactly what the LIBINTL-LTLIBINTL patches fixed.

Ingo, please re-add the patch and bump revision.

Re: UPDATE: math/R

2015-06-23 Thread David Coppa

Il 22/giu/2015 20:39, Ingo Feinerer feine...@logic.at ha scritto:

 Update math/R 3.2.0 - 3.2.1:

 - Use base readline (handling is still fine)

Right, no more need for this now that devel/readline has been fixed to not
conflict with readline from base.


 - patch-src_include_Rinterface_h is now included in upstream
 - Avoid LIBINTL-LTLIBINTL patches (works fine for me in various locales)
 - Simplify javareconf patch
 - Remove outdated comments

 OK?
ok dcoppa@

 Best regards,
 Ingo

Thanks,

David


  Index: Makefile
 ===
 RCS file: /cvs/ports/math/R/Makefile,v
 retrieving revision 1.71
 diff -u -p -r1.71 Makefile
 --- Makefile28 May 2015 08:09:46 -  1.71
 +++ Makefile22 Jun 2015 18:02:09 -
 @@ -3,8 +3,7 @@
  SHARED_ONLY=   Yes

  COMMENT=   powerful math/statistics/graphics language
 -DISTNAME=  R-3.2.0
 -REVISION=  1
 +DISTNAME=  R-3.2.1

  SHARED_LIBS=   R   3.1
  SHARED_LIBS+=  Rlapack 31.2# 31.2
 @@ -19,7 +18,7 @@ MAINTAINER=   Ingo Feinerer feinerer@logi
  PERMIT_PACKAGE_CDROM=  Yes

  WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
 -   cairo ereadline fontconfig freetype glib-2.0 \
 +   cairo readline fontconfig freetype glib-2.0 \
 gobject-2.0 icui18n icuuc idn jpeg lzma m \
 ncurses pango-1.0 pangocairo-1.0 \
 pangoft2-1.0 pcre png pthread ssl tiff z \
 @@ -57,7 +56,6 @@ LIB_DEPENDS=  ${MODFORTRAN_LIB_DEPENDS} \
 devel/glib2 \
 devel/libidn \
 devel/pango \
 -   devel/readline \
 graphics/cairo \
 graphics/jpeg \
 graphics/png \
 @@ -84,7 +82,7 @@ CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
 --with-tk-config=${MODTK_CONFIG}

  CONFIGURE_ENV= FFLAGS=${FFLAGS} \
 -   CPPFLAGS=-I${LOCALBASE}/include/ereadline
-I${LOCALBASE}/include \
 +   CPPFLAGS=-I${LOCALBASE}/include \
 LDFLAGS=-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib
\
 LIBnn=lib \
 ac_cv_path_PDFLATEX= \
 Index: distinfo
 ===
 RCS file: /cvs/ports/math/R/distinfo,v
 retrieving revision 1.24
 diff -u -p -r1.24 distinfo
 --- distinfo29 Apr 2015 21:53:43 -  1.24
 +++ distinfo22 Jun 2015 18:02:09 -
 @@ -1,2 +1,2 @@
 -SHA256 (R-3.2.0.tar.gz) = 9a6VPxi6bz1VtGVWu79zRBNQ+f0iYlQCtyOiuB/2TzU=
 -SIZE (R-3.2.0.tar.gz) = 29124927
 +SHA256 (R-3.2.1.tar.gz) = 1Z28PwT0YEpc8PshC46nA+8kOLPuZf1atTbsUjT0yYI=
 +SIZE (R-3.2.1.tar.gz) = 29197870
 Index: patches/patch-Makefile_in
 ===
 RCS file: /cvs/ports/math/R/patches/patch-Makefile_in,v
 retrieving revision 1.7
 diff -u -p -r1.7 patch-Makefile_in
 --- patches/patch-Makefile_in   2 May 2015 09:22:58 -   1.7
 +++ patches/patch-Makefile_in   22 Jun 2015 18:02:09 -
 @@ -1,7 +1,5 @@
  $OpenBSD: patch-Makefile_in,v 1.7 2015/05/02 09:22:58 zhuk Exp $

 -Do not build PDF versions of the R manuals
 -
  --- Makefile.in.orig   Thu Mar 19 02:02:06 2015
  +++ Makefile.inSat May  2 11:47:48 2015
  @@ -82,8 +82,6 @@ vignettes: stamp-recommended
 Index: patches/patch-configure
 ===
 RCS file: /cvs/ports/math/R/patches/patch-configure,v
 retrieving revision 1.23
 diff -u -p -r1.23 patch-configure
 --- patches/patch-configure 2 May 2015 09:22:58 -   1.23
 +++ patches/patch-configure 22 Jun 2015 18:02:09 -
 @@ -1,65 +1,9 @@
  $OpenBSD: patch-configure,v 1.23 2015/05/02 09:22:58 zhuk Exp $

 -Use GNU readline instead of our base readline
 -
  Unbreak build on powerpc (relocation truncated to fit: R_PPC_GOT16...)

 -Fix --export-dynamic linker flag
 -
 -Fix linking with external libintl
 -
  --- configure.orig Thu Apr  9 01:16:36 2015
  +++ configure  Sat May  2 11:47:48 2015
 -@@ -20921,12 +20921,12 @@ done
 -   ## don't use the cached value as we need to rebuild LIBS
 -   unset ac_cv_lib_readline_rl_callback_read_char
 -   { $as_echo $as_me:${as_lineno-$LINENO}: checking for
rl_callback_read_char in -lreadline 5
 --$as_echo_n checking for rl_callback_read_char in -lreadline...  6; }
 -+$as_echo_n checking for rl_callback_read_char in -lereadline...  6;
}
 - if ${ac_cv_lib_readline_rl_callback_read_char+:} false; then :
 -   $as_echo_n (cached)  6
 - else
 -   ac_check_lib_save_LIBS=$LIBS
 --LIBS=-lreadline  $LIBS
 -+LIBS=-lereadline  $LIBS
 - cat confdefs.h - _ACEOF conftest.$ac_ext
 - /* end confdefs.h.  */
 -
 -@@ -20961,7 +20961,7 @@ if test
x$ac_cv_lib_readline_rl_callback_read_char =
 - #define HAVE_LIBREADLINE 1
 - _ACEOF
 -
 --  LIBS=-lreadline $LIBS
 -+  LIBS=-lereadline $LIBS
 -
 - fi
 -
 -@@ -21088,13 +21088,13 @@ fi
 -
 - fi
 -
 --{ $as_echo $as_me:${as_lineno-$LINENO}: checking

UPDATE: math/R

2015-06-22 Thread Ingo Feinerer

Update math/R 3.2.0 - 3.2.1:

- Use base readline (handling is still fine)
- patch-src_include_Rinterface_h is now included in upstream
- Avoid LIBINTL-LTLIBINTL patches (works fine for me in various locales)
- Simplify javareconf patch
- Remove outdated comments

OK?

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.71
diff -u -p -r1.71 Makefile
--- Makefile28 May 2015 08:09:46 -  1.71
+++ Makefile22 Jun 2015 18:02:09 -
@@ -3,8 +3,7 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.2.0
-REVISION=  1
+DISTNAME=  R-3.2.1
 
 SHARED_LIBS=   R   3.1
 SHARED_LIBS+=  Rlapack 31.2# 31.2
@@ -19,7 +18,7 @@ MAINTAINER=   Ingo Feinerer feinerer@logi
 PERMIT_PACKAGE_CDROM=  Yes
 
 WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
-   cairo ereadline fontconfig freetype glib-2.0 \
+   cairo readline fontconfig freetype glib-2.0 \
gobject-2.0 icui18n icuuc idn jpeg lzma m \
ncurses pango-1.0 pangocairo-1.0 \
pangoft2-1.0 pcre png pthread ssl tiff z \
@@ -57,7 +56,6 @@ LIB_DEPENDS=  ${MODFORTRAN_LIB_DEPENDS} \
devel/glib2 \
devel/libidn \
devel/pango \
-   devel/readline \
graphics/cairo \
graphics/jpeg \
graphics/png \
@@ -84,7 +82,7 @@ CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
--with-tk-config=${MODTK_CONFIG}
 
 CONFIGURE_ENV= FFLAGS=${FFLAGS} \
-   CPPFLAGS=-I${LOCALBASE}/include/ereadline 
-I${LOCALBASE}/include \
+   CPPFLAGS=-I${LOCALBASE}/include \
LDFLAGS=-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib \
LIBnn=lib \
ac_cv_path_PDFLATEX= \
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.24
diff -u -p -r1.24 distinfo
--- distinfo29 Apr 2015 21:53:43 -  1.24
+++ distinfo22 Jun 2015 18:02:09 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.2.0.tar.gz) = 9a6VPxi6bz1VtGVWu79zRBNQ+f0iYlQCtyOiuB/2TzU=
-SIZE (R-3.2.0.tar.gz) = 29124927
+SHA256 (R-3.2.1.tar.gz) = 1Z28PwT0YEpc8PshC46nA+8kOLPuZf1atTbsUjT0yYI=
+SIZE (R-3.2.1.tar.gz) = 29197870
Index: patches/patch-Makefile_in
===
RCS file: /cvs/ports/math/R/patches/patch-Makefile_in,v
retrieving revision 1.7
diff -u -p -r1.7 patch-Makefile_in
--- patches/patch-Makefile_in   2 May 2015 09:22:58 -   1.7
+++ patches/patch-Makefile_in   22 Jun 2015 18:02:09 -
@@ -1,7 +1,5 @@
 $OpenBSD: patch-Makefile_in,v 1.7 2015/05/02 09:22:58 zhuk Exp $
 
-Do not build PDF versions of the R manuals
-
 --- Makefile.in.orig   Thu Mar 19 02:02:06 2015
 +++ Makefile.inSat May  2 11:47:48 2015
 @@ -82,8 +82,6 @@ vignettes: stamp-recommended
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.23
diff -u -p -r1.23 patch-configure
--- patches/patch-configure 2 May 2015 09:22:58 -   1.23
+++ patches/patch-configure 22 Jun 2015 18:02:09 -
@@ -1,65 +1,9 @@
 $OpenBSD: patch-configure,v 1.23 2015/05/02 09:22:58 zhuk Exp $
 
-Use GNU readline instead of our base readline
-
 Unbreak build on powerpc (relocation truncated to fit: R_PPC_GOT16...)
 
