UPDATE: math/R

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

UPDATE: math/R

Ingo Feinerer-2
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&m=150737856618497&w=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
--- Makefile 14 Nov 2018 20:48:21 -0000 1.104
+++ Makefile 21 Dec 2018 12:03:22 -0000
@@ -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 <feinerer@logi
 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 -0000 1.40
+++ distinfo 21 Dec 2018 12:03:22 -0000
@@ -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 -0000 1.35
+++ patches/patch-configure 21 Dec 2018 12:03:22 -0000
@@ -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 <zlib.h>
  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 -0000 1.40
+++ pkg/PLIST 21 Dec 2018 12:03:22 -0000
@@ -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

Reply | Threaded
Open this post in threaded view
|

Re: UPDATE: math/R

Paul Irofti-4
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&m=150737856618497&w=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 -0000 1.104
> +++ Makefile 21 Dec 2018 12:03:22 -0000
> @@ -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 <feinerer@logi
>  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 -0000 1.40
> +++ distinfo 21 Dec 2018 12:03:22 -0000
> @@ -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 -0000 1.35
> +++ patches/patch-configure 21 Dec 2018 12:03:22 -0000
> @@ -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 <zlib.h>
>   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 -0000 1.40
> +++ pkg/PLIST 21 Dec 2018 12:03:22 -0000
> @@ -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

Reply | Threaded
Open this post in threaded view
|

Re: UPDATE: math/R

Stuart Henderson
In reply to this post by Ingo Feinerer-2
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&m=150737856618497&w=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 (31K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: UPDATE: math/R

Ingo Feinerer-2
On Tue, Dec 25, 2018 at 11:52:01PM +0000, 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
    [hidden email]:/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

Reply | Threaded
Open this post in threaded view
|

Re: UPDATE: math/R

Stuart Henderson
On 2018/12/27 15:02, Ingo Feinerer wrote:

> On Tue, Dec 25, 2018 at 11:52:01PM +0000, 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
>     [hidden email]:/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?

Reply | Threaded
Open this post in threaded view
|

Re: UPDATE: math/R

Ingo Feinerer-2
On Thu, Dec 27, 2018 at 02:29:11PM +0000, 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