CVS commit: pkgsrc/math/R-RNetCDF

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Sep 20 23:12:15 UTC 2020

Modified Files:
        pkgsrc/math/R-RNetCDF: Makefile distinfo
        pkgsrc/math/R-RNetCDF/patches: patch-configure

Log Message:
(math/R-RNetCDF) Updated 1.9.1 to 2.4.2

Version 2.4-2, 2020-09-12
  * Support reading/writing special values (e.g. NA, Inf) without substitution,
    mainly in cases where type conversion between R and NetCDF is not required.
  * Fix selection of na.mode values 0,1,2
  * Fix range checks for numeric conversions with packing
  * Significantly increase test coverage of type conversion routines
  * Support parallel NetCDF when running with MPI
  * Allow creation of datasets in "data64" (CDF5) format
  * Support diskless files and in-memory manipulation of persistent files

Version 2.3-1, 2020-04-27
  * Fix problem when defining scalar variables with netcdf-4.7.4

Version 2.1-1, 2019-10-18
  * Remove automatic handling of fill values in user-defined types
  * Link rwinlib libraries by pathname to fix r-hub Windows builds
  * Correct quoting of external software names in DESCRIPTION

Version 2.0-4, 2019-10-13
  * Fix OSX packages by linking expat library

Version 2.0-3, 2019-10-05
  * Support NetCDF-4 features for reading and writing of datasets.
  * Suggest bit64 package for NC_INT64 and NC_UINT64 types.
  * Drop support for netcdf-3.x library, require netcdf-4.x.
  * Drop support for udunits-1 library.
  * Disable calendar functions if udunits-2.x is not found during build.


To generate a diff of this commit:
cvs rdiff -u -r1.12 -r1.13 pkgsrc/math/R-RNetCDF/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R-RNetCDF/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R-RNetCDF/patches/patch-configure

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-RNetCDF/Makefile
diff -u pkgsrc/math/R-RNetCDF/Makefile:1.12 pkgsrc/math/R-RNetCDF/Makefile:1.13
--- pkgsrc/math/R-RNetCDF/Makefile:1.12 Fri May 22 10:56:20 2020
+++ pkgsrc/math/R-RNetCDF/Makefile      Sun Sep 20 23:12:14 2020
@@ -1,9 +1,7 @@
-# $NetBSD: Makefile,v 1.12 2020/05/22 10:56:20 adam Exp $
+# $NetBSD: Makefile,v 1.13 2020/09/20 23:12:14 mef Exp $
 
 R_PKGNAME=     RNetCDF
-R_PKGVER=      1.9-1
-PKGREVISION=   9
-CATEGORIES=    math
+R_PKGVER=      2.4-2
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Interface to NetCDF datasets

Index: pkgsrc/math/R-RNetCDF/distinfo
diff -u pkgsrc/math/R-RNetCDF/distinfo:1.1 pkgsrc/math/R-RNetCDF/distinfo:1.2
--- pkgsrc/math/R-RNetCDF/distinfo:1.1  Mon Sep 17 13:24:18 2018
+++ pkgsrc/math/R-RNetCDF/distinfo      Sun Sep 20 23:12:14 2020
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.1 2018/09/17 13:24:18 maya Exp $
+$NetBSD: distinfo,v 1.2 2020/09/20 23:12:14 mef Exp $
 
-SHA1 (R/RNetCDF_1.9-1.tar.gz) = 720b4146271bd8a5156f9d3810d2c9bd1eee76ef
-RMD160 (R/RNetCDF_1.9-1.tar.gz) = b473a5eb57df4d48b96eea8b4b347bda2f2ded52
-SHA512 (R/RNetCDF_1.9-1.tar.gz) = 3a1cd3b9b7996ffc40b14f4ac6bee78c5ea68cad8e4f68e0ba64ecfd6bb26e9e349cfacac8dac910dd5c57d6f4e8dbad6f47e48632b57a7a2d962381e6ff75f7
-Size (R/RNetCDF_1.9-1.tar.gz) = 98628 bytes
-SHA1 (patch-configure) = 62e98e78ae4338ce7bad04dbcb69fdb60cef5b8f
+SHA1 (R/RNetCDF_2.4-2.tar.gz) = fd68dd7e1b5dc789e8d313ff9593cf56a8075ca0
+RMD160 (R/RNetCDF_2.4-2.tar.gz) = 8ff7615c3a43d83218914e9139a5bf00d9ad6c14
+SHA512 (R/RNetCDF_2.4-2.tar.gz) = afd314dd0a5735ccad3579c9b9091956e7277cf8e630016264f5adef9f31831c79d85b53459e160f09e37789b3518f3cb184a100036af082abfb0533b906e1a6
+Size (R/RNetCDF_2.4-2.tar.gz) = 124926 bytes
+SHA1 (patch-configure) = 0ff9f35b4c2ca1701c381be9f6761fd62fa33e39

Index: pkgsrc/math/R-RNetCDF/patches/patch-configure
diff -u pkgsrc/math/R-RNetCDF/patches/patch-configure:1.1 pkgsrc/math/R-RNetCDF/patches/patch-configure:1.2
--- pkgsrc/math/R-RNetCDF/patches/patch-configure:1.1   Mon Sep 17 13:24:18 2018
+++ pkgsrc/math/R-RNetCDF/patches/patch-configure       Sun Sep 20 23:12:15 2020
@@ -1,33 +1,24 @@
-$NetBSD: patch-configure,v 1.1 2018/09/17 13:24:18 maya Exp $
+$NetBSD: patch-configure,v 1.2 2020/09/20 23:12:15 mef Exp $
 
 Fix the use of == in shell scripts.
 
---- configure.orig     2016-11-06 16:18:40.084776697 +0000
+--- configure.orig     2020-09-12 01:56:31.000000000 +0000
 +++ configure
-@@ -3275,7 +3275,7 @@ fi
- done
+@@ -3628,7 +3628,7 @@ fi
  
+ fi
  
 -if test "x$have_nc_config" == xyes; then :
 +if test "x$have_nc_config" = xyes; then :
  
-     # Find libraries and cflags used to build netcdf:
+     # Prepend linker flags to LDFLAGS:
      { $as_echo "$as_me:${as_lineno-$LINENO}: checking netcdf linker flags" >&5
-@@ -3589,7 +3589,7 @@ fi
- # Define variables UDUNITS_LIB, UDUNITS_DBFILE and UDUNITS_DBVAR,
- # based on the version of udunits detected above.
- # Also define preprocessor macro HAVE_LIBUDUNITS or HAVE_LIBUDUNITS2.
--if test $udunits == 2; then :
-+if test $udunits = 2; then :
- 
-     UDUNITS_LIB=udunits2
-     UDUNITS_DBFILE=udunits2.xml
-@@ -3597,7 +3597,7 @@ if test $udunits == 2; then :
-     $as_echo "#define HAVE_LIBUDUNITS2 1" >>confdefs.h
+@@ -3910,7 +3910,7 @@ fi
  
  
--elif test $udunits == 1; then :
-+elif test $udunits = 1; then :
+ # Define HAVE_LIBUDUNITS2 if all udunits2 checks were successful:
+-if test "x$enable_calendar" == xyes; then :
++if test "x$enable_calendar" = xyes; then :
+   $as_echo "#define HAVE_LIBUDUNITS2 1" >>confdefs.h
  
-     UDUNITS_LIB=udunits
-     UDUNITS_DBFILE=udunits.dat
+ else