diff -Nru r-cran-ncdf4-1.16/configure.ac r-cran-ncdf4-1.16.1/configure.ac --- r-cran-ncdf4-1.16/configure.ac 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-ncdf4-1.16.1/configure.ac 2019-03-11 08:35:51.000000000 +0000 @@ -0,0 +1,149 @@ +AC_INIT(src/Makevars.in) +m4_include([tools/netcdf.m4]) + +echo "configure.ac: starting" + +: ${R_HOME=`R RHOME`} +if test -z "${R_HOME}"; then + echo "Could not determine R_HOME" + exit 1 +fi + +#--------------------------------------------------------------------------- +# The way R's package installation mechanism works, the C compiler and flags +# are set by R, and not changable at the package level. So this is really +# just for information purposes. Changing these values will NOT result in +# a different compiler being used!! +#--------------------------------------------------------------------------- +CC=`${R_HOME}/bin/R CMD config CC` +CFLAGS=`${R_HOME}/bin/R CMD config CFLAGS` + +# for ncdf4, I've chosen to REQUIRE the netcdf v4 interface +AC_PATH_NETCDF +if test $NETCDF_V4 = "no"; then + echo "-------------------------------------------------------------------" + echo "ncdf4 REQUIRES the netcdf library be version 4 or above," + echo "AND installed with HDF-5 support (i.e., the netcdf library must be" + echo "compiled with the --enable-netcdf-4 flag). If you don't want to install" + echo "the full version of netcdf-4 with HDF-5 support, then please install" + echo "the old, deprecated ncdf package instead." + echo "-------------------------------------------------------------------" + exit -1 +fi + +HAVE_NETCDF=TRUE + +NETCDF_LDFLAGS="$NETCDF_RPATH $NETCDF_LDFLAGS $LDFLAGS" + +AC_SUBST(NETCDF_CPPFLAGS) +AC_SUBST(NETCDF_LDFLAGS) +AC_SUBST(NETCDF_RPATH) +AC_SUBST(HAVE_NETCDF) + +AC_OUTPUT(src/Makevars) + +echo " " +echo "********************** Results of ncdf4 package configure *******************" +echo " " +echo "netCDF v4 CPP flags = $NETCDF_CPPFLAGS" +echo "netCDF v4 LD flags = $NETCDF_LDFLAGS" +echo "netCDF v4 runtime path = $NETCDF_RPATH" +echo " " +echo "netCDF C compiler used = $NETCDF_CC" +echo "R C compiler used = $CC $CFLAGS" +echo " " +echo "******************************************************************************" +echo " " + +#--------------------------------------------------------------------- +# Check to see if a different compiler is being used for netcdf and R +#--------------------------------------------------------------------- +set $NETCDF_CC +NETCDF_CC_ARG1=$1 +set $CC +R_CC_ARG1=$1 +TEST_EMIT_WARNING=0 +if test x$NETCDF_CC_ARG1 != x$R_CC_ARG1 -o $TEST_EMIT_WARNING -eq 1; then + + #------------------------------------------------------------------------------ + # By default, we emit a warning if the compilers of R and netcdf are different. + # This happens with some regularity to naive users. + #------------------------------------------------------------------------------ + emit_warning=1 + + #------------------------------------------------------------------------------------------------- + # Skip warning if one is gcc and the other is clang -- seems to bother some overly sensitive folks + #------------------------------------------------------------------------------------------------- + NETCDF_IS_GCC=0 + if echo "$NETCDF_CC_ARG1" | grep -q "gcc"; then + NETCDF_IS_GCC=1 + else + AC_PROG_CC([$NETCDF_CC_ARG1]) + if test "z$GCC" = zyes; then + NETCDF_IS_GCC=1 + fi + fi + NETCDF_IS_CLANG=0 + if echo "$NETCDF_CC_ARG1" | grep -q "clang"; then + NETCDF_IS_CLANG=1 + fi + + R_IS_GCC=0 + if echo "$R_CC_ARG1" | grep -q "gcc"; then + R_IS_GCC=1 + else + AC_PROG_CC([$R_CC_ARG1]) + if test "z$GCC" = zyes; then + R_IS_GCC=1 + fi + fi + R_IS_CLANG=0 + if echo "$R_CC_ARG1" | grep -q "clang"; then + R_IS_CLANG=1 + fi + + #------------------------------------------------------------- + # We don't bother emitting the warning if the two compilers in + # use are clang and gcc -- supposedly they are compatible + #------------------------------------------------------------- + if test $NETCDF_IS_CLANG -eq 1 -a $R_IS_GCC -eq 1; then + emit_warning=0 + fi + if test $NETCDF_IS_GCC -eq 1 -a $R_IS_CLANG -eq 1; then + emit_warning=0 + fi + + #----------------------------------------------------- + # Both same, but different exact names of compilers... + # not sure if this actually guarantees success?? + #----------------------------------------------------- + if test $NETCDF_IS_CLANG -eq 1 -a $R_IS_CLANG -eq 1; then + emit_warning=0 + fi + if test $NETCDF_IS_GCC -eq 1 -a $R_IS_GCC -eq 1; then + emit_warning=0 + fi + + echo "netcdf cc arg1: $NETCDF_CC_ARG1 R cc arg1: $R_CC_ARG1 R_IS_GCC: $R_IS_GCC R_IS_CLANG: $R_IS_CLANG NETCDF_IS_GCC: $NETCDF_IS_GCC NETCDF_IS_CLANG: $NETCDF_IS_CLANG emit_warning: $emit_warning" + + if test $emit_warning -eq 1 -o $TEST_EMIT_WARNING -eq 1; then + echo " " + echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" + echo "Dear ncdf4 user: The software configuration tool thinks that perhaps different compilers are being" + echo "used for R and the netcdf library. However, we all know that software configuration tools are" + echo "not that smart. If ncdf4 compiles fine for you, then please ignore this message. However, if" + echo "installation fails, it might be that you are using different compilers for R and the netcdf library." + echo "If so, then you must create a new version of the netcdf library that was compiled with the same" + echo "compiler that was used to install R (see information above). Then, try installing the ncdf4" + echo "package again using that new netcdf library. If necessary, you can specify the location of" + echo "the new nc-config (the one that uses the same compiler used by R) like this:" + echo " " + echo "R CMD INSTALL --configure-args=\"--with-nc-config=/home/joe/bin/nc-config\"" + echo " " + echo "(obviously, put in the correct path to YOUR nc-config, don't just use my example location!)" + echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" + echo " " + fi + +fi + diff -Nru r-cran-ncdf4-1.16/debian/changelog r-cran-ncdf4-1.16.1/debian/changelog --- r-cran-ncdf4-1.16/debian/changelog 2018-12-12 11:09:21.000000000 +0000 +++ r-cran-ncdf4-1.16.1/debian/changelog 2019-07-15 09:34:49.000000000 +0000 @@ -1,8 +1,12 @@ -r-cran-ncdf4 (1.16-2build1) disco; urgency=medium +r-cran-ncdf4 (1.16.1-1) unstable; urgency=medium - * Rebuild against new libhdf5-103. + * Bálint does not manage to keep on maintaining this package + * New upstream version + * debhelper 12 + * Standards-Version: 4.4.0 + * Secure URI in copyright format - -- Gianfranco Costamagna Wed, 12 Dec 2018 12:09:21 +0100 + -- Andreas Tille Mon, 15 Jul 2019 11:34:49 +0200 r-cran-ncdf4 (1.16-2) unstable; urgency=medium diff -Nru r-cran-ncdf4-1.16/debian/compat r-cran-ncdf4-1.16.1/debian/compat --- r-cran-ncdf4-1.16/debian/compat 2018-06-21 13:24:36.000000000 +0000 +++ r-cran-ncdf4-1.16.1/debian/compat 2019-07-15 09:34:49.000000000 +0000 @@ -1 +1 @@ -11 +12 diff -Nru r-cran-ncdf4-1.16/debian/control r-cran-ncdf4-1.16.1/debian/control --- r-cran-ncdf4-1.16/debian/control 2018-06-21 13:24:36.000000000 +0000 +++ r-cran-ncdf4-1.16.1/debian/control 2019-07-15 09:34:49.000000000 +0000 @@ -1,15 +1,15 @@ Source: r-cran-ncdf4 Maintainer: Debian R Packages Maintainers -Uploaders: Balint Reczey +Uploaders: Andreas Tille Section: gnu-r Testsuite: autopkgtest-pkg-r Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper (>= 12~), dh-r, r-base-dev, libnetcdf-dev, netcdf-bin -Standards-Version: 4.1.4 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-ncdf4 Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-ncdf4.git Homepage: https://cran.r-project.org/package=ncdf4 diff -Nru r-cran-ncdf4-1.16/debian/copyright r-cran-ncdf4-1.16.1/debian/copyright --- r-cran-ncdf4-1.16/debian/copyright 2018-06-21 13:24:36.000000000 +0000 +++ r-cran-ncdf4-1.16.1/debian/copyright 2019-07-15 09:34:49.000000000 +0000 @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ncdf4 Source: http://cran.r-project.org/web/packages/ncdf4/index.html diff -Nru r-cran-ncdf4-1.16/debian/patches/01_no_rpath.patch r-cran-ncdf4-1.16.1/debian/patches/01_no_rpath.patch --- r-cran-ncdf4-1.16/debian/patches/01_no_rpath.patch 2018-06-21 13:24:36.000000000 +0000 +++ r-cran-ncdf4-1.16.1/debian/patches/01_no_rpath.patch 2019-07-15 09:34:49.000000000 +0000 @@ -2,11 +2,9 @@ Forwarded: not-needed Author: Balint Reczey -diff --git a/tools/configure.ac b/tools/configure.ac -index 03329c6..aa09fc6 100644 ---- a/tools/configure.ac -+++ b/tools/configure.ac -@@ -32,11 +32,11 @@ fi +--- a/configure.ac ++++ b/configure.ac +@@ -33,11 +33,11 @@ fi HAVE_NETCDF=TRUE diff -Nru r-cran-ncdf4-1.16/debian/rules r-cran-ncdf4-1.16.1/debian/rules --- r-cran-ncdf4-1.16/debian/rules 2018-06-21 13:24:36.000000000 +0000 +++ r-cran-ncdf4-1.16.1/debian/rules 2019-07-15 09:34:49.000000000 +0000 @@ -4,10 +4,6 @@ %: dh $@ --buildsystem R -override_dh_auto_configure: - cd tools && ./regenerate - dh_auto_configure - override_dh_install: dh_install find debian -name HDF5_COPYING -delete diff -Nru r-cran-ncdf4-1.16/DESCRIPTION r-cran-ncdf4-1.16.1/DESCRIPTION --- r-cran-ncdf4-1.16/DESCRIPTION 2017-04-01 22:56:52.000000000 +0000 +++ r-cran-ncdf4-1.16.1/DESCRIPTION 2019-03-11 11:39:16.000000000 +0000 @@ -1,5 +1,5 @@ Package: ncdf4 -Version: 1.16 +Version: 1.16.1 Date: 2017-04-01 Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files @@ -10,6 +10,6 @@ License: GPL (>= 3) URL: http://cirrus.ucsd.edu/~pierce/ncdf NeedsCompilation: yes -Packaged: 2017-04-01 21:29:52 UTC; pierce +Packaged: 2019-03-11 08:43:47 UTC; ripley Repository: CRAN -Date/Publication: 2017-04-01 22:56:52 UTC +Date/Publication: 2019-03-11 11:39:16 UTC diff -Nru r-cran-ncdf4-1.16/MD5 r-cran-ncdf4-1.16.1/MD5 --- r-cran-ncdf4-1.16/MD5 2017-04-01 22:56:52.000000000 +0000 +++ r-cran-ncdf4-1.16.1/MD5 2019-03-11 11:39:16.000000000 +0000 @@ -1,7 +1,7 @@ 6349e4bb96c92e1f11ed21ccc87921a7 *ChangeLog -ba4d0693bb53f87c0d17eff7a132df83 *DESCRIPTION +cd76ac11939971929bb51fed85ee6644 *DESCRIPTION 36c1fbaaed8bc2fb94337130abd73011 *NAMESPACE -991a6594d03ec1a9d7172664b8ee0060 *R/ncdf4.R +d55a9cee7303135159edcb7518398d8f *R/ncdf4.R 777eba9944e67d13aac05649cd647add *R/ncdf4_priv.R d1115214348c8570d76389ba49626130 *R/ncdf4_priv_att.R 79b5675030428c59e2bcfa615e0b8ec3 *R/ncdf4_priv_dim.R @@ -9,6 +9,7 @@ 848679a3905f3019119cbfd996ab83e0 *R/ncdf4_priv_var.R 375cb891a49b0b7c57a1aff35daf1193 *cleanup d166b74624cd62256b6491b849d5e3ee *configure +08cc998ccc00e5ab6cbb6e67e7a5354c *configure.ac a06df3f633622526b02785e5442b4835 *inst/HDF5_COPYING b6edd0b113e654540165a2b53d1e81d8 *man/ancvar_put.Rd b256db50eaf9b1638ae3badef997ac4a *man/nc_close.Rd @@ -32,7 +33,4 @@ 78d681e25a4cad63030a0de445d13fa5 *src/Makevars.in 3f869799c5a06e5ccdeca7bb6ea5d29e *src/Makevars.win d525349389ed27a5b374052c1099d7fa *src/ncdf.c -b4d36900efe0d6045f65d132445a9b6d *tools/aclocal.m4 -54f32ede0c409c04707dd0ebb9175900 *tools/configure.ac c385dcbf01f753e75aee4c5db9a66337 *tools/netcdf.m4 -f695d66e71d8028902b4801b5ecb5023 *tools/regenerate diff -Nru r-cran-ncdf4-1.16/R/ncdf4.R r-cran-ncdf4-1.16.1/R/ncdf4.R --- r-cran-ncdf4-1.16/R/ncdf4.R 