-Fix --export-dynamic linker flag
-
-Fix linking with external libintl
-
 --- configure.orig Thu Apr  9 01:16:36 2015
 +++ configure  Sat May  2 11:47:48 2015
-@@ -20921,12 +20921,12 @@ done
-   ## don't use the cached value as we need to rebuild LIBS
-   unset ac_cv_lib_readline_rl_callback_read_char
-   { $as_echo $as_me:${as_lineno-$LINENO}: checking for rl_callback_read_char 
in -lreadline 5
--$as_echo_n checking for rl_callback_read_char in -lreadline...  6; }
-+$as_echo_n checking for rl_callback_read_char in -lereadline...  6; }
- if ${ac_cv_lib_readline_rl_callback_read_char+:} false; then :
-   $as_echo_n (cached)  6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS=-lreadline  $LIBS
-+LIBS=-lereadline  $LIBS
- cat confdefs.h - _ACEOF conftest.$ac_ext
- /* end confdefs.h.  */
- 
-@@ -20961,7 +20961,7 @@ if test x$ac_cv_lib_readline_rl_callback_read_char =
- #define HAVE_LIBREADLINE 1
- _ACEOF
- 
--  LIBS=-lreadline $LIBS
-+  LIBS=-lereadline $LIBS
- 
- fi
- 
-@@ -21088,13 +21088,13 @@ fi
- 
- fi
- 
--{ $as_echo $as_me:${as_lineno-$LINENO}: checking for 
rl_callback_read_char in -lreadline 5
--$as_echo_n checking for rl_callback_read_char in -lreadline...  6; }
-+{ $as_echo $as_me:${as_lineno-$LINENO}: checking for 
rl_callback_read_char in -lereadline 5
-+$as_echo_n checking for rl_callback_read_char in -lereadline...  6

Re: UPDATE: math/R

2015-04-21 Thread Rafael Sadowski

On Fri Apr 17, 2015 at 05:37:32PM +0200, Ingo Feinerer wrote:
 Update of math/R to 3.2.0 (released yesterday):
 
 - Delete patches/patch-src_main_Rstrptime_h
   This patch was processed upstream (in modified form) upon my request:
   
 https://github.com/wch/r-source/commit/93efce2d8eb870b0554272f392d6a2343ba6ede8

Nice to see, good work Ingo.

 
 - Remove PREFIX and INSTALL* in FAKE_FLAGS and MAKE_FLAGS
   Builds and installs fine without.

looks okay for me

 
 - Remove all --with-* configure options which are true by default

ACK;

 
 - Add devel/libidn and net/curl in LIB_DEPENDS
   (based on make port-lib-depends-check)
   and adapt WANTLIB accordingly

okay for curl, but it's not set as default option true.

 
 - Avoid setting ac_cv_path_TAR as it works without

Are your sure, R pick up gtar?

 
 - Remove non-working mirrors from MASTER_SITES
 
 - Increase SHARED_LIBS R version number as the exported symbols changed
   (checked by comparing old and new library with nm -g).

ACK;

 
 Passes all tests and works with my personal R packages and scripts.
 Tested on amd64.

Tested on amd64. All regressions passed.


 
 Remarks:
 
 - I have
 
   LDFLAGS=-L/usr/local/lib
   CFLAGS=-I/usr/local/include
 
   in my .R/Makevars. This is very useful if you install packages which
   need to compile some C code at installation. Should this info be
   included in pkg/README?

I think it's a good advice.

 
 - Moreover, I am willing to take MAINTAINERship just in case Rafael
   Sadowski is no longer interested. I plan to provide updates in the
   future as well as I need a current R version for my work/research.
 

I'm interested but I think you're the better men for this port. You're
closer to the R community and (more or less) a daily R user on OpenBSD.
I will not stand in the way.

Cheers, Rafael

Re: UPDATE: math/R

2015-04-21 Thread Vadim Zhukov

21 апр. 2015 г. 9:12 пользователь Rafael Sadowski raf...@sizeofvoid.org
написал:

 On Fri Apr 17, 2015 at 05:37:32PM +0200, Ingo Feinerer wrote:
  Update of math/R to 3.2.0 (released yesterday):
 
  - Delete patches/patch-src_main_Rstrptime_h
This patch was processed upstream (in modified form) upon my request:
 
https://github.com/wch/r-source/commit/93efce2d8eb870b0554272f392d6a2343ba6ede8

 Nice to see, good work Ingo.

 
  - Remove PREFIX and INSTALL* in FAKE_FLAGS and MAKE_FLAGS
Builds and installs fine without.

 looks okay for me

 
  - Remove all --with-* configure options which are true by default

 ACK;

 
  - Add devel/libidn and net/curl in LIB_DEPENDS
(based on make port-lib-depends-check)
and adapt WANTLIB accordingly

 okay for curl, but it's not set as default option true.

 
  - Avoid setting ac_cv_path_TAR as it works without

 Are your sure, R pick up gtar?

 
  - Remove non-working mirrors from MASTER_SITES
 
  - Increase SHARED_LIBS R version number as the exported symbols changed
(checked by comparing old and new library with nm -g).

 ACK;

I see SHARED_LIBS minor bumped twice: 3.0 = 3.2. This should be 3.1
instead.

  Passes all tests and works with my personal R packages and scripts.
  Tested on amd64.

 Tested on amd64. All regressions passed.


 
  Remarks:
 
  - I have
 
LDFLAGS=-L/usr/local/lib
CFLAGS=-I/usr/local/include
 
in my .R/Makevars. This is very useful if you install packages which
need to compile some C code at installation. Should this info be
included in pkg/README?

 I think it's a good advice.

 
  - Moreover, I am willing to take MAINTAINERship just in case Rafael
Sadowski is no longer interested. I plan to provide updates in the
future as well as I need a current R version for my work/research.
 

 I'm interested but I think you're the better men for this port. You're
 closer to the R community and (more or less) a daily R user on OpenBSD.
 I will not stand in the way.

Given that there were problems in that area previously (PIC related), I
think this update worths trying on i386 before going in. If noone could do
that, I'll try do in the next few days.

If build will go smoothly, I'll commit the update (with SHARED_LIBS tweak
mentioned above).

--
Vadim Zhukov

First and foremost thanks and praises to Ingo for all the hard work
patching R and the guts for trying to push patches upstream (people who
complain about Theo's manners clearly never had to deal with Brian
Ripley).

On Tue, Apr 21, 2015 at 06:13:15PM +0200, Ingo Feinerer wrote:
On Tue, Apr 21, 2015 at 08:12:56AM +0200, Rafael Sadowski wrote:
- Add devel/libidn and net/curl in LIB_DEPENDS
(based on make port-lib-depends-check)
and adapt WANTLIB accordingly

okay for curl, but it's not set as default option true.

As far as I see there is no explicit configure option to enable/disable
it. If curl is there, it picks it up. So I added it to WANTLIB and
LIB_DEPENDS.

I don't think curl is a strict dependency, at least not at runtime. R
Installation and administration manual states that

libcurl version 7.28.0 or later can be used to support curlGetHeaders
and the libcurl methods of download.file and url.

but the help page for download.file says

For methods ‘wget’, ‘curl’ and ‘lynx’ a system call is made
to the tool given by ‘method’, and the respective program must be
installed on your system and be in the search path for executables.
They will block all other activity on the R process until they
complete: this may make a GUI unresponsive.

and

Method ‘wget’ is mainly for historical compatibility, but it and
‘curl’ can be used for URLs (e.g., ‘https://’ URLs or those that use
cookies) which the internal method does not support.

So I'm guessing its something R likes to have around for the
aforementioned methods of download.file and url, but not exactly
essential...

idn is needed by

R-3.2.0(math/R):
Missing: idn.17 from libidn-1.30 (/usr/local/lib/R/modules/internet.so)
WANTLIB += idn

so I added it as well.

- Avoid setting ac_cv_path_TAR as it works without

Are your sure, R pick up gtar?

I am pretty confident. The configure script checks for ${TAR} gtar
gnutar tar in that order. Since we do not set $TAR, gtar is found (as
we have it in BUILD_DEPENDS) and used.

Remarks:

- I have

LDFLAGS=-L/usr/local/lib
CFLAGS=-I/usr/local/include

in my .R/Makevars. This is very useful if you install packages which
need to compile some C code at installation. Should this info be
included in pkg/README?

I think it's a good advice.

I added a corresponding statement to pkg/README (based on
http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Customizing-package-compilation)

- Moreover, I am willing to take MAINTAINERship just in case Rafael
Sadowski is no longer interested. I plan to provide updates in the
future as well as I need a current R version for my work/research.

I'm interested but I think you're the better men for this port. You're
closer to the R community and (more or less) a daily R user on OpenBSD.
I will not stand in the way.

Thanks. On your approval I changed the MAINTAINER line as well. Future
updates will be posted to ports@ anyway, so you will be kept up-to-date
if something relevant happens.

Now to Vadim's comments:

I see SHARED_LIBS minor bumped twice: 3.0 = 3.2. This should be 3.1
instead.

Fixed. (The idea was to resemble that the R version is 3.2.)

Given that there were problems in that area previously (PIC related),
I think this update worths trying on i386 before going in. If noone
could do that, I'll try do in the next few days.

If build will go smoothly, I'll commit the update (with SHARED_LIBS
tweak mentioned above).

That would be great!

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.68
diff -u -p -u -p -r1.68 Makefile
--- Makefile 13 Apr 2015 10:41:13 - 1.68
+++ Makefile 21 Apr 2015 15:55:29 -
@@ -3,42 +3,38 @@
SHARED_ONLY= Yes

COMMENT= powerful math/statistics/graphics language
-DISTNAME=R-3.1.3
-REVISION=1
+DISTNAME=R-3.2.0

-SHARED_LIBS= R 3.0
+SHARED_LIBS= R 3.1
SHARED_LIBS+=Rlapack 31.2# 31.2
SHARED_LIBS+=Rblas 31.2# 31.2

CATEGORIES= math
HOMEPAGE=http://www.r-project.org/

-MAINTAINER= Rafael Sadowski raf...@sizeofvoid.org
+MAINTAINER= Ingo Feinerer feine...@logic.at

# GPL
PERMIT_PACKAGE_CDROM=Yes

-WANTLIB= ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
- ereadline fontconfig freetype glib-2.0 \
- gobject-2.0 icui18n icuuc jpeg lzma m \
+WANTLIB= ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
+ cairo ereadline fontconfig freetype glib-2.0 \
+ gobject-2.0 icui18n icuuc idn jpeg lzma m \
ncurses pango-1.0 pangocairo-1.0 \
- pangoft2-1.0 pcre png pthread tiff z \
+ pangoft2-1.0 pcre png pthread ssl tiff z \

Re: UPDATE: math/R

2015-04-21 Thread Ingo Feinerer

On Tue, Apr 21, 2015 at 08:12:56AM +0200, Rafael Sadowski wrote:
  - Add devel/libidn and net/curl in LIB_DEPENDS
(based on make port-lib-depends-check)
and adapt WANTLIB accordingly
 
 okay for curl, but it's not set as default option true.

