reassign 1069842 r-base thanks
On 25 April 2024 at 18:27, Santiago Vila wrote: | Package: src:rjava | Version: 1.0-11-1 | Severity: serious | Tags: ftbfs | | Dear maintainer: | | During a rebuild of all packages in unstable, your package failed to build: Thanks for this. It is caused by the just released R 4.4.0 which now uses libdeflate, gets it somehow already via its Build-Depends but then does not implicitly pass it on via its virtual (child) package r-base-dev and its depends. (Both have a list of lib*-dev compression packages.) I will make a r-base 4.4.0-2 either today or tomorrow to correct this and have r-base-dev explicitly list libdeflate-dev. Dirk | | -------------------------------------------------------------------------------- | [...] | debian/rules build | dh build --buildsystem R | dh_update_autotools_config -O--buildsystem=R | cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead | cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead | 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 | fakeroot debian/rules binary | dh binary --buildsystem R | dh_testroot -O--buildsystem=R | dh_prep -O--buildsystem=R | dh_auto_install --destdir=debian/r-cran-rjava/ -O--buildsystem=R | I: R Package: rJava Version: 1.0-11 | I: Building using R version 4.4.0-1 | I: R API version: r-api-4.0 | I: Using built-time from d/changelog: Fri, 26 Jan 2024 11:10:09 -0600 | mkdir -p /<<PKGBUILDDIR>>/debian/r-cran-rjava/usr/lib/R/site-library | R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rjava/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 26 Jan 2024 11:10:09 -0600'" | * installing *source* package ‘rJava’ ... | files ‘configure’, ‘jri/tools/config.guess’, ‘jri/tools/config.sub’, ‘src/config.h.in’ have the wrong MD5 checksums | ** using staged installation | checking for gcc... gcc | 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 the compiler supports GNU C... yes | checking whether gcc accepts -g... yes | checking for gcc option to enable C11 features... none needed | checking for sys/wait.h that is POSIX.1 compatible... yes | checking for stdio.h... yes | checking for stdlib.h... yes | checking for string.h... yes | checking for inttypes.h... yes | checking for stdint.h... yes | checking for strings.h... yes | checking for sys/stat.h... yes | checking for sys/types.h... yes | checking for unistd.h... yes | checking for string.h... (cached) yes | checking for sys/time.h... yes | checking for unistd.h... (cached) yes | checking for an ANSI C-conforming const... yes | configure: checking whether gcc supports static inline... | yes | checking whether setjmp.h is POSIX.1 compatible... yes | checking for gcc options needed to detect all undeclared functions... none needed | checking whether sigsetjmp is declared... yes | checking whether siglongjmp is declared... yes | checking Java support in R... present: | interpreter : '/usr/lib/jvm/default-java/bin/java' | archiver : '/usr/lib/jvm/default-java/bin/jar' | compiler : '/usr/lib/jvm/default-java/bin/javac' | header prep.: '' | cpp flags : '-I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux' | java libs : '-L/usr/lib/jvm/default-java/lib/server -ljvm' | checking whether Java run-time works... yes | checking whether -Xrs is supported... yes | checking whether -Xrs will be used... yes | checking whether JVM will be loaded dynamically... no | checking whether JNI programs can be compiled... yes | checking whether JNI programs run... yes | checking JNI data types... ok | checking whether JRI should be compiled (autodetect)... yes | checking whether debugging output should be enabled... no | checking whether memory profiling is desired... no | checking whether threads support is requested... no | checking whether callbacks support is requested... no | checking whether JNI cache support is requested... no | checking whether headless init is enabled... no | checking whether JRI is requested... yes | configure: creating ./config.status | config.status: creating src/Makevars | config.status: creating R/zzz.R | config.status: creating src/config.h | === configuring in jri (/<<PKGBUILDDIR>>/jri) | configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local' 'CC=gcc' 'CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection' 'LDFLAGS=-Wl,-z,relro' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' --cache-file=/dev/null --srcdir=. | checking build system type... x86_64-pc-linux-gnu | checking host system type... x86_64-pc-linux-gnu | checking for gcc... gcc | 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 the compiler supports GNU C... yes | checking whether gcc accepts -g... yes | checking for gcc option to enable C11 features... none needed | checking for stdio.h... yes | checking for stdlib.h... yes | checking for string.h... yes | checking for inttypes.h... yes | checking for stdint.h... yes | checking for strings.h... yes | checking for sys/stat.h... yes | checking for sys/types.h... yes | checking for unistd.h... yes | checking for sys/time.h... yes | checking for sys/types.h... (cached) yes | checking for sys/select.h... yes | checking Java version... 17.0.11 | checking Java compatibility version (integer)... 