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. -------------------------------------------------------------------------------- [...] 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 âalabaster.baseâ ... ** this is package âalabaster.baseâ version â1.6.1â ** using staged installation ** libs specified C++17 using C++ compiler: âx86_64-linux-gnu-g++ (Debian 16.2.0-1) 16.2.0â 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 âalabaster.baseâ * removing â/<<PKGBUILDDIR>>/debian/r-bioc-alabaster.base/usr/lib/R/site-library/alabaster.baseâ 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 --------------------------------------------------------------------------------