As far as I see there is no explicit configure option to enable/disable
it. If curl is there, it picks it up. So I added it to WANTLIB and
LIB_DEPENDS.

idn is needed by

R-3.2.0(math/R):
Missing: idn.17 from libidn-1.30 (/usr/local/lib/R/modules/internet.so)
WANTLIB += idn

so I added it as well.

  - Avoid setting ac_cv_path_TAR as it works without
 
 Are your sure, R pick up gtar?

I am pretty confident. The configure script checks for ${TAR} gtar
gnutar tar in that order. Since we do not set $TAR, gtar is found (as
we have it in BUILD_DEPENDS) and used.

  Remarks:
  
  - I have
  
LDFLAGS=-L/usr/local/lib
CFLAGS=-I/usr/local/include
  
in my .R/Makevars. This is very useful if you install packages which
need to compile some C code at installation. Should this info be
included in pkg/README?
 
 I think it's a good advice.

I added a corresponding statement to pkg/README (based on
http://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Customizing-package-compilation)

  - Moreover, I am willing to take MAINTAINERship just in case Rafael
Sadowski is no longer interested. I plan to provide updates in the
future as well as I need a current R version for my work/research.
  
 
 I'm interested but I think you're the better men for this port. You're
 closer to the R community and (more or less) a daily R user on OpenBSD.
 I will not stand in the way.

Thanks. On your approval I changed the MAINTAINER line as well. Future
updates will be posted to ports@ anyway, so you will be kept up-to-date
if something relevant happens.

Now to Vadim's comments:

 I see SHARED_LIBS minor bumped twice: 3.0 = 3.2. This should be 3.1
 instead.

Fixed. (The idea was to resemble that the R version is 3.2.)

 Given that there were problems in that area previously (PIC related),
 I think this update worths trying on i386 before going in. If noone
 could do that, I'll try do in the next few days.

 If build will go smoothly, I'll commit the update (with SHARED_LIBS
 tweak mentioned above).

That would be great!

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.68
diff -u -p -u -p -r1.68 Makefile
--- Makefile13 Apr 2015 10:41:13 -  1.68
+++ Makefile21 Apr 2015 15:55:29 -
@@ -3,42 +3,38 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.1.3
-REVISION=  1
+DISTNAME=  R-3.2.0
 
-SHARED_LIBS=   R   3.0
+SHARED_LIBS=   R   3.1
 SHARED_LIBS+=  Rlapack 31.2# 31.2
 SHARED_LIBS+=  Rblas   31.2# 31.2
 
 CATEGORIES=math
 HOMEPAGE=  http://www.r-project.org/
 
-MAINTAINER=Rafael Sadowski raf...@sizeofvoid.org
+MAINTAINER=Ingo Feinerer feine...@logic.at
 
 # GPL
 PERMIT_PACKAGE_CDROM=  Yes
 
-WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
-   ereadline fontconfig freetype glib-2.0 \
-   gobject-2.0 icui18n icuuc jpeg lzma m \
+WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
+   cairo ereadline fontconfig freetype glib-2.0 \
+   gobject-2.0 icui18n icuuc idn jpeg lzma m \
ncurses pango-1.0 pangocairo-1.0 \
-   pangoft2-1.0 pcre png pthread tiff z \
+   pangoft2-1.0 pcre png pthread ssl tiff z \
${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB}
 
 MASTER_SITES=  http://cran.r-project.org/src/base/R-3/ \
ftp://cran.r-project.org/pub/R/src/base/R-3/ \
ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://cran.at.r-project.org/src/base/R-3/ \
-   http://cran.au.r-project.org/src/base/R-3/ \
http://cran.br.r-project.org/src/base/R-3/ \
http://cran.ch.r-project.org/src/base/R-3/ \
http://cran.dk.r-project.org/src/base/R-3/ \
http://cran.es.r-project.org/src/base/R-3/ \
-   http://cran.hu.r-project.org/src/base/R-3/ \
http://cran.stat.ucla.edu/src/base/R-3/ \
http://cran.uk.r-project.org/src/base/R-3/ \
http://cran.us.r-project.org/src/base/R-3/ \
-   http://cran.za.r-project.org/src/base/R-3/ \
http://lib.stat.cmu.edu/R/CRAN/src/base/R-3/ \
http://probability.ca/cran/src/base/R-3/
 
@@ -59,12 +55,14 @@ LIB_DEPENDS=${MODFORTRAN_LIB_DEPENDS} \
archivers/bzip2 \
archivers/xz \
devel/glib2 \
+   devel/libidn \
devel/pango \
devel/readline \
graphics/cairo \
graphics/jpeg \

UPDATE: math/R

2015-04-17 Thread Ingo Feinerer

Update of math/R to 3.2.0 (released yesterday):

- Delete patches/patch-src_main_Rstrptime_h
  This patch was processed upstream (in modified form) upon my request:
  
https://github.com/wch/r-source/commit/93efce2d8eb870b0554272f392d6a2343ba6ede8

- Remove PREFIX and INSTALL* in FAKE_FLAGS and MAKE_FLAGS
  Builds and installs fine without.

- Remove all --with-* configure options which are true by default

- Add devel/libidn and net/curl in LIB_DEPENDS
  (based on make port-lib-depends-check)
  and adapt WANTLIB accordingly

- Avoid setting ac_cv_path_TAR as it works without

- Remove non-working mirrors from MASTER_SITES

- Increase SHARED_LIBS R version number as the exported symbols changed
  (checked by comparing old and new library with nm -g).

Passes all tests and works with my personal R packages and scripts.
Tested on amd64.

Remarks:

- I have

  LDFLAGS=-L/usr/local/lib
  CFLAGS=-I/usr/local/include

  in my .R/Makevars. This is very useful if you install packages which
  need to compile some C code at installation. Should this info be
  included in pkg/README?

- Moreover, I am willing to take MAINTAINERship just in case Rafael
  Sadowski is no longer interested. I plan to provide updates in the
  future as well as I need a current R version for my work/research.

Best regards,
Ingo

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.68
diff -u -p -u -p -r1.68 Makefile
--- Makefile13 Apr 2015 10:41:13 -  1.68
+++ Makefile17 Apr 2015 15:10:48 -
@@ -3,10 +3,9 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.1.3
-REVISION=  1
+DISTNAME=  R-3.2.0
 
-SHARED_LIBS=   R   3.0
+SHARED_LIBS=   R   3.2
 SHARED_LIBS+=  Rlapack 31.2# 31.2
 SHARED_LIBS+=  Rblas   31.2# 31.2
 
@@ -18,27 +17,24 @@ MAINTAINER= Rafael Sadowski rafael@size
 # GPL
 PERMIT_PACKAGE_CDROM=  Yes
 
-WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
-   ereadline fontconfig freetype glib-2.0 \
-   gobject-2.0 icui18n icuuc jpeg lzma m \
+WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c crypto curl \
+   cairo ereadline fontconfig freetype glib-2.0 \
+   gobject-2.0 icui18n icuuc idn jpeg lzma m \
ncurses pango-1.0 pangocairo-1.0 \
-   pangoft2-1.0 pcre png pthread tiff z \
+   pangoft2-1.0 pcre png pthread ssl tiff z \
${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB}
 
 MASTER_SITES=  http://cran.r-project.org/src/base/R-3/ \
ftp://cran.r-project.org/pub/R/src/base/R-3/ \
ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://cran.at.r-project.org/src/base/R-3/ \
-   http://cran.au.r-project.org/src/base/R-3/ \
http://cran.br.r-project.org/src/base/R-3/ \
http://cran.ch.r-project.org/src/base/R-3/ \
http://cran.dk.r-project.org/src/base/R-3/ \
http://cran.es.r-project.org/src/base/R-3/ \
-   http://cran.hu.r-project.org/src/base/R-3/ \
http://cran.stat.ucla.edu/src/base/R-3/ \
http://cran.uk.r-project.org/src/base/R-3/ \
http://cran.us.r-project.org/src/base/R-3/ \
-   http://cran.za.r-project.org/src/base/R-3/ \
http://lib.stat.cmu.edu/R/CRAN/src/base/R-3/ \
http://probability.ca/cran/src/base/R-3/
 
@@ -59,12 +55,14 @@ LIB_DEPENDS=${MODFORTRAN_LIB_DEPENDS} \
archivers/bzip2 \
archivers/xz \
devel/glib2 \
+   devel/libidn \
devel/pango \
devel/readline \
graphics/cairo \
graphics/jpeg \
graphics/png \
graphics/tiff \
+   net/curl \
textproc/icu4c
 
 RUN_DEPENDS=   archivers/gtar \
@@ -82,17 +80,7 @@ CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
--enable-BLAS-shlib \
--enable-R-shlib \
--enable-prebuilt-html \
-   --with-ICU \
-   --with-cairo \
-   --with-jpeglib \
-   --with-libpng \
-   --with-libtiff \
-   --with-readline \
-   --with-system-bzlib \
-   --with-system-pcre \
-   --with-system-xz \
--with-tcl-config=${MODTCL_CONFIG} \
-   --with-tcltk \
--with-tk-config=${MODTK_CONFIG}
 
 CONFIGURE_ENV= FFLAGS=${FFLAGS} \
@@ -100,21 +88,11 @@ CONFIGURE_ENV= FFLAGS=${FFLAGS} \
LDFLAGS=-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib \
LIBnn=lib \
ac_cv_path_PDFLATEX= \
-   ac_cv_path_TAR=${LOCALBASE}/bin/gtar \
rdocdir=${PREFIX}/share/doc/R
 
-MAKE_FLAGS=

Re: UPDATE: math/R

2015-03-26 Thread David Coppa

On Thu, 26 Mar 2015, Vadim Zhukov wrote:

 Please, don't remove patches that allow to avoid texlive dependency.
 They do help heavily in bulk builds. The best would be to find way to
 be able do it either way - by picking up automatically during
 configure state, or forcing state with configure switches/environment.
 If that's too hard or won't be accepted upstream, then those patches
 should stay in.

Also, R requires the inconsolata.sty package[1] to build the PDF
manuals, which is not in texlive_base:

dcoppa@t420:/usr/ports/print/texlive$ grep -r inconsolata.sty * 
texmf/pkg/PLIST-full:share/texmf-dist/tex/latex/inconsolata/inconsolata.sty

So you'd need a build dependency on the full TeXLive package: simply
impractical.

