.travis.yml

@@ -12,7 +12,7 @@ before_install:
   - if [[ "${CC}" == "gcc" || "${CC}" == "g++" ]]; then export CXX=g++; fi
   - if [[ "${CC}" == "clang" || "${CC}" == "clang++" ]]; then export CXX=clang++; fi
   - sudo apt-get update -qq
-  - sudo apt-get install -y -qq antlr libantlr-dev libnetcdfc7 libnetcdf-dev netcdf-bin udunits-bin libudunits2-0 libudunits2-dev
+  - sudo apt-get install -y -qq antlr libantlr-dev libnetcdf11 libnetcdf-dev netcdf-bin udunits-bin libudunits2-0 libudunits2-dev
   - ./configure
   - export DATA='/home/travis'
 

bld/Makefile

@@ -1270,7 +1270,7 @@ endif # endif OMP
 endif
 # endif LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, FREEBSD, MACOSX
 
-# NB: Deprecated as of 201403. Now MACOSX is subsumed in LINUX
+# NB: Deprecated as of 201403. Now LINUX* subsumes MACOSX
 ifeq (${PVM_ARCH},MACOSXOLD)
 CXX := ${LINUX_CXX}
 # NB: -D_POSIX_SOURCE breaks MACOSX build in nco_fl_utl.c, nco_mmr.c

bld/nco.spec

@@ -2,17 +2,17 @@
 # http://cvs.fedoraproject.org/viewvc/devel/nco/nco.spec?view=co
 
 Name:           nco
-Version:        4.8.1
+Version:        4.9.0
 Release:        1%{?dist}
 Summary:        Programs that manipulate netCDF files
 Group:          Applications/Engineering
 License:        GPL3
 URL:            http://nco.sf.net/
 
-# Obtain NCO version 4.8.1-1 tar.gz from Sourceforge using CVS:
+# Obtain NCO version 4.9.0-1 tar.gz from Sourceforge using CVS:
 # cvs -d:pserver:anonymous@nco.cvs.sf.net:/cvsroot/nco login
-# cvs -z3 -d:pserver:anonymous@nco.cvs.sf.net:/cvsroot/nco co -r nco-4.8.1-1 -d nco-%{version} nco
-# tar czf nco-%{version}.tar.gz --exclude='nco-4.8.1/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude='ncap_yacc.[ch]' ./nco-%{version}
+# cvs -z3 -d:pserver:anonymous@nco.cvs.sf.net:/cvsroot/nco co -r nco-4.9.0-1 -d nco-%{version} nco
+# tar czf nco-%{version}.tar.gz --exclude='nco-4.9.0/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude='ncap_yacc.[ch]' ./nco-%{version}
 Source0:        nco-%{version}.tar.gz
 #Patch0:		nco_install_C_headers.patch
 #Patch1:         nco_find_udunits-dat.patch
@@ -108,6 +108,9 @@ fi
 # %{_libdir}/libnco++.so
 
 %changelog
+* Mon Dec 04 2019 Charlie Zender <zender@uci.edu> - 4.9.0-1
+- new upstream 4.9.0
+
 * Mon Jul 01 2019 Charlie Zender <zender@uci.edu> - 4.8.1-1
 - new upstream 4.8.1
 

bld/nco_dst.pl

@@ -5,20 +5,20 @@
 
 # Usage:
 # Export tagged, public versions
-# /usr/bin/scp ${DATA}/nco-4.8.1.tar.gz zender,nco@web.sf.net:/home/project-web/nco/htdocs/src
-
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4.8.1 # Build, do not release on SF
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --sf nco-4.8.1 # Build, release on SF
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --nst_all nco-4.8.1 # Install, do not build
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --nst_all nco-4.8.1 # Build and install
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_cnt nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_prs nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cgd_cnt nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cray_prs nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --bbl_cnt nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --blk_cnt nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --dat_cnt nco-4.8.1
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --ute_prs nco-4.8.1
+# /usr/bin/scp ${DATA}/nco-4.9.0.tar.gz zender,nco@web.sf.net:/home/project-web/nco/htdocs/src
+
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4.9.0 # Build, do not release on SF
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --sf nco-4.9.0 # Build, release on SF
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --nst_all nco-4.9.0 # Install, do not build
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --nst_all nco-4.9.0 # Build and install
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_cnt nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_prs nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cgd_cnt nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cray_prs nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --bbl_cnt nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --blk_cnt nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --dat_cnt nco-4.9.0
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --ute_prs nco-4.9.0
 
