[R-pkg-team] Bug#951655: r-cran-sf: FTBFS with PROJ 7.0.0 (configure: error: proj_api.h not found in standard or given locations.)

[Bas Couwenberg]

Source: r-cran-sf
Version: 0.8-1+dfsg-1
Severity: important
Tags: ftbfs
User: debian-gis at lists.debian.org
Usertags: proj-7.0

Dear Maintainer,

Your package FTBFS with PROJ 7 from experimental:

 configure: error: proj_api.h not found in standard or given locations.

The full buildlog is attached.

Kind Regards,

Bas
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dpkg-checkbuilddeps: error: Unmet build dependencies: r-cran-classint (>= 0.4-1) r-cran-dbi (>= 0.8) r-cran-magrittr r-cran-rcpp (>= 0.12.18) r-cran-units libgdal-dev
W: Unmet build-dependency in source
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building r-cran-sf using existing ./r-cran-sf_0.8-1+dfsg.orig.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building r-cran-sf in r-cran-sf_0.8-1+dfsg-2.debian.tar.xz
dpkg-source: info: building r-cran-sf in r-cran-sf_0.8-1+dfsg-2.dsc
I: Generating source changes file for original dsc
dpkg-genchanges: info: not including original source code in upload
I: Copying COW directory
I: forking: rm -rf /var/cache/pbuilder/build/cow.340
I: forking: cp -al /var/cache/pbuilder/base-sid+rebuild.cow /var/cache/pbuilder/build/cow.340
I: removed stale ilistfile /var/cache/pbuilder/build/cow.340/.ilist
I: forking: chroot /var/cache/pbuilder/build/cow.340 cowdancer-ilistcreate /.ilist 'find . -xdev -path ./home -prune -o \( \( -type l -o -type f \) -a -links +1 -print0 \) | xargs -0 stat --format '%d %i ''
I: Invoking pbuilder
I: forking: pbuilder build --debbuildopts  --debbuildopts  --buildplace /var/cache/pbuilder/build/cow.340 --buildresult /var/cache/pbuilder/result/ --mirror http://ftp.nl.debian.org/debian/ --distribution sid --no-targz --internal-chrootexec 'chroot /var/cache/pbuilder/build/cow.340 cow-shell' /home/bas/tmp/debian/r-cran-sf_0.8-1+dfsg-2.dsc
I: Running in no-targz mode
I: pbuilder: network access will be disabled during build
I: Current time: Wed Feb 19 08:33:14 CET 2020
I: pbuilder-time-stamp: 1582097594
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: Copying source file
I: copying [/home/bas/tmp/debian/r-cran-sf_0.8-1+dfsg-2.dsc]
I: copying [/home/bas/tmp/debian/r-cran-sf_0.8-1+dfsg.orig.tar.xz]
I: copying [/home/bas/tmp/debian/r-cran-sf_0.8-1+dfsg-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: extracting unsigned source package (r-cran-sf_0.8-1+dfsg-2.dsc)
dpkg-source: info: extracting r-cran-sf in r-cran-sf-0.8-1+dfsg
dpkg-source: info: unpacking r-cran-sf_0.8-1+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-cran-sf_0.8-1+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying exclude_test_requiring_rgeos.patch
dpkg-source: info: applying exclude_test_requiring_rgdal.patch
I: using fakeroot in build.
I: Installing the build-deps
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint at lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 12), dh-r, r-base-dev, r-cran-classint (>= 0.4-1), r-cran-dbi (>= 0.8), r-cran-magrittr, r-cran-rcpp (>= 0.12.18), r-cran-units, libgdal-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 14426 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on dh-r; however:
  Package dh-r is not installed.
 pbuilder-satisfydepends-dummy depends on r-base-dev; however:
  Package r-base-dev is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-classint (>= 0.4-1); however:
  Package r-cran-classint is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-dbi (>= 0.8); however:
  Package r-cran-dbi is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-magrittr; however:
  Package r-cran-magrittr is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-rcpp (>= 0.12.18); however:
  Package r-cran-rcpp is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-units; however:
  Package r-cran-units is not installed.
 pbuilder-satisfydepends-dummy depends on libgdal-dev; however:
  Package libgdal-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
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The following packages are RECOMMENDED but will NOT be installed:
  bzip2-doc curl devscripts krb5-locales libarchive-cpio-perl libcfitsio-doc libfile-mimeinfo-perl libglib2.0-data libmail-sendmail-perl libnet-dbus-perl libpng-tools libtasn1-doc libx11-protocol-perl lynx poppler-data proj-bin publicsuffix r-cran-crayon r-cran-testthat r-cran-xml2 r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 
0 packages upgraded, 256 newly installed, 0 to remove and 0 not upgraded.
Need to get 6081 kB/165 MB of archives. After unpacking 687 MB will be used.
Writing extended state information...
Get: 1 http://ftp.nl.debian.org/debian sid/main amd64 libnetcdf15 amd64 1:4.7.3-1 [391 kB]
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Creating config file /etc/papersize with new version
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Building database of manual pages ...
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
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update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libnetcdf-dev (1:4.7.3-1) ...