[1] checking for tex... /usr/local/bin/tex
checking for pdftex... /usr/local/bin/pdftex
checking for pdflatex... /usr/local/bin/pdflatex
checking for makeindex... /usr/local/bin/makeindex
checking for makeinfo... /usr/bin/makeinfo
checking whether makeinfo version is at least 4.7... yes
checking for ginstall-info... no
checking for install-info... /usr/bin/install-info
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/local/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes 
and package manuals will not be rendered optimally

Ciao!
David

Re: UPDATE: math/R

2015-03-26 Thread Stuart Henderson

On 2015/03/25 20:13, Ingo Feinerer wrote:
 - Deleted patch-src_main_connections_c
..
   For the signed char c vs. char c I see no difference in this use case.
   But maybe because of my amd64 platform.
 
 - Deleted patch-src_main_gram_y
   Again signed char c vs. char c

If you want to remove these, you need to test on powerpc or arm.

Re: UPDATE: math/R

2015-03-25 Thread Vadim Zhukov

2015-03-25 22:13 GMT+03:00 Ingo Feinerer feine...@logic.at:
 Dear OpenBSD useRs,

 please consider the following update of math/R to 3.1.3.

 Although this update is minor (3.1.2 - 3.1.3) the diff is quite large
 as I used the opportunity to get rid of as many patches as possible. The
 plan is to make future updates (like to 3.2.0 which is scheduled for
 2015-04-16) a lot easier.

 The current proposed diff builds fine for me on amd64 and passes the
 same regression tests as 3.1.2 with all patches did. Moreover, all my
 private R scripts run without problems with this new patch-reduced
 version.

 Please find below a detailed list of comments for each modified/deleted
 patch. I appreciate all comments.

 - Deleted patch-Makeconf_in
   Replaced by MAKE_FLAGS += DYLIB_EXT=.so.${LIBR_VERSION}

 - patch-Makefile_in
   Build and install PDFs; works with BUILD_DEPENDS=print/texlive/base

 - patch-configure
   -Wl,-export-dynamic appears to work as well
   DYLIB_EXT correctly set by MAKE_FLAGS += DYLIB_EXT=.so.${LIBR_VERSION}

 - Deleted patch-doc_Makefile_in
   Build NEWS.pdf; works with BUILD_DEPENDS=print/texlive/base

 - Deleted patch-etc_Makeconf_in
   Replaced by MAKE_FLAGS += DYLIB_EXT=.so.${LIBR_VERSION}

 - Deleted patch-src_appl_Makefile_in
   Replaced by MAKE_FLAGS += Rblas_la=libRblas.so.${LIBRblas_VERSION}

 - Deleted patch-src_extra_blas_Makefile_in
   Replaced by MAKE_FLAGS += Rblas_la=libRblas.so.${LIBRblas_VERSION}

 - Deleted patch-src_include_R_ext_eventloop_h
   Not needed; works without

 - Deleted patch-src_main_CommandLineArgs_c
   10 years old patch, unchanged for 10 years upstream, just syntactic sugar

 - patch-src_main_Makefile_in
   DYLIB_EXT correctly set by MAKE_FLAGS += DYLIB_EXT=.so.${LIBR_VERSION}

 - Deleted patch-src_main_connections_c
   Not strictly needed. This patches replaces one vsprintf with vsnprintf
   but there are many similar cases that could be addressed. So skip this
   one as well to minimize differences.
   For the signed char c vs. char c I see no difference in this use case.
   But maybe because of my amd64 platform.

 - Deleted patch-src_main_gram_y
   Again signed char c vs. char c

 - Deleted patch-src_main_main_c
   I was not able to reproduce the warning failed to set alternate
   signal stack

 - Deleted patch-src_main_platform_c
   The port also builds without this patch with USE_SYSTRACE=Yes for me

 - Deleted patch-src_modules_lapack_Makefile_in
   Replaced by MAKE_FLAGS += Rlapack_la=libRlapack.so.$(LIBRlapack_VERSION)

 - Deleted patch-src_nmath_standalone_Makefile_in
   DYLIB_EXT correctly set by MAKE_FLAGS += DYLIB_EXT=.so.${LIBR_VERSION}

 - Deleted patch-src_scripts_config
   DYLIB_EXT correctly set by MAKE_FLAGS += DYLIB_EXT=.so.${LIBR_VERSION}

 Moreover, I sent patch-src_main_Rstrptime_h upstream. Let's see if it
 gets processed and accepted.

Please, don't remove patches that allow to avoid texlive dependency.
They do help heavily in bulk builds. The best would be to find way to
be able do it either way - by picking up automatically during
configure state, or forcing state with configure switches/environment.
If that's too hard or won't be accepted upstream, then those patches
should stay in.

--
  WBR,
  Vadim Zhukov

Re: UPDATE: math/R 3.1.2

2015-01-20 Thread Vadim Zhukov

2014-12-21 23:06 GMT+03:00 Rafael Sadowski raf...@sizeofvoid.org:
 Hey @ports,

 Christmas and holiday season is OpenBSD-ports season.

 Here is an update for math/R.

 - update to Version 3.2.1- New FLAVOR java
 - documentation goes in /usr/local/share/doc/R
 - New FLAVOR java
 -- ... idea and README from David Coppa - thanks David
 - sorted in Makefile

 Tested @amd64.

 Regards,

 Rafael Sadowksi


 Index: Makefile
 ===
 RCS file: /cvs/ports/math/R/Makefile,v
 retrieving revision 1.63
 diff -u -p -u -p -r1.63 Makefile
 --- Makefile2 Sep 2014 14:55:37 -   1.63
 +++ Makefile21 Dec 2014 19:55:22 -
 @@ -3,7 +3,7 @@
  SHARED_ONLY=   Yes

  COMMENT=   powerful math/statistics/graphics language
 -DISTNAME=  R-3.1.1
 +DISTNAME=  R-3.1.2

  SHARED_LIBS=   R   2.1 # 2.1
  SHARED_LIBS+=  Rlapack 31.2# 31.2
 @@ -17,6 +17,9 @@ MAINTAINER=   Rafael Sadowski rafael@size
  # GPL
  PERMIT_PACKAGE_CDROM=  Yes

 +FLAVORS=java
 +FLAVOR?=
 +
  WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
 ereadline fontconfig freetype glib-2.0 \
 gobject-2.0 icui18n icuuc jpeg lzma m \
 @@ -26,19 +29,19 @@ WANTLIB=ICE SM X11 Xext Xmu Xss Xt bz2

  MASTER_SITES=  http://cran.r-project.org/src/base/R-3/ \
 ftp://cran.r-project.org/pub/R/src/base/R-3/ \
 +   ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
 http://cran.at.r-project.org/src/base/R-3/ \
 http://cran.au.r-project.org/src/base/R-3/ \
 http://cran.br.r-project.org/src/base/R-3/ \
 http://cran.ch.r-project.org/src/base/R-3/ \
 -   http://cran.es.r-project.org/src/base/R-3/ \
 http://cran.dk.r-project.org/src/base/R-3/ \
 +   http://cran.es.r-project.org/src/base/R-3/ \
 http://cran.hu.r-project.org/src/base/R-3/ \
 +   http://cran.stat.ucla.edu/src/base/R-3/ \
 http://cran.uk.r-project.org/src/base/R-3/ \
 http://cran.us.r-project.org/src/base/R-3/ \
 http://cran.za.r-project.org/src/base/R-3/ \
 -   ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
 http://lib.stat.cmu.edu/R/CRAN/src/base/R-3/ \
 -   http://cran.stat.ucla.edu/src/base/R-3/ \
 http://probability.ca/cran/src/base/R-3/

  MODULES=   fortran \
 @@ -52,6 +55,7 @@ BUILD_DEPENDS=${MODFORTRAN_BUILD_DEPEND
 archivers/unzip \
 archivers/zip \
 devel/xdg-utils
 +
  LIB_DEPENDS=   ${MODFORTRAN_LIB_DEPENDS} \
 ${MODTK_LIB_DEPENDS} \
 archivers/bzip2 \
 @@ -64,15 +68,20 @@ LIB_DEPENDS=${MODFORTRAN_LIB_DEPENDS} \
 graphics/png \
 graphics/tiff \
 textproc/icu4c
 +
  RUN_DEPENDS=   archivers/gtar \
 archivers/unzip \
 archivers/zip \
 devel/gmake \
 -   devel/xdg-utils
 +   devel/xdg-utils \
 +   print/texlive/base

  CONFIGURE_STYLE=gnu
 +
  MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
 +
  CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
 +   rdocdir=${LOCALBASE}/share/doc/R \
 --enable-BLAS-shlib \
 --enable-R-shlib \
 --enable-prebuilt-html \
 @@ -85,8 +94,8 @@ CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
 --with-system-bzlib \
 --with-system-pcre \
 --with-system-xz \
 -   --with-tcltk \
 --with-tcl-config=${MODTCL_CONFIG} \
 +   --with-tcltk \
 --with-tk-config=${MODTK_CONFIG}

  CONFIGURE_ENV= FFLAGS=${FFLAGS} \
 @@ -113,9 +122,16 @@ USE_GMAKE= Yes

  TEXMFLOCAL=${PREFIX}/share/texmf-local

 +# see README-java
 +.if ${FLAVOR:Mjava}
 +MODULES+=  java
 +MODJAVA_VER=   1.7+
 +RUN_DEPENDS+=  java/javaPathHelper
 +CONFIGURE_ENV+= JAVA_HOME=`${TRUEPREFIX}/bin/javaPathHelper -h R`
 +.endif
 +
  post-install:
 mv ${WRKINST}/${LOCALBASE}/lib/R/share/texmf ${TEXMFLOCAL}
 @perl -i -pe 's:^R_HOME_DIR=.*:R_HOME_DIR=${TRUEPREFIX}/lib/R:' \
 ${PREFIX}/bin/R
 -
  .include bsd.port.mk
 Index: distinfo
 ===
 RCS file: /cvs/ports/math/R/distinfo,v
 retrieving revision 1.21
 diff -u -p -u -p -r1.21 distinfo
 --- distinfo2 Sep 2014 14:55:37 -   1.21
 +++ distinfo21 Dec 2014 19:55:22 -
 @@ -1,2 +1,2 @@
 -SHA256 (R-3.1.1.tar.gz) = zlxNXjRBTOjx7C1WQoYUNfod3EzYm9M2Fyu+JaYsehk=
 -SIZE (R-3.1.1.tar.gz) = 28606569
 +SHA256 (R-3.1.2.tar.gz) = vNFQr8rg4C9u+181pqtyQyvoLoSexSzgu4nYw0Ko+no=
 +SIZE (R-3.1.2.tar.gz) = 28655941
 Index: pkg/PLIST
 ===
 RCS file:

Re: UPDATE: math/R 3.1.2

2015-01-20 Thread David Coppa

On Tue, Jan 20, 2015 at 7:02 PM, Vadim Zhukov persg...@gmail.com wrote:

 Can't this be done in post-install target rather instead?