17 | checking whether actually works... no | checking whether javah was replaced by javac -h... yes | checking for target flags... -h . -target 1.8 -source 1.8 | checking whether Java interpreter works... checking whether JNI programs can be compiled... yes | checking whether JNI programs can be run... yes | checking JNI data types... ok | checking whether Rinterface.h exports R_CStackXXX variables... yes | checking whether Rinterface.h exports R_SignalHandlers... yes | configure: creating ./config.status | config.status: creating src/Makefile | config.status: creating Makefile | config.status: creating run | config.status: creating src/config.h | ** libs | using C compiler: ‘gcc (Debian 13.2.0-23) 13.2.0’ | make[1]: Entering directory '/<<PKGBUILDDIR>>/src' | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Rglue.c -o Rglue.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c arrayc.c -o arrayc.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c callJNI.c -o callJNI.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c callback.c -o callback.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c fields.c -o fields.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c jri_glue.c -o jri_glue.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c loader.c -o loader.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c otables.c -o otables.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c rJava.c -o rJava.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c registration.c -o registration.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c rjstring.c -o rjstring.o | gcc -I"/usr/share/R/include" -DNDEBUG -I. -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c tools.c -o tools.o | gcc -shared -L/usr/lib/R/lib -Wl,-z,relro -o rJava.so Rglue.o arrayc.o callJNI.o callback.o fields.o init.o jri_glue.o loader.o otables.o rJava.o registration.o rjstring.o tools.o -L/usr/lib/jvm/default-java/lib/server -ljvm -L/usr/lib/R/lib -lR | (cd ../jri && make) | make[2]: Entering directory '/<<PKGBUILDDIR>>/jri' | make -C src JRI.jar | make[3]: Entering directory '/<<PKGBUILDDIR>>/jri/src' | /usr/lib/jvm/default-java/bin/javac -h . -target 1.8 -source 1.8 -d . ../Mutex.java ../RBool.java ../RConsoleOutputStream.java ../REXP.java ../RFactor.java ../RList.java ../RMainLoopCallbacks.java ../RVector.java ../Rengine.java ../package-info.java | warning: [options] bootstrap class path not set in conjunction with -source 8 | Note: ../REXP.java uses or overrides a deprecated API. | Note: Recompile with -Xlint:deprecation for details. | Note: Some input files use unchecked or unsafe operations. | Note: Recompile with -Xlint:unchecked for details. | 1 warning | if [ -n "" ]; then -d . -classpath . org.rosuda.JRI.Rengine; fi | gcc -c -o Rengine.o Rengine.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include | gcc -c -o jri.o jri.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include | gcc -c -o Rcallbacks.o Rcallbacks.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include | gcc -c -o Rinit.o Rinit.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/share/R/include -I/usr/share/R/include | gcc -c -o globals.o globals.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux | gcc -c -o rjava.o rjava.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux | gcc -c -o rjstring.o rjstring.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -g -Iinclude -DRIF_HAS_CSTACK -DRIF_HAS_RSIGHAND -DHAVE_CONFIG_H -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -I/usr/share/R/include -I/usr/share/R/include | gcc -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o rjstring.o -Wl,-z,relro -Wl,-z,relro -shared -L/usr/lib/jvm/default-java/lib/server -ljvm -Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n | /usr/bin/ld: cannot find -ldeflate: No such file or directory | collect2: error: ld returned 1 exit status | make[3]: *** [Makefile.all:40: libjri.so] Error 1 | make[3]: Leaving directory '/<<PKGBUILDDIR>>/jri/src' | make[2]: *** [Makefile.all:19: src/JRI.jar] Error 2 | make[2]: Leaving directory '/<<PKGBUILDDIR>>/jri' | make[1]: *** [Makevars:14: jri] Error 2 | make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' | make[1]: Entering directory '/<<PKGBUILDDIR>>/src' | make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' | ERROR: compilation failed for package ‘rJava’ | * removing ‘/<<PKGBUILDDIR>>/debian/r-cran-rjava/usr/lib/R/site-library/rJava’ | dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rjava/usr/lib/R/site-library --clean . "--built-timestamp='Fri, 26 Jan 2024 11:10:09 -0600'" returned exit code 1 | make: *** [debian/rules:7: binary] Error 25 | dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2 | -------------------------------------------------------------------------------- | | The above is just how the build ends and not necessarily the most relevant part. | If required, the full build log is available here: | | https://people.debian.org/~sanvila/build-logs/202404/ | | About the archive rebuild: The build was made on virtual machines | of type m6a.large from AWS, using sbuild and a reduced chroot | with only build-essential packages. | | If you could not 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 affects, so that this is still visible in the BTS web | page for this package. | | Thanks. -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
