[R-pkg-team] Bug#978891: r-cran-ncdf4: ftbfs with autoconf 2.70

[Matthias Klose]

Package: src:r-cran-ncdf4
Version: 1.17-1
Severity: normal
Tags: sid bookworm
User: doko at debian.org
Usertags: ftbfs-ac270

[This bug report is not targeted to the upcoming bullseye release]

The package fails to build in a test rebuild on at least amd64 with
autoconf 2.70, but succeeds to build with autoconf 2.69. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://qa-logs.debian.net/2020/09/26.ac270/r-cran-ncdf4_1.17-1_unstable_ac270.log
The last lines of the build log are at the end of this report.

To build with autoconf 2.70, please install the autoconf package from
experimental:  apt-get -t=experimental install autoconf 

[...]
SCHROOT_UID=1001
SCHROOT_USER=user42
SHELL=/bin/sh
USER=user42

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -sa -rfakeroot
dpkg-buildpackage: info: source package r-cran-ncdf4
dpkg-buildpackage: info: source version 1.17-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Dylan Aïssi <daissi at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 fakeroot debian/rules clean
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 dpkg-source -b .
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building r-cran-ncdf4 using existing ./r-cran-ncdf4_1.17.orig.tar.gz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building r-cran-ncdf4 in r-cran-ncdf4_1.17-1.debian.tar.xz
dpkg-source: info: building r-cran-ncdf4 in r-cran-ncdf4_1.17-1.dsc
 debian/rules build
dh build --buildsystem R
   dh_update_autotools_config -O--buildsystem=R
   dh_autoreconf -O--buildsystem=R
configure.ac:44: warning: AC_OUTPUT should be used without arguments.
configure.ac:44: You should run autoupdate.
configure.ac:44: warning: AC_OUTPUT should be used without arguments.
configure.ac:44: You should run autoupdate.
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd tools && ./regenerate
rm: cannot remove '../Makefile': No such file or directory
rm: cannot remove '../src/Makevars': No such file or directory
configure.ac:44: warning: AC_OUTPUT should be used without arguments.
configure.ac:44: You should run autoupdate.
configure.ac:44: warning: AC_OUTPUT should be used without arguments.
configure.ac:44: You should run autoupdate.
dh_auto_configure
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_build -O--buildsystem=R
   dh_auto_test -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary
dh binary --buildsystem R
   dh_testroot -O--buildsystem=R
   dh_prep -O--buildsystem=R
   dh_auto_install -O--buildsystem=R
I: R Package: ncdf4 Version: 1.17
I: Building using R version 4.0.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 03 Jan 2020 18:51:25 +0100
	mkdir -p /<<PKGBUILDDIR>>/debian/r-cran-ncdf4/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-ncdf4/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 03 Jan 2020 18:51:25 +0100'"
* installing *source* package ‘ncdf4’ ...
files ‘configure’, ‘configure.ac’, ‘tools/aclocal.m4’, ‘tools/configure.ac’ have the wrong MD5 checksums
** using staged installation
configure.ac: starting
./configure: line 1764: syntax error near unexpected token `;;'
./configure: line 1764: ` as_dir=./ ;;'
ERROR: configuration failed for package ‘ncdf4’
* removing ‘/<<PKGBUILDDIR>>/debian/r-cran-ncdf4/usr/lib/R/site-library/ncdf4’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-ncdf4/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 03 Jan 2020 18:51:25 +0100'" returned exit code 1
make: *** [debian/rules:5: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2