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:
--------------------------------------------------------------------------------
[...]
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.