 # Export daily snapshot
 # ${HOME}/nco/bld/nco_dst.pl --dbg=2 
@@ -256,7 +256,7 @@ if($bld){
 # Set up FTP server
     chdir $dst_pth_pfx or die "$prg_nm: ERROR unable to chdir to $dst_pth_pfx: $!\n"; # $! is system error string
     cmd_prc("$cp_cmd $doc_fl ./$dst_vrs/doc"); # Copy derived documentation to source directory
-    cmd_prc("$tar_cmd cvzf $dst_fl --exclude='nco-4.8.1/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude=ncap_yacc.[ch] ./$dst_vrs"); # Create gzipped tarfile
+    cmd_prc("$tar_cmd cvzf $dst_fl --exclude='nco-4.9.0/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude=ncap_yacc.[ch] ./$dst_vrs"); # Create gzipped tarfile
     cmd_prc("$rsh_cmd $www_mch $rm_cmd $www_drc/src/$dst_fl"); # Remove any distribution with same name
     if($dly_snp){cmd_prc("$rsh_cmd $www_mch $rm_cmd -r $www_drc/src/nco-????????.tar.gz");} # Remove previous daily snapshots from WWW server
     cmd_prc("$rcp_cmd $dst_fl $www_mch:$www_drc/src"); # Copy local tarfile to WWW server

bm/NCO_rgr.pm

@@ -117,6 +117,8 @@ sub tst_rgr {
     # 470 (for library 4.7.0)
     # 471 (for library 4.7.1)
     # 472 (for library 4.7.2)
+    # 473 (for library 4.7.3)
+    # 474 (for library 4.7.4)
 
   if($exit_value == 410){print "netCDF version 4.1.x detected\n";}
   if($exit_value == 431){print "netCDF version 4.3.1 detected\n";}
@@ -134,6 +136,8 @@ sub tst_rgr {
   if($exit_value == 470){print "netCDF version 4.7.0 detected\n";}
   if($exit_value == 471){print "netCDF version 4.7.1 detected\n";}
   if($exit_value == 472){print "netCDF version 4.7.2 detected\n";}
+  if($exit_value == 473){print "netCDF version 4.7.3 detected\n";}
+  if($exit_value == 474){print "netCDF version 4.7.4 detected\n";}
 
   if($exit_value >= 400){$RUN_NETCDF4_TESTS=1;}
   if($exit_value >= 431){$RUN_NETCDF4_TESTS_VERSION_GE_431=1;}
@@ -2608,7 +2612,7 @@ if($RUN_NETCDF4_TESTS_VERSION_GE_431){
 #ncks #85
 #ncks -O -L 0 --cnk_min=1 --cnk_dmn lat,1 -v one ~/nco/data/hdn.nc ~/foo.nc
 #ncks -C -m --trd --hdn -v one -g g13 ~/foo.nc | grep _ChunkSizes
-    $dsc_sng="(Groups) Imposing zero deflation (-L 0) on already-chunked variable keeps uses specified not netCDF-default chunksizes (expect failure with netCDF 4.1.1-)";
+    $dsc_sng="(Groups) Imposing zero deflation (-L 0) on already-chunked variable keeps/uses specified chunksizes not netCDF-default chunksizes (expect failure with netCDF 4.1.1-)";
     $tst_cmd[0]="ncks -O -4 -L 0 --cnk_min=1 --cnk_dmn lat,1 -v one $nco_D_flg $in_pth_arg hdn.nc %tmp_fl_00%";
     $tst_cmd[1]="ncks -C -m --trd --hdn -v one -g g13 %tmp_fl_00% | grep _ChunkSizes";
     $tst_cmd[2]="one attribute 2: _ChunkSizes, size = 1 NC_INT, value = 1";

