[R-pkg-team] Bug#1135464: r-bioc-rhdf5: FTBFS: H5D.c:461:25: error: implicit declaration of function 'STRING_PTR'; did you mean 'STRING_ELT'? [-Wimplicit-function-declaration]
Santiago Vila
sanvila at debian.org
Sat May 2 00:14:39 BST 2026
Package: src:r-bioc-rhdf5
Version: 2.50.2+dfsg-2
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202605/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:r-bioc-rhdf5, so that this is still
visible in the BTS web page for this package.
Thanks.
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[...]
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules binary
dh binary --buildsystem R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
autoreconf: export WARNINGS=
autoreconf: Entering directory '.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force
autoreconf: configure.ac: tracing
autoreconf: configure.ac: not using Libtool
autoreconf: configure.ac: not using Intltool
autoreconf: configure.ac: not using Gtkdoc
autoreconf: running: /usr/bin/autoconf --force
autoreconf: configure.ac: not using Autoheader
autoreconf: configure.ac: not using Automake
autoreconf: Leaving directory '.'
debian/rules execute_before_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# see debian/hdf5-1.14-private/README
ln -s /<<PKGBUILDDIR>>/debian/hdf5-1.14-private/H5private.h /<<PKGBUILDDIR>>/src/H5private.h
ln -s /<<PKGBUILDDIR>>/debian/hdf5-1.14-private/H5TSprivate.h /<<PKGBUILDDIR>>/src/H5TSprivate.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 --destdir=debian/r-bioc-rhdf5/ -O--buildsystem=R
I: R Package: rhdf5 Version: 2.50.2
I: Building using R version 4.6.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 13 Mar 2026 19:24:08 +0900
mkdir -p /<<BUILDDIR>>/r-bioc-rhdf5-2.50.2\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-rhdf5-2.50.2\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 19:24:08 +0900'"
* installing *source* package ‘rhdf5’ ...
** this is package ‘rhdf5’ version ‘2.50.2’
files ‘inst/doc/practical_tips.html’, ‘inst/doc/rhdf5.html’, ‘inst/doc/rhdf5_cloud_reading.html’ are missing
files ‘configure’, ‘src/H5R.c’, ‘src/H5constants.c’, ‘src/Makevars’, ‘src/h5testLock.h’, ‘src/myhdf5.h’, ‘src/utils.c’, ‘tests/testthat/test_H5P.R’, ‘tests/testthat/test_external_filters.R’, ‘tests/testthat/test_h5read.R’ have the wrong MD5 checksums
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
using C compiler: ‘x86_64-linux-gnu-gcc (Debian 15.2.0-17) 15.2.0’
using C++ compiler: ‘x86_64-linux-gnu-g++ (Debian 15.2.0-17) 15.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -DH5_USE_110_API -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c H5.c -o H5.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -DH5_USE_110_API -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c H5A.c -o H5A.o
x86_64-linux-gnu-gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rhdf5lib/include' -DH5_USE_110_API -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c H5D.c -o H5D.o
H5D.c: In function ‘H5Dread_helper_STRING’:
H5D.c:461:25: error: implicit declaration of function ‘STRING_PTR’; did you mean ‘STRING_ELT’? [-Wimplicit-function-declaration]
461 | PERMUTE(Rval, STRING_PTR, mem_space_id);
| ^~~~~~~~~~
H5D.c:50:5: note: in definition of macro ‘PERMUTE’
50 | ACCESSOR(to)[li] = ACCESSOR(FROM)[lj]; \
| ^~~~~~~~
H5D.c:50:17: error: subscripted value is neither array nor pointer nor vector
50 | ACCESSOR(to)[li] = ACCESSOR(FROM)[lj]; \
| ^
H5D.c:461:11: note: in expansion of macro ‘PERMUTE’
461 | PERMUTE(Rval, STRING_PTR, mem_space_id);
| ^~~~~~~
H5D.c:50:38: error: subscripted value is neither array nor pointer nor vector
50 | ACCESSOR(to)[li] = ACCESSOR(FROM)[lj]; \
| ^
H5D.c:461:11: note: in expansion of macro ‘PERMUTE’
461 | PERMUTE(Rval, STRING_PTR, mem_space_id);
| ^~~~~~~
H5D.c: In function ‘_H5Dwrite’:
H5D.c:50:17: error: subscripted value is neither array nor pointer nor vector
50 | ACCESSOR(to)[li] = ACCESSOR(FROM)[lj]; \
| ^
H5D.c:1080:13: note: in expansion of macro ‘PERMUTE’
1080 | PERMUTE(_buf, STRING_PTR, dim_space_id);
| ^~~~~~~
H5D.c:50:38: error: subscripted value is neither array nor pointer nor vector
50 | ACCESSOR(to)[li] = ACCESSOR(FROM)[lj]; \
| ^
H5D.c:1080:13: note: in expansion of macro ‘PERMUTE’
1080 | PERMUTE(_buf, STRING_PTR, dim_space_id);
| ^~~~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:190: H5D.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘rhdf5’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-rhdf5/usr/lib/R/site-library/rhdf5’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-rhdf5-2.50.2\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library --clean . --built-timestamp="'Fri, 13 Mar 2026 19:24:08 +0900'" returned exit code 1
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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