[R-pkg-team] Bug#1144177: r-bioc-alabaster.base: FTBFS: collect2: error: ld returned 1 exit status

[Santiago Vila]

Package: src:r-bioc-alabaster.base
Version: 1.6.1+ds-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/202608/

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-alabaster.base, 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
   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-alabaster.base/ -O--buildsystem=R
I: R Package: alabaster.base Version: 1.6.1
I: Building using R version 4.6.1-4
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Sun, 12 Jan 2025 11:19:49 +0100
	mkdir -p /<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library
	R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library --clean . --built-timestamp="'Sun, 12 Jan 2025 11:19:49 +0100'"
* installing *source* package ‘alabaster.base’ ...
** this is package ‘alabaster.base’ version ‘1.6.1’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘x86_64-linux-gnu-g++ (Debian 16.2.0-1) 16.2.0’
using C++17
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c RcppExports.cpp -o RcppExports.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c check_csv.cpp -o check_csv.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c check_list.cpp -o check_list.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c is_rfc3339.cpp -o is_rfc3339.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c load_csv.cpp -o load_csv.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c load_list.cpp -o load_list.o
x86_64-linux-gnu-g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/hdf5/serial/ -I'/usr/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2   -c validate.cpp -o validate.o
x86_64-linux-gnu-g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o -fPIC /usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5 -lhdf5_cpp -lcrypto -lcurl -lpthread -lsz -lz -L/usr/lib/R/lib -lR
/usr/bin/x86_64-linux-gnu-ld.bfd: cannot find /usr/lib/R/site-library/Rhdf5lib/libs/Rhdf5lib.so: No such file or directory
collect2: error: ld returned 1 exit status
make[1]: *** [/usr/share/R/share/make/shlib.mk:10: alabaster.base.so] 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 ‘alabaster.base’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-alabaster.base/usr/lib/R/site-library/alabaster.base’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-alabaster.base-1.6.1\+ds/debian/r-bioc-alabaster.base/usr/lib/R/site-library --clean . --built-timestamp="'Sun, 12 Jan 2025 11:19:49 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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