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for NCO netCDF Operators 4.8.1.
+# Generated by GNU Autoconf 2.69 for NCO netCDF Operators 4.9.0.
 #
 # Report bugs to <nco-bugs@lists.sourceforge.net>.
 #
@@ -592,8 +592,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='NCO netCDF Operators'
 PACKAGE_TARNAME='nco'
-PACKAGE_VERSION='4.8.1'
-PACKAGE_STRING='NCO netCDF Operators 4.8.1'
+PACKAGE_VERSION='4.9.0'
+PACKAGE_STRING='NCO netCDF Operators 4.9.0'
 PACKAGE_BUGREPORT='nco-bugs@lists.sourceforge.net'
 PACKAGE_URL=''
@@ -1388,7 +1388,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures NCO netCDF Operators 4.8.1 to adapt to many kinds of systems.
+\`configure' configures NCO netCDF Operators 4.9.0 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1459,7 +1459,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of NCO netCDF Operators 4.8.1:";;
+     short | recursive ) echo "Configuration of NCO netCDF Operators 4.9.0:";;
    esac
   cat <<\_ACEOF
@@ -1625,7 +1625,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-NCO netCDF Operators configure 4.8.1
+NCO netCDF Operators configure 4.9.0
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2491,7 +2491,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
-It was created by NCO netCDF Operators $as_me 4.8.1, which was
+It was created by NCO netCDF Operators $as_me 4.9.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -3746,7 +3746,7 @@ fi
 # Define the identity of the package.
  PACKAGE='nco'
- VERSION='4.8.1'
+ VERSION='4.9.0'
 cat >>confdefs.h <<_ACEOF
@@ -21575,7 +21575,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by NCO netCDF Operators $as_me 4.8.1, which was
+This file was extended by NCO netCDF Operators $as_me 4.9.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -21641,7 +21641,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-NCO netCDF Operators config.status 4.8.1
+NCO netCDF Operators config.status 4.9.0
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

configure.ac

@@ -54,7 +54,7 @@
 # 20170808: Choose between traditional version and Git-based version
 # If Git, consider that Linux dynamic libraries will have full messy name, MacOSX will not
 # https://stackoverflow.com/questions/43526939/how-to-insert-git-based-version-in-autoconf-managed-project
-AC_INIT([NCO netCDF Operators],[4.8.1],[nco-bugs@lists.sourceforge.net],[nco])
+AC_INIT([NCO netCDF Operators],[4.9.0],[nco-bugs@lists.sourceforge.net],[nco])
 
 # Print GNU copyright in configure script
 AC_COPYRIGHT

configure.eg

@@ -354,7 +354,7 @@ scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU
 # Latest ticket: AREQ0215917 on 20180413
 # Latest sysadmin-compiled module usage: soft add +netcdf-4.6.1 soft add +nco-4.7.4 # 20180417
 # Personal recipe last modified: 20180729
-# Personal recipe last used successfully: 20190510
+# Personal recipe last used successfully: 20191113
 # Fails to link to system-installed udunits...why?
 # nm -a /soft/udunits/2.1.21/lib/libudunits2.a | grep ut_read_xml
 # soft add +antlr-2.7.7 # 20161223 this ANTLR appears to be stock and not NCO-compatible
@@ -373,23 +373,25 @@ make check >> nco.make.${GNU_TRP}.foo 2>&1
 make install >> nco.make.${GNU_TRP}.foo 2>&1
 scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU_TRP}.foo nco.make.${GNU_TRP}.foo dust.ess.uci.edu:Sites/nco/rgr
 