 Why does separate FLAVOR needed, I see no FLAVOR-specific files in
 diff? Is JDK really used at the build time?

Vadim, this is an old diff.
I've already committed a different one.

cheers,
David

Re: UPDATE: math/R 3.1.2

2015-01-20 Thread Vadim Zhukov

2015-01-20 23:10 GMT+03:00 David Coppa dco...@gmail.com:
 On Tue, Jan 20, 2015 at 7:02 PM, Vadim Zhukov persg...@gmail.com wrote:

 Can't this be done in post-install target rather instead?

 Why does separate FLAVOR needed, I see no FLAVOR-specific files in
 diff? Is JDK really used at the build time?

 Vadim, this is an old diff.
 I've already committed a different one.

Ah, okay. I'm going through backlog now, sorry for the noise.

--
  WBR,
  Vadim Zhukov

UPDATE: math/R 3.1.2

2014-12-21 Thread Rafael Sadowski

Hey @ports,

Christmas and holiday season is OpenBSD-ports season.

Here is an update for math/R.

- update to Version 3.2.1- New FLAVOR java
- documentation goes in /usr/local/share/doc/R
- New FLAVOR java
-- ... idea and README from David Coppa - thanks David
- sorted in Makefile

Tested @amd64.

Regards,

Rafael Sadowksi


Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.63
diff -u -p -u -p -r1.63 Makefile
--- Makefile2 Sep 2014 14:55:37 -   1.63
+++ Makefile21 Dec 2014 19:55:22 -
@@ -3,7 +3,7 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.1.1
+DISTNAME=  R-3.1.2
 
 SHARED_LIBS=   R   2.1 # 2.1
 SHARED_LIBS+=  Rlapack 31.2# 31.2
@@ -17,6 +17,9 @@ MAINTAINER=   Rafael Sadowski rafael@size
 # GPL
 PERMIT_PACKAGE_CDROM=  Yes
 
+FLAVORS=java
+FLAVOR?=
+
 WANTLIB=   ICE SM X11 Xext Xmu Xss Xt bz2 c cairo \
ereadline fontconfig freetype glib-2.0 \
gobject-2.0 icui18n icuuc jpeg lzma m \
@@ -26,19 +29,19 @@ WANTLIB=ICE SM X11 Xext Xmu Xss Xt bz2 
 
 MASTER_SITES=  http://cran.r-project.org/src/base/R-3/ \
ftp://cran.r-project.org/pub/R/src/base/R-3/ \
+   ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://cran.at.r-project.org/src/base/R-3/ \
http://cran.au.r-project.org/src/base/R-3/ \
http://cran.br.r-project.org/src/base/R-3/ \
http://cran.ch.r-project.org/src/base/R-3/ \
-   http://cran.es.r-project.org/src/base/R-3/ \
http://cran.dk.r-project.org/src/base/R-3/ \
+   http://cran.es.r-project.org/src/base/R-3/ \
http://cran.hu.r-project.org/src/base/R-3/ \
+   http://cran.stat.ucla.edu/src/base/R-3/ \
http://cran.uk.r-project.org/src/base/R-3/ \
http://cran.us.r-project.org/src/base/R-3/ \
http://cran.za.r-project.org/src/base/R-3/ \
-   ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-3/ \
http://lib.stat.cmu.edu/R/CRAN/src/base/R-3/ \
-   http://cran.stat.ucla.edu/src/base/R-3/ \
http://probability.ca/cran/src/base/R-3/
 
 MODULES=   fortran \
@@ -52,6 +55,7 @@ BUILD_DEPENDS=${MODFORTRAN_BUILD_DEPEND
archivers/unzip \
archivers/zip \
devel/xdg-utils
+
 LIB_DEPENDS=   ${MODFORTRAN_LIB_DEPENDS} \
${MODTK_LIB_DEPENDS} \
archivers/bzip2 \
@@ -64,15 +68,20 @@ LIB_DEPENDS=${MODFORTRAN_LIB_DEPENDS} \
graphics/png \
graphics/tiff \
textproc/icu4c
+
 RUN_DEPENDS=   archivers/gtar \
archivers/unzip \
archivers/zip \
devel/gmake \
-   devel/xdg-utils
+   devel/xdg-utils \
+   print/texlive/base
 
 CONFIGURE_STYLE=gnu
+
 MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
+
 CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
+   rdocdir=${LOCALBASE}/share/doc/R \
--enable-BLAS-shlib \
--enable-R-shlib \
--enable-prebuilt-html \
@@ -85,8 +94,8 @@ CONFIGURE_ARGS= ${CONFIGURE_SHARED} \
--with-system-bzlib \
--with-system-pcre \
--with-system-xz \
-   --with-tcltk \
--with-tcl-config=${MODTCL_CONFIG} \
+   --with-tcltk \
--with-tk-config=${MODTK_CONFIG}
 
 CONFIGURE_ENV= FFLAGS=${FFLAGS} \
@@ -113,9 +122,16 @@ USE_GMAKE= Yes
 
 TEXMFLOCAL=${PREFIX}/share/texmf-local
 
+# see README-java
+.if ${FLAVOR:Mjava}
+MODULES+=  java
+MODJAVA_VER=   1.7+
+RUN_DEPENDS+=  java/javaPathHelper
+CONFIGURE_ENV+= JAVA_HOME=`${TRUEPREFIX}/bin/javaPathHelper -h R`
+.endif
+
 post-install:
mv ${WRKINST}/${LOCALBASE}/lib/R/share/texmf ${TEXMFLOCAL}
@perl -i -pe 's:^R_HOME_DIR=.*:R_HOME_DIR=${TRUEPREFIX}/lib/R:' \
${PREFIX}/bin/R
-
 .include bsd.port.mk
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.21
diff -u -p -u -p -r1.21 distinfo
--- distinfo2 Sep 2014 14:55:37 -   1.21
+++ distinfo21 Dec 2014 19:55:22 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.1.1.tar.gz) = zlxNXjRBTOjx7C1WQoYUNfod3EzYm9M2Fyu+JaYsehk=
-SIZE (R-3.1.1.tar.gz) = 28606569
+SHA256 (R-3.1.2.tar.gz) = vNFQr8rg4C9u+181pqtyQyvoLoSexSzgu4nYw0Ko+no=
+SIZE (R-3.1.2.tar.gz) = 28655941
Index: pkg/PLIST
===
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.23
diff -u -p -u -p -r1.23 PLIST
--- pkg/PLIST   2 Sep 2014 14:55:37 -   1.23
+++ pkg/PLIST   21 Dec 2014 19:55:22 -
@@ -1,4 +1,4 @@

Re: UPDATE: math/R 3.0.3 - 3.1.0

2014-05-15 Thread Rafael Sadowski

On Sun May 04, 2014 at 01:40:22PM +0200, Rafael Sadowski wrote:
 On Fri May 02, 2014 at 11:03:29PM +0200, Rafael Sadowski wrote:
  Hi @ports and R-users,
  
  attached is an maintainer-update for mathe/R. All test pass @amd64.
  
  - Update  3.0.3 = 3.1.0
  - SHARED_LIBS-syntax, okay?
  
  Comments? OKs? 
  
  cheers, Rafael
  
  
   @exec %D/bin/mktexlsr  /dev/null 21
  -@unexec-delete %D/bin/mktexlsr  /dev/null 21
  +@unexec-delete %D/bin/mktexlsr  /dev/null 2
  
  ups, this is wrong.

okay, heads up, correct and 100% working (all tests pass) R ports
update.

comments? okays? commit it, please!


cheers Rafael


Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.61
diff -u -p -u -r1.61 Makefile
--- Makefile24 Mar 2014 09:08:46 -  1.61
+++ Makefile15 May 2014 16:35:00 -
@@ -3,11 +3,11 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.0.3
+DISTNAME=  R-3.1.0
 
-SHARED_LIBS=   R   2.0  \
-   Rlapack 31.1 \
-   Rblas   31.0
+SHARED_LIBS=   R   2.1 # 2.0
+SHARED_LIBS+=  Rlapack 31.2# 31.1
+SHARED_LIBS+=  Rblas   31.1# 31.0
 
 CATEGORIES=math
 HOMEPAGE=  http://www.r-project.org/
@@ -41,7 +41,10 @@ MASTER_SITES=http://cran.r-project.org/
http://cran.stat.ucla.edu/src/base/R-3/ \
http://probability.ca/cran/src/base/R-3/
 
-MODULES=   fortran devel/gettext x11/tk
+MODULES=   fortran \
+   devel/gettext \
+   x11/tk
+
 MODFORTRAN_COMPILER= gfortran
 
 BUILD_DEPENDS= ${MODFORTRAN_BUILD_DEPENDS} \
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.19
diff -u -p -u -r1.19 distinfo
--- distinfo12 Mar 2014 11:04:41 -  1.19
+++ distinfo15 May 2014 16:35:00 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.0.3.tar.gz) = uXz9lUDylKt4boRhU/PdhgVhDX4nYWv7QpZ5W8T95tY=
-SIZE (R-3.0.3.tar.gz) = 28075821
+SHA256 (R-3.1.0.tar.gz) = imgDkPhMWMAdze/Wguqg6QOJ8J5tLy4JDHGvQAZfX+I=
+SIZE (R-3.1.0.tar.gz) = 28469975
Index: patches/patch-Makeconf_in
===
RCS file: patches/patch-Makeconf_in
diff -N patches/patch-Makeconf_in
--- patches/patch-Makeconf_in   12 Mar 2014 11:04:41 -  1.2
+++ /dev/null   1 Jan 1970 00:00:00 -
@@ -1,11 +0,0 @@
-$OpenBSD: patch-Makeconf_in,v 1.2 2014/03/12 11:04:41 dcoppa Exp $
 Makeconf.in.orig   Wed Mar  6 00:02:46 2013
-+++ Makeconf.inMon May 27 14:00:25 2013
-@@ -19,7 +19,6 @@ CPICFLAGS = @CPICFLAGS@
- CPPFLAGS = @CPPFLAGS@
- DEFS = @DEFS@ @R_DEFS@
- DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude=*.o 
--exclude=*$(SHLIB_EXT) --exclude=*~
--DYLIB_EXT = @DYLIB_EXT@
- DYLIB_LD = @DYLIB_LD@
- DYLIB_LDFLAGS = @DYLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(DYLIBS_LTO)
- DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
Index: patches/patch-Makefile_in
===
RCS file: /cvs/ports/math/R/patches/patch-Makefile_in,v
retrieving revision 1.3
diff -u -p -u -r1.3 patch-Makefile_in
--- patches/patch-Makefile_in   12 Mar 2014 11:04:41 -  1.3
+++ patches/patch-Makefile_in   15 May 2014 16:35:00 -
@@ -1,75 +1,20 @@
-$OpenBSD: patch-Makefile_in,v 1.3 2014/03/12 11:04:41 dcoppa Exp $
+$OpenBSD$
 