2017-04-01 21:07:11.000000000 +0000 +++ r-cran-ncdf4-1.16.1/R/ncdf4.R 2019-03-11 08:43:39.000000000 +0000 @@ -1952,7 +1952,7 @@ varsize <- ncvar_size ( ncid2use, varid2use ) ndims <- ncvar_ndims( ncid2use, varid2use ) - is_scalar = (varsize == 1) && (ndims == 0) + is_scalar = all(varsize == 1) && all(ndims == 0) if( verbose ) { print(paste("ncvar_put: varsize=")) print(varsize) diff -Nru r-cran-ncdf4-1.16/tools/aclocal.m4 r-cran-ncdf4-1.16.1/tools/aclocal.m4 --- r-cran-ncdf4-1.16/tools/aclocal.m4 2016-05-14 15:38:27.000000000 +0000 +++ r-cran-ncdf4-1.16.1/tools/aclocal.m4 1970-01-01 00:00:00.000000000 +0000 @@ -1,15 +0,0 @@ -# generated automatically by aclocal 1.11.3 -*- Autoconf -*- - -# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, -# 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software Foundation, -# Inc. -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY, to the extent permitted by law; without -# even the implied warranty of MERCHANTABILITY or FITNESS FOR A -# PARTICULAR PURPOSE. - -m4_include([netcdf.m4]) diff -Nru r-cran-ncdf4-1.16/tools/configure.ac r-cran-ncdf4-1.16.1/tools/configure.ac --- r-cran-ncdf4-1.16/tools/configure.ac 2016-05-14 15:38:27.000000000 +0000 +++ r-cran-ncdf4-1.16.1/tools/configure.ac 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AC_INIT(src/Makevars.in) - -echo "configure.ac: starting" - -: ${R_HOME=`R RHOME`} -if test -z "${R_HOME}"; then - echo "Could not determine R_HOME" - exit 1 -fi - -#--------------------------------------------------------------------------- -# The way R's package installation mechanism works, the C compiler and flags -# are set by R, and not changable at the package level. So this is really -# just for information purposes. Changing these values will NOT result in -# a different compiler being used!! -#--------------------------------------------------------------------------- -CC=`${R_HOME}/bin/R CMD config CC` -CFLAGS=`${R_HOME}/bin/R CMD config CFLAGS` - -# for ncdf4, I've chosen to REQUIRE the netcdf v4 interface -AC_PATH_NETCDF -if test $NETCDF_V4 = "no"; then - echo "-------------------------------------------------------------------" - echo "ncdf4 REQUIRES the netcdf library be version 4 or above," - echo "AND installed with HDF-5 support (i.e., the netcdf library must be" - echo "compiled with the --enable-netcdf-4 flag). If you don't want to install" - echo "the full version of netcdf-4 with HDF-5 support, then please install" - echo "the old, deprecated ncdf package instead." - echo "-------------------------------------------------------------------" - exit -1 -fi - -HAVE_NETCDF=TRUE - -NETCDF_LDFLAGS="$NETCDF_RPATH $NETCDF_LDFLAGS $LDFLAGS" - -AC_SUBST(NETCDF_CPPFLAGS) -AC_SUBST(NETCDF_LDFLAGS) -AC_SUBST(NETCDF_RPATH) -AC_SUBST(HAVE_NETCDF) - -AC_OUTPUT(src/Makevars) - -echo " " -echo "********************** Results of ncdf4 package configure *******************" -echo " " -echo "netCDF v4 CPP flags = $NETCDF_CPPFLAGS" -echo "netCDF v4 LD flags = $NETCDF_LDFLAGS" -echo "netCDF v4 runtime path = $NETCDF_RPATH" -echo " " -echo "netCDF C compiler used = $NETCDF_CC" -echo "R C compiler used = $CC $CFLAGS" -echo " " -echo "******************************************************************************" -echo " " - -#--------------------------------------------------------------------- -# Check to see if a different compiler is being used for netcdf and R -#--------------------------------------------------------------------- -set $NETCDF_CC -NETCDF_CC_ARG1=$1 -set $CC -R_CC_ARG1=$1 -TEST_EMIT_WARNING=0 -if test x$NETCDF_CC_ARG1 != x$R_CC_ARG1 -o $TEST_EMIT_WARNING -eq 1; then - - #------------------------------------------------------------------------------ - # By default, we emit a warning if the compilers of R and netcdf are different. - # This happens with some regularity to naive users. - #------------------------------------------------------------------------------ - emit_warning=1 - - #------------------------------------------------------------------------------------------------- - # Skip warning if one is gcc and the other is clang -- seems to bother some overly sensitive folks - #------------------------------------------------------------------------------------------------- - NETCDF_IS_GCC=0 - if echo "$NETCDF_CC_ARG1" | grep -q "gcc"; then - NETCDF_IS_GCC=1 - else - AC_PROG_CC([$NETCDF_CC_ARG1]) - if test "z$GCC" = zyes; then - NETCDF_IS_GCC=1 - fi - fi - NETCDF_IS_CLANG=0 - if echo "$NETCDF_CC_ARG1" | grep -q "clang"; then - NETCDF_IS_CLANG=1 - fi - - R_IS_GCC=0 - if echo "$R_CC_ARG1" | grep -q "gcc"; then - R_IS_GCC=1 - else - AC_PROG_CC([$R_CC_ARG1]) - if test "z$GCC" = zyes; then - R_IS_GCC=1 - fi - fi - R_IS_CLANG=0 - if echo "$R_CC_ARG1" | grep -q "clang"; then - R_IS_CLANG=1 - fi - - #------------------------------------------------------------- - # We don't bother emitting the warning if the two compilers in - # use are clang and gcc -- supposedly they are compatible - #------------------------------------------------------------- - if test $NETCDF_IS_CLANG -eq 1 -a $R_IS_GCC -eq 1; then - emit_warning=0 - fi - if test $NETCDF_IS_GCC -eq 1 -a $R_IS_CLANG -eq 1; then - emit_warning=0 - fi - - #----------------------------------------------------- - # Both same, but different exact names of compilers... - # not sure if this actually guarantees success?? - #----------------------------------------------------- - if test $NETCDF_IS_CLANG -eq 1 -a $R_IS_CLANG -eq 1; then - emit_warning=0 - fi - if test $NETCDF_IS_GCC -eq 1 -a $R_IS_GCC -eq 1; then - emit_warning=0 - fi - - echo "netcdf cc arg1: $NETCDF_CC_ARG1 R cc arg1: $R_CC_ARG1 R_IS_GCC: $R_IS_GCC R_IS_CLANG: $R_IS_CLANG NETCDF_IS_GCC: $NETCDF_IS_GCC NETCDF_IS_CLANG: $NETCDF_IS_CLANG emit_warning: $emit_warning" - - if test $emit_warning -eq 1 -o $TEST_EMIT_WARNING -eq 1; then - echo " " - echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - echo "Dear ncdf4 user: The software configuration tool thinks that perhaps different compilers are being" - echo "used for R and the netcdf library. However, we all know that software configuration tools are" - echo "not that smart. If ncdf4 compiles fine for you, then please ignore this message. However, if" - echo "installation fails, it might be that you are using different compilers for R and the netcdf library." - echo "If so, then you must create a new version of the netcdf library that was compiled with the same" - echo "compiler that was used to install R (see information above). Then, try installing the ncdf4" - echo "package again using that new netcdf library. If necessary, you can specify the location of" - echo "the new nc-config (the one that uses the same compiler used by R) like this:" - echo " " - echo "R CMD INSTALL --configure-args=\"--with-nc-config=/home/joe/bin/nc-config\"" - echo " " - echo "(obviously, put in the correct path to YOUR nc-config, don't just use my example location!)" - echo "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<" - echo " " - fi - -fi - diff -Nru r-cran-ncdf4-1.16/tools/regenerate r-cran-ncdf4-1.16.1/tools/regenerate --- r-cran-ncdf4-1.16/tools/regenerate 2016-05-14 15:38:27.000000000 +0000 +++ r-cran-ncdf4-1.16.1/tools/regenerate 1970-01-01 00:00:00.000000000 +0000 @@ -1,13 +0,0 @@ -#!/bin/sh - -rm ../Makefile -rm ../configure -rm ../src/Makevars - -aclocal -I . - -autoconf - -mv configure .. - -