-# icc/icpc 20171013 Zender uses this to develop/install/update netCDF4-enabled NCO in personal directories on cheyenne:
+# gcc/g++ 20171013 Zender uses this to develop/install/update netCDF4-enabled NCO in personal directories on cheyenne:
 # Sysadmin upgrade request: cislhelp@ucar.edu # NCAR Maintainer = Pat Nichols
 # Latest ticket: 216373 on 20180413
 # Latest sysadmin-compiled module usage: module load netcdf/4.6.1 module load nco/4.7.4 # 20180417
-# Personal recipe last modified: 20180427
-# Personal recipe last used successfully: 20180921 (getopt errors were eliminated by removing ~/include/getopt*.h)
+# Personal recipe last modified: 20190813
+# Personal recipe last used successfully: 20190813
+# Personal recipe last failed: 20190812 (antlr needed GCC 9.1.0 recompile)
+# Cheyenne GNU:
 module purge
-module load ncarenv intel ncarcompilers mpt netcdf
-module add intel
-module add netcdf/4.6.1
+module load ncarenv gnu/9.1.0 ncarcompilers mpt netcdf/4.6.3
+module add gnu/9.1.0
+module add netcdf/4.6.3
 module add mpt
 export PATH=${PATH}:/opt/pbs/bin # needed for qsub
-export PATH=${PATH}:/glade/u/apps/ch/opt/netcdf/4.6.1/intel/17.0.1/bin # needed for ncgen
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/glade/u/apps/ch/opt/netcdf/4.6.1/intel/17.0.1/lib:/glade/u/apps/ch/opt/udunits/2.2.20/gnu/4.8.2/lib # needed to run NCO
+export PATH=${PATH}:/glade/u/apps/ch/opt/netcdf/4.6.3/gnu/9.1.0/bin # needed for ncgen
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/glade/u/apps/ch/opt/netcdf/4.6.3/gnu/9.1.0/lib:/glade/u/apps/ch/opt/udunits/2.2.26/gnu/9.1.0/lib:/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0/lib # needed to run NCO
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
 cd ~/nco;git reset --hard origin/master
-cd ~/nco/bld;make ANTLR_ROOT=${HOME} GSL_ROOT='/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0' GSL_INC='/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0/include' SL_LIB='/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0/lib' NETCDF_ROOT='/glade/u/apps/ch/opt/netcdf/4.6.1/intel/17.0.1' UDUNITS_INC='/glade/u/apps/ch/opt/udunits/2.2.20/gnu/4.8.2/include' UDUNITS_LIB='/glade/u/apps/ch/opt/udunits/2.2.20/gnu/4.8.2/lib' OPTS=D allinone;cd -
+cd ~/nco/bld;make ANTLR_ROOT=${HOME} GSL_ROOT='/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0' GSL_INC='/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0/include' SL_LIB='/glade/u/apps/ch/opt/gsl/2.4/gnu/6.3.0/lib' NETCDF_ROOT='/glade/u/apps/ch/opt/netcdf/4.6.3/gnu/9.1.0' UDUNITS_INC='/glade/u/apps/ch/opt/udunits/2.2.26/gnu/9.1.0/include' UDUNITS_LIB='/glade/u/apps/ch/opt/udunits/2.2.26/gnu/9.1.0/lib' OPTS=D allinone;cd -
 