 Do not build PDF versions of the R manuals
 
 Makefile.in.orig   Tue Sep 10 00:05:05 2013
-+++ Makefile.inTue Feb  4 09:15:53 2014
-@@ -95,7 +95,7 @@ install install-strip: installdirs svnonly
-   @for f in $(INSTFILES); do \
- $(INSTALL_DATA) $(srcdir)/$${f} $(DESTDIR)$(rhome); \
-   done
--  @for f in NEWS NEWS.pdf $(NON_SVN_INSTFILES); do \
-+  @for f in NEWS $(NON_SVN_INSTFILES); do \
- $(INSTALL_DATA) $${f} $(DESTDIR)$(rhome); \
-   done
- @WANT_R_FRAMEWORK_TRUE@   $(MAKE) -f $(srcdir)/Makefile.fw 
top_srcdir=$(top_srcdir) $@
-@@ -121,7 +121,7 @@ svnonly:
- fi \
-   fi
- 
--libR_la = lib/libR$(DYLIB_EXT)
-+libR_la = lib/libR.so.$(LIBR_VERSION)
- install-libR:
-   @if test -f $(libR_la); then $(MAKE) install-libR-exists; fi
- install-libR-exists:
-@@ -133,13 +133,13 @@ installdirs:
- uninstall:
-   @(for d in $(SUBDIRS); do rsd=$${d} $${rsd}; done; \
- for d in $${rsd}; do (cd $${d}  $(MAKE) $@); done)
--  @for f in NEWS NEWS.pdf $(INSTFILES) $(NON_SVN_INSTFILES); do \
-+  @for f in NEWS  $(INSTFILES) $(NON_SVN_INSTFILES); do \
- rm -f $(DESTDIR)$(rhome)/$${f}; \
-   done
-   @rm -rf $(DESTDIR)$(Rexecbindir) $(DESTDIR)$(rhome)/lib
-   @rmdir $(DESTDIR)$(rhome) 2/dev/null \
-   || $(ECHO)   dir $(DESTDIR)$(rhome) not removed
--  @rm -f $(DESTDIR)${libdir}/libR$(DYLIB_EXT)
-+  @rm -f $(DESTDIR)${libdir}/libR.so.$(LIBR_VERSION)
- 
- mostlyclean: clean

Re: UPDATE: math/R 3.0.3 - 3.1.0

2014-05-15 Thread Zé Loff

On Thu, May 15, 2014 at 06:41:56PM +0200, Rafael Sadowski wrote:
 On Sun May 04, 2014 at 01:40:22PM +0200, Rafael Sadowski wrote:
  On Fri May 02, 2014 at 11:03:29PM +0200, Rafael Sadowski wrote:
   Hi @ports and R-users,
   
   attached is an maintainer-update for mathe/R. All test pass @amd64.
   
   - Update  3.0.3 = 3.1.0
   - SHARED_LIBS-syntax, okay?
   
   Comments? OKs? 
   
   cheers, Rafael
   
   
@exec %D/bin/mktexlsr  /dev/null 21
   -@unexec-delete %D/bin/mktexlsr  /dev/null 21
   +@unexec-delete %D/bin/mktexlsr  /dev/null 2
   
   ups, this is wrong.
 
 okay, heads up, correct and 100% working (all tests pass) R ports
 update.
 
 comments? okays? commit it, please!

Sorry for coming late to the show, but I just realised that the X11cairo
plotting device is not working properly on R 3.0.3, running on amd64
-current. To be more specific, parts of the plot aren't immediately
drawn when the device comes up or when resizing the plot's window.

Can anyone reproduce this?

Cheers
Zé

--

Re: UPDATE: math/R 3.0.3 - 3.1.0

2014-05-04 Thread Rafael Sadowski

On Fri May 02, 2014 at 11:03:29PM +0200, Rafael Sadowski wrote:
 Hi @ports and R-users,
 
 attached is an maintainer-update for mathe/R. All test pass @amd64.
 
 - Update  3.0.3 = 3.1.0
 - SHARED_LIBS-syntax, okay?
 
 Comments? OKs? 
 
 cheers, Rafael
 
 
  @exec %D/bin/mktexlsr  /dev/null 21
 -@unexec-delete %D/bin/mktexlsr  /dev/null 21
 +@unexec-delete %D/bin/mktexlsr  /dev/null 2
 
 ups, this is wrong.

UPDATE: math/R 3.0.3 - 3.1.0

2014-05-02 Thread Rafael Sadowski

Hi @ports and R-users,

attached is an maintainer-update for mathe/R. All test pass @amd64.

- Update  3.0.3 = 3.1.0
- SHARED_LIBS-syntax, okay?

Comments? OKs? 

cheers, Rafael


Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.61
diff -u -p -u -r1.61 Makefile
--- Makefile24 Mar 2014 09:08:46 -  1.61
+++ Makefile2 May 2014 20:57:15 -
@@ -3,11 +3,11 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   powerful math/statistics/graphics language
-DISTNAME=  R-3.0.3
+DISTNAME=  R-3.1.0
 
-SHARED_LIBS=   R   2.0  \
-   Rlapack 31.1 \
-   Rblas   31.0
+SHARED_LIBS=   R   2.1 # 2.0
+SHARED_LIBS+=  Rlapack 31.2# 31.1
+SHARED_LIBS+=  Rblas   31.1# 31.0
 
 CATEGORIES=math
 HOMEPAGE=  http://www.r-project.org/
@@ -41,7 +41,10 @@ MASTER_SITES=http://cran.r-project.org/
http://cran.stat.ucla.edu/src/base/R-3/ \
http://probability.ca/cran/src/base/R-3/
 
-MODULES=   fortran devel/gettext x11/tk
+MODULES=   fortran \
+   devel/gettext \
+   x11/tk
+
 MODFORTRAN_COMPILER= gfortran
 
 BUILD_DEPENDS= ${MODFORTRAN_BUILD_DEPENDS} \
Index: distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.19
diff -u -p -u -r1.19 distinfo
--- distinfo12 Mar 2014 11:04:41 -  1.19
+++ distinfo2 May 2014 20:57:15 -
@@ -1,2 +1,2 @@
-SHA256 (R-3.0.3.tar.gz) = uXz9lUDylKt4boRhU/PdhgVhDX4nYWv7QpZ5W8T95tY=
-SIZE (R-3.0.3.tar.gz) = 28075821
+SHA256 (R-3.1.0.tar.gz) = imgDkPhMWMAdze/Wguqg6QOJ8J5tLy4JDHGvQAZfX+I=
+SIZE (R-3.1.0.tar.gz) = 28469975
Index: patches/patch-Makeconf_in
===
RCS file: patches/patch-Makeconf_in
diff -N patches/patch-Makeconf_in
--- patches/patch-Makeconf_in   12 Mar 2014 11:04:41 -  1.2
+++ /dev/null   1 Jan 1970 00:00:00 -
@@ -1,11 +0,0 @@
-$OpenBSD: patch-Makeconf_in,v 1.2 2014/03/12 11:04:41 dcoppa Exp $
 Makeconf.in.orig   Wed Mar  6 00:02:46 2013
-+++ Makeconf.inMon May 27 14:00:25 2013
-@@ -19,7 +19,6 @@ CPICFLAGS = @CPICFLAGS@
- CPPFLAGS = @CPPFLAGS@
- DEFS = @DEFS@ @R_DEFS@
- DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude=*.o 
--exclude=*$(SHLIB_EXT) --exclude=*~
--DYLIB_EXT = @DYLIB_EXT@
- DYLIB_LD = @DYLIB_LD@
- DYLIB_LDFLAGS = @DYLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(DYLIBS_LTO)
- DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
Index: patches/patch-Makefile_in
===
RCS file: /cvs/ports/math/R/patches/patch-Makefile_in,v
retrieving revision 1.3
diff -u -p -u -r1.3 patch-Makefile_in
--- patches/patch-Makefile_in   12 Mar 2014 11:04:41 -  1.3
+++ patches/patch-Makefile_in   2 May 2014 20:57:15 -
@@ -1,75 +1,20 @@
-$OpenBSD: patch-Makefile_in,v 1.3 2014/03/12 11:04:41 dcoppa Exp $
+$OpenBSD$
 
 Do not build PDF versions of the R manuals
 
 Makefile.in.orig   Tue Sep 10 00:05:05 2013
-+++ Makefile.inTue Feb  4 09:15:53 2014
-@@ -95,7 +95,7 @@ install install-strip: installdirs svnonly
-   @for f in $(INSTFILES); do \
- $(INSTALL_DATA) $(srcdir)/$${f} $(DESTDIR)$(rhome); \
-   done
--  @for f in NEWS NEWS.pdf $(NON_SVN_INSTFILES); do \
-+  @for f in NEWS $(NON_SVN_INSTFILES); do \
- $(INSTALL_DATA) $${f} $(DESTDIR)$(rhome); \
-   done
- @WANT_R_FRAMEWORK_TRUE@   $(MAKE) -f $(srcdir)/Makefile.fw 
top_srcdir=$(top_srcdir) $@
-@@ -121,7 +121,7 @@ svnonly:
- fi \
-   fi
- 
--libR_la = lib/libR$(DYLIB_EXT)
-+libR_la = lib/libR.so.$(LIBR_VERSION)
- install-libR:
-   @if test -f $(libR_la); then $(MAKE) install-libR-exists; fi
- install-libR-exists:
-@@ -133,13 +133,13 @@ installdirs:
- uninstall:
-   @(for d in $(SUBDIRS); do rsd=$${d} $${rsd}; done; \
- for d in $${rsd}; do (cd $${d}  $(MAKE) $@); done)
--  @for f in NEWS NEWS.pdf $(INSTFILES) $(NON_SVN_INSTFILES); do \
-+  @for f in NEWS  $(INSTFILES) $(NON_SVN_INSTFILES); do \
- rm -f $(DESTDIR)$(rhome)/$${f}; \
-   done
-   @rm -rf $(DESTDIR)$(Rexecbindir) $(DESTDIR)$(rhome)/lib
-   @rmdir $(DESTDIR)$(rhome) 2/dev/null \
-   || $(ECHO)   dir $(DESTDIR)$(rhome) not removed
--  @rm -f $(DESTDIR)${libdir}/libR$(DYLIB_EXT)
-+  @rm -f $(DESTDIR)${libdir}/libR.so.$(LIBR_VERSION)
- 
- mostlyclean: clean
- clean:
-@@ -154,7 +154,7 @@ distclean: clean
-   @rm -f po/Makefile
-   -@rm -rf bin include lib library modules gnome
-   @if test -f non-tarball ; then \
--rm -f $(NON_SVN_INSTFILES) NEWS NEWS.pdf non-tarball doc/FAQ 
doc/RESOURCES doc/html/resources.html doc/html/NEWS.html; \
-+rm -f $(NON_SVN_INSTFILES) NEWS non-tarball doc/FAQ doc/RESOURCES 
doc/html/resources.html doc/html/NEWS.html; \
-   fi
-