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Creating config file /etc/R/Renviron with new version
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Setting up libmariadb-dev (1:10.3.22-1) ...
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Setting up r-cran-magrittr (1.5-5) ...
Setting up r-cran-littler (0.3.9-1) ...
Setting up libmariadb-dev-compat:amd64 (1:10.3.22-1) ...
Setting up r-cran-rcpp (1.0.3-1) ...
Setting up r-base-dev (3.6.2-2) ...
Setting up littler (0.3.9-1) ...
Setting up libgeotiff-dev:amd64 (1.5.1-3) ...
Setting up r-cran-dbi (1.1.0-2) ...
Setting up r-cran-mass (7.3-51.5-2) ...
Setting up r-cran-units (0.6-5-1) ...
Setting up r-cran-kernsmooth (2.23-16-1+1) ...
Setting up default-libmysqlclient-dev:amd64 (1.0.5) ...
Setting up r-cran-class (7.3-15-1+b1) ...
Setting up r-cran-e1071 (1.7-3-1) ...
Setting up r-cran-classint (0.4-2-1) ...
Setting up odbcinst (2.3.6-0.1+b1) ...
Setting up dh-autoreconf (19) ...
Setting up odbcinst1debian2:amd64 (2.3.6-0.1+b1) ...
Setting up unixodbc-dev:amd64 (2.3.6-0.1+b1) ...
Setting up libgdal26 (3.0.4+dfsg-2) ...
Setting up debhelper (12.9) ...
Setting up libgdal-dev (3.0.4+dfsg-2) ...
Setting up dh-r (20200104) ...
Processing triggers for libc-bin (2.29-10) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libfakeroot
The following NEW packages will be installed:
  fakeroot libfakeroot
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/132 kB of archives.
After this operation, 393 kB of additional disk space will be used.
Selecting previously unselected package libfakeroot:amd64.
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(Reading database ... 40033 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.24-1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.24-1_amd64.deb ...
Unpacking fakeroot (1.24-1) ...
Setting up libfakeroot:amd64 (1.24-1) ...
Setting up fakeroot (1.24-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Processing triggers for man-db (2.9.0-2) ...
Processing triggers for libc-bin (2.29-10) ...
I: Copying back the cached apt archive contents
I: new cache content 'littler_0.3.9-1_all.deb' added
I: new cache content 'r-cran-pkgkitten_0.1.5-1_all.deb' added
I: new cache content 'r-cran-littler_0.3.9-1_amd64.deb' added
I: new cache content 'r-cran-e1071_1.7-3-1_amd64.deb' added
I: new cache content 'r-cran-mass_7.3-51.5-2_amd64.deb' added
I: new cache content 'r-cran-rcpp_1.0.3-1_amd64.deb' added
I: new cache content 'r-cran-dbi_1.1.0-2_all.deb' added
I: new cache content 'r-cran-classint_0.4-2-1_amd64.deb' added
I: new cache content 'r-cran-units_0.6-5-1_amd64.deb' added
I: Building the package
I: Running cd /build/r-cran-sf-0.8-1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc 
dpkg-buildpackage: info: source package r-cran-sf
dpkg-buildpackage: info: source version 0.8-1+dfsg-2
dpkg-buildpackage: info: source distribution UNRELEASED
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-sf using existing ./r-cran-sf_0.8-1+dfsg.orig.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building r-cran-sf in r-cran-sf_0.8-1+dfsg-2.debian.tar.xz
dpkg-source: info: building r-cran-sf in r-cran-sf_0.8-1+dfsg-2.dsc
 debian/rules build
make: 'build' is up to date.
 fakeroot debian/rules binary
dh binary --buildsystem R
   dh_update_autotools_config -O--buildsystem=R
   dh_autoreconf -O--buildsystem=R
   dh_auto_configure -O--buildsystem=R
   dh_auto_build -O--buildsystem=R
   dh_auto_test -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=R
   dh_prep -O--buildsystem=R
   dh_auto_install -O--buildsystem=R
I: R packages needed for DEP8: testthat, sp, lwgeom, dplyr, tidyr, rsqlite, maps, maptools, ggplot2, raster, rpostgresql, spatstat
I: R Package: sf Version: 0.8-1
I: Building using R version 3.6.2-2
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Wed, 19 Feb 2020 08:33:09 +0100
	mkdir -p /build/r-cran-sf-0.8-1\+dfsg/debian/r-cran-sf/usr/lib/R/site-library
	R CMD INSTALL -l /build/r-cran-sf-0.8-1\+dfsg/debian/r-cran-sf/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 19 Feb 2020 08:33:09 +0100'"
* installing *source* package 'sf' ...
files 'inst/doc/sf1.html', 'inst/doc/sf2.html', 'inst/doc/sf3.html', 'inst/doc/sf4.html', 'inst/doc/sf5.html', 'inst/doc/sf6.html', 'tests/roundtrip.Rout.save' are missing
files 'tests/graticule.R', 'tests/graticule.Rout.save', 'tests/roundtrip.R', 'tests/testthat/test_geos.R', 'tests/testthat/test_tidy.R' have the wrong MD5 checksums
** using staged installation
configure: CC: gcc -std=gnu99
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.4
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj_api.h usability... no
checking proj_api.h presence... no
checking for proj_api.h... no
configure: error: proj_api.h not found in standard or given locations.
ERROR: configuration failed for package 'sf'
* removing '/build/r-cran-sf-0.8-1+dfsg/debian/r-cran-sf/usr/lib/R/site-library/sf'
dh_auto_install: error: R CMD INSTALL -l /build/r-cran-sf-0.8-1\+dfsg/debian/r-cran-sf/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 19 Feb 2020 08:33:09 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: Cleaning COW directory
I: forking: rm -rf /var/cache/pbuilder/build/cow.340