 # gcc/g++ Zender uses this to develop/install/update netCDF4-enabled NCO in personal directories on compy
 # https://acme-climate.atlassian.net/wiki/spaces/ED/pages/928973795/CompyMcNodeFace+-+E3SM+RGMA+ESMD+dedicated+system+at+PNNL
@@ -399,6 +401,7 @@ cd ~/nco/bld;make ANTLR_ROOT=${HOME} GSL_ROOT='/glade/u/apps/ch/opt/gsl/2.4/gnu/
 # Personal recipe last modified: 20190525
 # Personal recipe last used successfully: 20190525
 # 20190526: DAP functionality is present in libnetcdf but missing in my NCO because configure does not find libcurl although it is definitely in /lib64/libcurl.so.*
+# 20190806: Must load modules prior to (re-)building otherwise system GCC 4.8.5 C++ compiler will not link to g++ 8.1.0 Antlr library
 module purge
 module load gcc/8.1.0
 module load mvapich2/2.3.1 # Required for ncclimo/ncremap in MPI-mode
@@ -434,12 +437,13 @@ scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU
 # Sysadmin upgrade request: https://nersc.service-now.com/navpage.do # NERSC Maintainer = Yun (Helen) He
 # Latest ticket: INC0118469 on 20180413
 # Latest sysadmin-compiled module usage: module load nco/4.7.4 # 20180430 (without ncap2)
-# Personal recipe last modified: 20190607 (converted from intel to gnu)
-# Personal recipe last used successfully: 20190607 (currently not linking ncap2 because needs -L${HOME}/lib_cori to find -lantlr. Moreover, ldd cannot find system libraries.)
+# Personal recipe last modified: 20190801 (converted from intel to gnu)
+# Personal recipe last used successfully: 20191108 (currently not linking ncap2 because needs -L${HOME}/lib_cori to find -lantlr. Moreover, ldd cannot find system libraries.)
 module load gcc
+#module load udunits
 export GNU_TRP=`~/nco/autobld/config.guess`
 cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
-ANTLR_ROOT=${HOME} ANTLR_LIB=${HOME}/lib_cori CC='gcc' CXX='g++' GSL_ROOT='/usr/common/software/gsl/2.1/gnu' NETCDF_INC='/opt/cray/pe/netcdf/4.6.1.3/gnu/7.1/include' NETCDF_LIB='/opt/cray/pe/netcdf/4.6.1.3/gnu/7.1/lib' NETCDF_ROOT='/opt/cray/pe/netcdf/4.6.1.3' UDUNITS2_PATH='/usr/common/software/udunits/2.2.19/hsw/gnu' ./configure --prefix=${HOME} --bindir=${HOME}/bin_cori --datadir=${HOME}/nco/data --libdir=${HOME}/lib_cori --mandir=${HOME}/man > nco.configure.${GNU_TRP}.foo 2>&1
+ANTLR_ROOT=${HOME} ANTLR_LIB=${HOME}/lib_cori CC='gcc' CXX='g++' GSL_ROOT='/usr/common/software/gsl/2.1/gnu' NETCDF_INC='/opt/cray/pe/netcdf/4.6.3.0/gnu/8.2/include' NETCDF_LIB='/opt/cray/pe/netcdf/4.6.3.0/gnu/8.2/lib' NETCDF_ROOT='/opt/cray/pe/netcdf/4.6.3.0' UDUNITS2_PATH='/global/common/sw/cray/cnl7/haswell/udunits2/2.2.24/gcc/8.2.0/y4j6eez' ./configure --prefix=${HOME} --bindir=${HOME}/bin_cori --datadir=${HOME}/nco/data --libdir=${HOME}/lib_cori --mandir=${HOME}/man > nco.configure.${GNU_TRP}.foo 2>&1
 /bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
 /bin/cp -f libtool nco.libtool.${GNU_TRP}.foo
 make clean;make > nco.make.${GNU_TRP}.foo 2>&1
@@ -493,37 +497,18 @@ make check >> nco.make.${GNU_TRP}.foo 2>&1
 make install >> nco.make.${GNU_TRP}.foo 2>&1
 scp nco.configure.${GNU_TRP}.foo nco.config.log.${GNU_TRP}.foo nco.libtool.${GNU_TRP}.foo nco.make.${GNU_TRP}.foo dust.ess.uci.edu:Sites/nco/rgr
 