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-07-03 Thread Stefan Unterweger

* Stefan Unterweger on Mon, Jul 02, 2012 at 04:23:48PM +0200:
   | begin installing recommended package MASS
   | systrace: deny user: stefan, prog: 
   /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
   policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), 
   filename: /usr
   | systrace: deny user: stefan, prog: 
   /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
   policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), 
   filename: /usr/ports
   | systrace: deny user: stefan, prog: 
   /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
   policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), 
   filename: /usr/ports/pobj
   | systrace: deny user: stefan, prog: 
   /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
   policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), 
   filename: /usr
   | systrace: deny user: stefan, prog: 
   /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
   policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), 
   filename: /usr/ports

  Without the patch (patches/patch-src_main_platform_c), the build
  fails. With the patch you get these warnings, but at least the build
  continues...

 Ah, ok. Then I'll leave it running and report back in a few hours if it
 finishes.

The build succeeds and installs fine apart from the warning messages.
R seems to start and at least some hello-world-esque things seem to run
without problem. I'm a relative newbie at R so i cannot really say if
everything works, but at least it seems that way for now. I'll pipe up
if I encounter anything unusual in the next few days.

Thanks for the effort of porting the update! :o)


s//un

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-07-02 Thread Stefan Unterweger

Hi!

* David Coppa on Fri, Jun 29, 2012 at 03:50:14PM +0200:
 Attached you have my fixed/updated diff for R-2.15.1...
 
 Some highlights:
 
 - updated to R-2.15.1 (released on 2012-06-22)
 - fixed handling of shared lib versions
 - fixed building with USE_SYSTRACE
 - fixed configure to use the external libintl from ports instead of
 its internal one
 - use xdg-utils so there's no need to depend on a particular browser/pdf 
 viewer

Since you mention systrace: Can it be that trying to build it as a
normal user (via the SUDO-flag in mk.conf) is partially broken as a
result? The build is not yet through and everything up to that point
runs fine, but now I get tons of warning messages like the following:

| begin installing recommended package MASS
| systrace: deny user: stefan, prog: 
/usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
/usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr
| systrace: deny user: stefan, prog: 
/usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
/usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr/ports
| systrace: deny user: stefan, prog: 
/usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
/usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
/usr/ports/pobj
| systrace: deny user: stefan, prog: 
/usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
/usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr
| systrace: deny user: stefan, prog: 
/usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
/usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr/ports

For reference, my mk.conf reads the following:
| FETCH_PACKAGES=Yes
| SUDO=/usr/bin/sudo
| USE_SYSTRACE=Yes


Cheers,
s//un

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-07-02 Thread David Coppa

On Mon, Jul 2, 2012 at 4:00 PM, Stefan Unterweger ste...@aleturo.com wrote:
 Hi!

 * David Coppa on Fri, Jun 29, 2012 at 03:50:14PM +0200:
 Attached you have my fixed/updated diff for R-2.15.1...

 Some highlights:

 - updated to R-2.15.1 (released on 2012-06-22)
 - fixed handling of shared lib versions
 - fixed building with USE_SYSTRACE
 - fixed configure to use the external libintl from ports instead of
 its internal one
 - use xdg-utils so there's no need to depend on a particular browser/pdf 
 viewer

 Since you mention systrace: Can it be that trying to build it as a
 normal user (via the SUDO-flag in mk.conf) is partially broken as a
 result? The build is not yet through and everything up to that point
 runs fine, but now I get tons of warning messages like the following:

 | begin installing recommended package MASS
 | systrace: deny user: stefan, prog: 
 /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
 /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr
 | systrace: deny user: stefan, prog: 
 /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
 /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr/ports
 | systrace: deny user: stefan, prog: 
 /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
 /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
 /usr/ports/pobj
 | systrace: deny user: stefan, prog: 
 /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
 /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr
 | systrace: deny user: stefan, prog: 
 /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], policy: 
 /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: /usr/ports

 For reference, my mk.conf reads the following:
 | FETCH_PACKAGES=Yes
 | SUDO=/usr/bin/sudo
 | USE_SYSTRACE=Yes

Hi,

Without the patch (patches/patch-src_main_platform_c), the build
fails. With the patch you get these warnings, but at least the build
continues...

ciao
David

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-07-02 Thread Stefan Unterweger

Hi!

* David Coppa on Mon, Jul 02, 2012 at 04:11:31PM +0200:
  | begin installing recommended package MASS
  | systrace: deny user: stefan, prog: 
  /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
  policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
  /usr
  | systrace: deny user: stefan, prog: 
  /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
  policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
  /usr/ports
  | systrace: deny user: stefan, prog: 
  /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
  policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
  /usr/ports/pobj
  | systrace: deny user: stefan, prog: 
  /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
  policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
  /usr
  | systrace: deny user: stefan, prog: 
  /usr/ports/pobj/R-2.15.1/build-i386/bin/exec/R, pid: 23647(0)[10587], 
  policy: /usr/bin/env, filters: 241, syscall: native-fswrite(136), filename: 
  /usr/ports

 Without the patch (patches/patch-src_main_platform_c), the build
 fails. With the patch you get these warnings, but at least the build
 continues...

Ah, ok. Then I'll leave it running and report back in a few hours if it
finishes.


Bye,
s//un

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-07-01 Thread Benjamin Nadland

On Fri, Jun 29, 2012 at 03:16:03PM -0500, Amit Kulkarni wrote:
  Rafael / Amit: please test this with cantor from kde4 and report 
  success/failure
 
 cantor still crashes with the R backend. But the other two cantor
 backends are ok i.e qalculate and kalgebra. we can revisit this later.
 the R diff is the best combined effort i have seen so far. i am
 emailing benjamin so he can test R.

My scripts (mostly plots) work with this version on i386.

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-07-01 Thread David Coppa

On Sun, Jul 1, 2012 at 2:31 PM, Benjamin Nadland
benjamin.nadl...@freenet.de wrote:
 On Fri, Jun 29, 2012 at 03:16:03PM -0500, Amit Kulkarni wrote:
  Rafael / Amit: please test this with cantor from kde4 and report 
  success/failure

 cantor still crashes with the R backend. But the other two cantor
 backends are ok i.e qalculate and kalgebra. we can revisit this later.
 the R diff is the best combined effort i have seen so far. i am
 emailing benjamin so he can test R.

 My scripts (mostly plots) work with this version on i386.


Thanks for testing!

if I have the ok from another developer I'll commit this update...

Ciao
David

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-06-29 Thread Amit Kulkarni

 Rafael / Amit: please test this with cantor from kde4 and report 
 success/failure

cantor still crashes with the R backend. But the other two cantor
backends are ok i.e qalculate and kalgebra. we can revisit this later.
the R diff is the best combined effort i have seen so far. i am
emailing benjamin so he can test R.

thanks

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-06-27 Thread Stuart Henderson

On 2012/06/26 16:56, Amit Kulkarni wrote:
 rafael's patches need to be reviewed and dcoppa@ is scheduled to
 review it when he gets the time. please be patient.

scheduled? where is this schedule, I want to see it :)

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-06-26 Thread Benjamin Nadland

On Mon, Jun 25, 2012 at 12:10:42AM +0200, Rafael Sadowski wrote:
 On Thu Jun 21, 2012 at 07:52:02PM +0200, Rafael Sadowski wrote:
  On Thu Jun 21, 2012 at 12:09:30PM +0200, Rafael Sadowski wrote:
   Hey @ports,
   
   here is my R[1] update from 2.8.1 to 2.15.0. After long time and many
   fixes and tests R works with x11/kde4/contor[2] and it pass regress
   test. All demo() calls works fine.
   
   Big step between this two versions, see:
   http://cran.r-project.org/src/base/NEWS
   
   comments? OK? commit?
   
   Thanks David Coppa!
   Cheers, Rafael
   
   [1]: https://github.com/jasperla/openbsd-wip/tree/master/math/R
   [2]: https://github.com/jasperla/openbsd-wip/tree/master/x11/kde4/cantor
   
  
  After tango dance with `cvs rm/mv` here is the final patch. It hope it
  works. Thanks Amit ...
  
  I need one advice. The port built good without modify `ulimit -d` but `make
  regress` crashed, if we don't set ulimit -d value upper. So, should I set
  VMEM_WARNING=Yes?
  
 
 No comments? I want to push it to cvs!

The patches in math/R/patches don't apply for me after the update.
Not sure though if it's a problem on my side.

After I do `rm math/R/patches/*` the port builds and installs.

I tested it a bit on my i386 machine and it works for me.

It also is a recent enough version to install and use the ggplot2
package, so I would like to see this update imported.

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-06-26 Thread Amit Kulkarni

   Hey @ports,
  
   here is my R[1] update from 2.8.1 to 2.15.0. After long time and many
   fixes and tests R works with x11/kde4/contor[2] and it pass regress
   test. All demo() calls works fine.
  
   Big step between this two versions, see:
   http://cran.r-project.org/src/base/NEWS
  
   comments? OK? commit?
  
   Thanks David Coppa!
   Cheers, Rafael
  
   [1]: https://github.com/jasperla/openbsd-wip/tree/master/math/R
   [2]: https://github.com/jasperla/openbsd-wip/tree/master/x11/kde4/cantor
  
 
  After tango dance with `cvs rm/mv` here is the final patch. It hope it
  works. Thanks Amit ...
 