-# gcc/g++ 20160107 Zender uses this to develop/install/update netCDF4-enabled NCO in personal directories on rhea with system (old) netCDF:
-# Sysadmin upgrade request: https://www.olcf.ornl.gov/support/submit-ticket
-# Latest ticket: 381695 on 20180413
-# Latest sysadmin-compiled module usage: module load netcdf/4.6.1 nco/4.7.4 # 20180423
-# Personal recipe last modified: 20170814
-# Personal recipe last used successfully: 20190227 
-# 20190420: Everything broke due to major system upgrade (Summit?). Most packages no longer present.
-# Block below no longer works, just keeping it until I cobble together a replacement in the following block
-export LINUX_CC='gcc -std=c99 -pedantic -D_DEFAULT_SOURCE -D_BSD_SOURCE -D_POSIX_SOURCE'
-export LINUX_CXX='g++ -std=c++11'
-export LINUX_FC='gfortran'
-module load intel
-export LD_LIBRARY_PATH=/autofs/nccs-svm1_sw/rhea/.swci/0-core/opt/spack/20170224/linux-rhel6-x86_64/gcc-4.4.7/netcdf-4.4.1-uroyzcwi6fc3kerfidguoof7g2vimo57/lib:/sw/redhat6/szip/2.1/rhel6.6_gnu4.8.2/lib:${LD_LIBRARY_PATH}
-export NETCDF_ROOT=/autofs/nccs-svm1_sw/rhea/.swci/0-core/opt/spack/20170224/linux-rhel6-x86_64/gcc-4.4.7/netcdf-4.4.1-uroyzcwi6fc3kerfidguoof7g2vimo57 
-export PATH=/autofs/nccs-svm1_sw/rhea/.swci/0-core/opt/spack/20170224/linux-rhel6-x86_64/gcc-4.4.7/netcdf-4.4.1-uroyzcwi6fc3kerfidguoof7g2vimo57/bin:${PATH}
-cd ~/nco;git reset --hard origin/master
-cd ~/nco/bld;make ANTLR_ROOT=${HOME} NETCDF_ROOT='/autofs/nccs-svm1_sw/rhea/.swci/0-core/opt/spack/20170224/linux-rhel6-x86_64/gcc-4.4.7/netcdf-4.4.1-uroyzcwi6fc3kerfidguoof7g2vimo57' SZ=Y SZ_LIB='/sw/redhat6/szip/2.1/rhel6.6_gnu4.8.2/lib' UDUNITS_INC='/sw/redhat6/udunits/2.1.24/rhel6.4_intel13.1.3/include' UDUNITS_LIB='/sw/redhat6/udunits/2.1.24/rhel6.4_intel13.1.3/lib' OPTS=D OMP=Y allinone;cd -
-
 # gcc/g++ 20160107 Zender uses this to develop/install/update netCDF4-enabled NCO in personal directories on rhea:
 # Sysadmin upgrade request: https://www.olcf.ornl.gov/support/submit-ticket
 # Latest ticket: 381695 on 20180413
 # Latest sysadmin-compiled module usage: module load netcdf/4.6.1 nco/4.7.4 # 20180423
-# Personal recipe last modified: 20190420
-# Personal recipe last used successfully: 20190227
-source /ccs/proj/cli900/sw/rhea/e3sm-unified/load_latest_e3sm_unified.sh
+# Personal recipe last modified: 20190828
+# Personal recipe last used successfully: 20190827 (except ncgen does not link)
 export LINUX_CC='gcc -std=c99 -pedantic -D_DEFAULT_SOURCE -D_BSD_SOURCE -D_POSIX_SOURCE'
 export LINUX_CXX='g++ -std=c++11'
 export LINUX_FC='gfortran'
-export LD_LIBRARY_PATH=/ccs/proj/cli900/sw/rhea/e3sm-unified/base/envs/e3sm_unified_1.2.5_py3.7_nox/lib:${LD_LIBRARY_PATH}
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/ccs/proj/cli900/sw/rhea/e3sm-unified/base/envs/e3sm_unified_1.2.5_py3.7_nox/lib
 export NETCDF_ROOT=/ccs/proj/cli900/sw/rhea/e3sm-unified/base/envs/e3sm_unified_1.2.5_py3.7_nox
-export PATH=/ccs/proj/cli900/sw/rhea/e3sm-unified/base/envs/e3sm_unified_1.2.5_py3.7_nox/bin:${PATH}
+export PATH=${PATH}:/ccs/proj/cli900/sw/rhea/e3sm-unified/base/envs/e3sm_unified_1.2.5_py3.7_nox/bin
 cd ~/nco;git reset --hard origin/master
 cd ~/nco/bld;make ANTLR_ROOT=${HOME} NETCDF_ROOT='/ccs/proj/cli900/sw/rhea/e3sm-unified/base/envs/e3sm_unified_1.2.5_py3.7_nox' OPTS=D OMP=Y allinone;cd -
 
@@ -816,7 +801,9 @@ cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
 CC='gcc' CFLAGS='' CXX='g++' CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
 # Firn 20180729 (works)
 ANTLR_ROOT=${HOME} CC='gcc' CFLAGS='' CXX='g++' CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
-# Sastrugi 20180729 (works)
+# Sastrugi 20180729 (works with both gcc and clang)
+ANTLR_ROOT=${HOME} CC=${LINUX_CC} CFLAGS='' CXX=${LINUX_CXX} CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
+# Rigb 20190912 (fxm)
 ANTLR_ROOT=${HOME} CC=${LINUX_CC} CFLAGS='' CXX=${LINUX_CXX} CXXFLAGS='' ./configure --prefix=${HOME} --bindir=${MY_BIN_DIR} --datadir=${HOME}/nco/data --libdir=${MY_LIB_DIR} --mandir=${HOME}/nco/man > nco.configure.${GNU_TRP}.foo 2>&1
 /bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
 /bin/cp -f libtool nco.libtool.${GNU_TRP}.foo

data/map_file_stats.nco

+// check the totals in a map file
+// usage:  ncap2 -v -O -S map_file_checker.nco  map_in.nc tot.nc
+
+
+pi=3.14159265358979323844;
+
+a=1;
+a@area_ttl=area_a.ttl();
+a@mask_ttl=mask_a.ttl().int();;
+a@frac_ttl=frac_a.ttl();
+a@frac_min=frac_a.min();
+a@frac_max=frac_a.max();
+a@frac_rms=(frac_a-1.0).rms();
+
+b=1;
+b@area_ttl=area_b.ttl();
+b@mask_ttl=mask_b.ttl();
+b@frac_ttl=frac_b.ttl();
+b@frac_min=frac_b.min();
+b@frac_max=frac_b.max();
+b@frac_rms=(frac_b-1.0).rms();
+
+s=1;
+s@S_ttl=S.ttl();
+
+
+print("map file statistics\n");
+print(a@area_ttl,"area_a total=%.15g steradians");
+print(a@area_ttl / 4.0 / pi *100.0, "  ( %.15f%% )\n"); 
+
+print(a@mask_ttl, "mask_a total=%d\n");
+print(a@frac_ttl, "frac_a total=%.15f ");
+print(a@frac_min, "min=%.15f ");
+print(a@frac_max, "max=%.15f ");
+print(a@frac_rms, "rms=%.15f\n");  
+
+print("\n");
+print(b@area_ttl,"area_b total=%.15g steradians");
+print(b@area_ttl / 4.0 / pi *100.0, "  ( %.15f%% )\n"); 
+
+print(b@mask_ttl, "mask_b total=%d\n");
+print(b@frac_ttl, "frac_b total=%.15f ");
+print(b@frac_min, "min=%.15f ");
+print(b@frac_max, "max=%.15f ");
+print(b@frac_rms, "rms=%.15f\n");  
+
+print("\n");
+print(s@S_ttl,"S weights  total=%.15f\n");

debian/changelog

-nco (4.8.1-2) UNRELEASED; urgency=medium
+nco (4.9.0-1) unstable; urgency=medium
 
+  * New upstream release.
   * Bump Standards-Version to 4.4.1, no changes.
+  * Drop spelling-errors.patch, applied upstream.
+  * Drop unused override for spelling-error-in-binary.
 
- -- Bas Couwenberg <sebastic@debian.org>  Wed, 10 Jul 2019 18:33:34 +0200
+ -- Bas Couwenberg <sebastic@debian.org>  Thu, 05 Dec 2019 05:32:58 +0100
 
 nco (4.8.1-1) unstable; urgency=medium
 

debian/lintian-overrides

-# False positive, string not included in source
-spelling-error-in-binary usr/bin/nc* ment meant
-
 # False positive on abbreviation for 'degree east'
 spelling-error-in-binary * degreeE degree
 