  I need one advice. The port built good without modify `ulimit -d` but `make
  regress` crashed, if we don't set ulimit -d value upper. So, should I set
  VMEM_WARNING=Yes?
 

 No comments? I want to push it to cvs!

 The patches in math/R/patches don't apply for me after the update.
 Not sure though if it's a problem on my side.

you have to use the https://github.com/jasperla/openbsd-wip tree by
checking it out at /usr/ports
then set PORTSDIR=/home/benjamin/openbsd/wherever_ports_is_extracted
in /etc/mk.conf
then adjust PORTSDIR_PATH=$(PORTSDIR)/openbsd-wip:${PORTSDIR} in /etc/mk.conf


 After I do `rm math/R/patches/*` the port builds and installs.

this is obviously not correct.

 I tested it a bit on my i386 machine and it works for me.

 It also is a recent enough version to install and use the ggplot2
 package, so I would like to see this update imported.


rafael's patches need to be reviewed and dcoppa@ is scheduled to
review it when he gets the time. please be patient.

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-06-24 Thread Rafael Sadowski

On Thu Jun 21, 2012 at 07:52:02PM +0200, Rafael Sadowski wrote:
 On Thu Jun 21, 2012 at 12:09:30PM +0200, Rafael Sadowski wrote:
  Hey @ports,
  
  here is my R[1] update from 2.8.1 to 2.15.0. After long time and many
  fixes and tests R works with x11/kde4/contor[2] and it pass regress
  test. All demo() calls works fine.
  
  Big step between this two versions, see:
  http://cran.r-project.org/src/base/NEWS
  
  comments? OK? commit?
  
  Thanks David Coppa!
  Cheers, Rafael
  
  [1]: https://github.com/jasperla/openbsd-wip/tree/master/math/R
  [2]: https://github.com/jasperla/openbsd-wip/tree/master/x11/kde4/cantor
  
 
 After tango dance with `cvs rm/mv` here is the final patch. It hope it
 works. Thanks Amit ...
 
 I need one advice. The port built good without modify `ulimit -d` but `make
 regress` crashed, if we don't set ulimit -d value upper. So, should I set
 VMEM_WARNING=Yes?
 

No comments? I want to push it to cvs!

Cheers, Rafael

Re: UPDATE math/R 2.8.1 - 2.15.0

2012-06-21 Thread David Coppa

On Thu, Jun 21, 2012 at 12:09 PM, Rafael Sadowski raf...@sizeofvoid.org wrote:
 Hey @ports,

 here is my R[1] update from 2.8.1 to 2.15.0. After long time and many
 fixes and tests R works with x11/kde4/contor[2] and it pass regress
 test. All demo() calls works fine.

 Big step between this two versions, see:
 http://cran.r-project.org/src/base/NEWS

 comments? OK? commit?

 Thanks David Coppa!
 Cheers, Rafael

 [1]: https://github.com/jasperla/openbsd-wip/tree/master/math/R
 [2]: https://github.com/jasperla/openbsd-wip/tree/master/x11/kde4/cantor


 ? patches/patch-Makefile_in
 ? patches/patch-doc_Makefile_in

Forgot to cvs add these patches?

ciao,
David

Update math/R to 2.6.0

2007-10-07 Thread Marc Balmer

this updates math/R to the new version 2.6.0.

comments, ok?

Index: math/R/Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.21
diff -u -r1.21 Makefile
--- math/R/Makefile 15 Sep 2007 18:44:36 -  1.21
+++ math/R/Makefile 7 Oct 2007 09:32:29 -
@@ -3,10 +3,9 @@
 SHARED_ONLY=   Yes
 
 COMMENT=   clone of S, a powerful math/statistics/graphics language
-DISTNAME=  R-2.5.0
-PKGNAME=   ${DISTNAME}p0
-SHARED_LIBS=   Rlapack 25.0 \
-   Rblas   25.0
+DISTNAME=  R-2.6.0
+SHARED_LIBS=   Rlapack 26.0 \
+   Rblas   26.0
 
 CATEGORIES=math
 HOMEPAGE=  http://www.r-project.org/
@@ -30,7 +29,7 @@
 LIB_DEPENDS=   jpeg.=62::graphics/jpeg \
tk84.=1:tk-8.4.*:x11/tk/8.4
 
-CONFIGURE_STYLE=gnu dest
+CONFIGURE_STYLE=gnu
 MODGNU_CONFIG_GUESS_DIRS=${WRKSRC}/tools
 CONFIGURE_ARGS=${CONFIGURE_SHARED} \
--with-readline --with-tcltk \
Index: math/R/distinfo
===
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.10
diff -u -r1.10 distinfo
--- math/R/distinfo 26 Apr 2007 20:26:12 -  1.10
+++ math/R/distinfo 7 Oct 2007 09:32:29 -
@@ -1,5 +1,5 @@
-MD5 (R-2.5.0.tar.gz) = uQiGY/xTnAWaz68Z1tkKaQ==
-RMD160 (R-2.5.0.tar.gz) = rhR3UoG1Oi/8WCl37sTDbGvcUE8=
-SHA1 (R-2.5.0.tar.gz) = p1u7WY1/lXrsPEvnnxgqkG+xRUE=
-SHA256 (R-2.5.0.tar.gz) = UlBMdwD4+ICJGzRiL3OkHd5m4HUqhVLSuN9chXVqju8=
-SIZE (R-2.5.0.tar.gz) = 15117375
+MD5 (R-2.6.0.tar.gz) = l+XSVCNJkllit0aUVtRXMQ==
+RMD160 (R-2.6.0.tar.gz) = VLPRg9+xWvf4Yee2KQSZiGWtGUw=
+SHA1 (R-2.6.0.tar.gz) = /1FXj8Yw5lzg4ruSsOH4MkyUkl0=
+SHA256 (R-2.6.0.tar.gz) = ipFuZTr/qDWEEZ3AiosS4w5DDe4Zo5hRNRUAPEPXkdo=
+SIZE (R-2.6.0.tar.gz) = 15447985
Index: math/R/patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.6
diff -u -r1.6 patch-configure
--- math/R/patches/patch-configure  9 Aug 2007 22:22:17 -   1.6
+++ math/R/patches/patch-configure  7 Oct 2007 09:32:29 -
@@ -1,16 +1,16 @@
 $OpenBSD: patch-configure,v 1.6 2007/08/09 22:22:17 steven Exp $
 configure.orig Thu Aug  9 00:44:12 2007
-+++ configure  Thu Aug  9 00:44:46 2007
-@@ -60699,7 +60699,7 @@ HAVE_POSIX_PRINTF!$HAVE_POSIX_PRINTF$ac_delim
- HAVE_ASPRINTF!$HAVE_ASPRINTF$ac_delim
- HAVE_SNPRINTF!$HAVE_SNPRINTF$ac_delim
- HAVE_WPRINTF!$HAVE_WPRINTF$ac_delim
+--- configure.orig Wed Sep 26 04:06:08 2007
 configure  Sun Oct  7 10:02:32 2007
+@@ -63170,7 +63170,7 @@ LIBTHREAD!$LIBTHREAD$ac_delim
+ LTLIBTHREAD!$LTLIBTHREAD$ac_delim
+ LIBMULTITHREAD!$LIBMULTITHREAD$ac_delim
+ LTLIBMULTITHREAD!$LTLIBMULTITHREAD$ac_delim
 -LIBICONV!$LIBICONV$ac_delim
 +LIBICONV!$LTLIBICONV$ac_delim
  LTLIBICONV!$LTLIBICONV$ac_delim
  INTLBISON!$INTLBISON$ac_delim
- BUILD_INCLUDED_LIBINTL!$BUILD_INCLUDED_LIBINTL$ac_delim
-@@ -60711,7 +60711,7 @@ GENCAT!$GENCAT$ac_delim
+ GLIBC21!$GLIBC21$ac_delim
+@@ -63230,7 +63230,7 @@ GENCAT!$GENCAT$ac_delim
  INTLOBJS!$INTLOBJS$ac_delim
  INTL_LIBTOOL_SUFFIX_PREFIX!$INTL_LIBTOOL_SUFFIX_PREFIX$ac_delim
  INTLLIBS!$INTLLIBS$ac_delim
Index: math/R/patches/patch-src_include_R_ext_eventloop_h
===
RCS file: /cvs/ports/math/R/patches/patch-src_include_R_ext_eventloop_h,v
retrieving revision 1.1
diff -u -r1.1 patch-src_include_R_ext_eventloop_h
--- math/R/patches/patch-src_include_R_ext_eventloop_h  8 Oct 2005 09:47:37 
-   1.1
+++ math/R/patches/patch-src_include_R_ext_eventloop_h  7 Oct 2007 09:32:29 
-
@@ -1,11 +1,11 @@
 $OpenBSD: patch-src_include_R_ext_eventloop_h,v 1.1 2005/10/08 09:47:37 
mbalmer Exp $
 src/include/R_ext/eventloop.h.orig Wed Aug 10 15:00:50 2005
-+++ src/include/R_ext/eventloop.h  Wed Aug 10 15:01:10 2005
-@@ -24,6 +24,7 @@
-Needed at least on FreeBSD so that fd_set is defined.
- */
- #include sys/types.h
-+#include sys/time.h
+--- src/include/R_ext/eventloop.h.orig Wed Sep  5 00:12:24 2007
 src/include/R_ext/eventloop.h  Sun Oct  7 10:03:46 2007
+@@ -26,6 +26,7 @@
+ #endif
+ /* NOTE: Needed at least on FreeBSD so that fd_set is defined. */
+ # include sys/types.h
++# include sys/time.h
+ #endif
  
  #ifdef  __cplusplus
- extern C {
Index: math/R/patches/patch-src_main_CommandLineArgs_c
===
RCS file: /cvs/ports/math/R/patches/patch-src_main_CommandLineArgs_c,v
retrieving revision 1.3
diff -u -r1.3 patch-src_main_CommandLineArgs_c
--- math/R/patches/patch-src_main_CommandLineArgs_c 9 Aug 2007 22:22:17 
-   1.3
+++ math/R/patches/patch-src_main_CommandLineArgs_c 7 Oct 2007 09:32:29 
-
@@ -1,7 +1,7 @@
 $OpenBSD: patch-src_main_CommandLineArgs_c,v 1.3 2007/08/09 22:22:17 steven 
Exp $
 src/main/CommandLineArgs.c.orig

92 matches

Mail list logo