debian/patches/series

-spelling-errors.patch

debian/patches/spelling-errors.patch

-Description: Fix spelling errors.
- * didnt -> didn't
-Author: Bas Couwenberg <sebastic@debian.org>
-Forwarded: https://github.com/nco/nco/pull/141
-Applied-Upstream: https://github.com/nco/nco/commit/cf2a29f647d1755d600ad7184aae674c4ac1f50f
-
---- a/src/nco/nco_ply_lst.c
-+++ b/src/nco/nco_ply_lst.c
-@@ -218,7 +218,7 @@ int *pl_nbr)
-     else
-     {
-       if(nco_dbg_lvl_get() >=  nco_dbg_std ){
--        (void)fprintf(stdout, "%s: split wrapping didnt work on this polygon(%lu)\n", nco_prg_nm_get(), idx );
-+        (void)fprintf(stdout, "%s: split wrapping didn't work on this polygon(%lu)\n", nco_prg_nm_get(), idx );
-         (void)fprintf(stdout, "/********************************/\n");
-       }
- 

doc/MANIFEST

@@ -241,12 +241,14 @@ nco/src/nco/nco_cnf_dmn.c
 nco/src/nco/nco_cnf_dmn.h
 nco/src/nco/nco_cnf_typ.c
 nco/src/nco/nco_cnf_typ.h
-nco/src/nco/nco_cnk.h
 nco/src/nco/nco_cnk.c
+nco/src/nco/nco_cnk.h
 nco/src/nco/nco_cnv_arm.c
 nco/src/nco/nco_cnv_arm.h
 nco/src/nco/nco_cnv_csm.c
 nco/src/nco/nco_cnv_csm.h
+nco/src/nco/nco_crt.c
+nco/src/nco/nco_crt.h
 nco/src/nco/nco_ctl.c
 nco/src/nco/nco_ctl.h
 nco/src/nco/nco_dbg.c
@@ -261,29 +263,35 @@ nco/src/nco/nco_grp_trv.c
 nco/src/nco/nco_grp_trv.h
 nco/src/nco/nco_grp_utl.c
 nco/src/nco/nco_grp_utl.h
+nco/src/nco/nco_kd.c
+nco/src/nco/nco_kd.h
 nco/src/nco/nco_lmt.c
 nco/src/nco/nco_lmt.h
 nco/src/nco/nco_lst_utl.c
 nco/src/nco/nco_lst_utl.h
 nco/src/nco/nco_map.c
 nco/src/nco/nco_map.h
-nco/src/nco/nco_md5.h
 nco/src/nco/nco_md5.c
+nco/src/nco/nco_md5.h
 nco/src/nco/nco_mmr.c
 nco/src/nco/nco_mmr.h
 nco/src/nco/nco_mpi.h
 nco/src/nco/nco_msa.c
 nco/src/nco/nco_msa.h
-nco/src/nco/nco_mta.c
-nco/src/nco/nco_mta.h
 nco/src/nco/nco_mss_val.c
 nco/src/nco/nco_mss_val.h
+nco/src/nco/nco_mta.c
+nco/src/nco/nco_mta.h
 nco/src/nco/nco_netcdf.c	NCO-independent C wrappers for libnetcdf
 nco/src/nco/nco_netcdf.h	NCO-independent C wrappers for libnetcdf
 nco/src/nco/nco_omp.c
 nco/src/nco/nco_omp.h
 nco/src/nco/nco_pck.c
 nco/src/nco/nco_pck.h
+nco/src/nco/nco_ply.c
+nco/src/nco/nco_ply.h
+nco/src/nco/nco_ply_lst.c
+nco/src/nco/nco_ply_lst.h
 nco/src/nco/nco_ppc.c
 nco/src/nco/nco_ppc.h
 nco/src/nco/nco_prn.c
@@ -304,6 +312,8 @@ nco/src/nco/nco_sld.c
 nco/src/nco/nco_sld.h
 nco/src/nco/nco_sng_utl.c
 nco/src/nco/nco_sng_utl.h
+nco/src/nco/nco_sph.c
+nco/src/nco/nco_sph.h
 nco/src/nco/nco_srm.c
 nco/src/nco/nco_srm.h
 nco/src/nco/nco_typ.h