On 15 April 2025 at 00:19, Santiago Vila wrote:
| Package: src:rjava
| Version: 1.0-11-1
| Severity: serious
| Tags: ftbfs trixie sid
|
| Dear maintainer:
|
| During a rebuild of all packages in unstable, your package failed to build:
|
| --------------------------------------------------------------------------------
| [...]
| 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-cran-rjava/ -O--buildsystem=R
| I: R Package: rJava Version: 1.0-11
| I: Building using R version 4.5.0-1
| 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’ ...
| ** this is package ‘rJava’ version ‘1.0-11’
| files ‘configure’, ‘jri/configure’, ‘jri/src/config.h.in’, ‘jri/tools/config.guess’, ‘jri/tools/config.sub’, ‘src/config.h.in’ have the wrong MD5 checksums
| ** using staged installation
| checking for gcc... gcc -std=gnu23
| 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 -std=gnu23 accepts -g... yes
| checking for gcc -std=gnu23 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 -std=gnu23 supports static inline...
| yes
| checking whether setjmp.h is POSIX.1 compatible... yes
| checking for gcc -std=gnu23 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 -std=gnu23' '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 -std=gnu23
| 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 -std=gnu23 accepts -g... yes
| checking for gcc -std=gnu23 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... 21.0.7-ea
| checking Java compatibility version (integer)... 21
| 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 14.2.0-19) 14.2.0’
| make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
| gcc -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 | warning: [options] source value 8 is obsolete and will be removed in a future release
| warning: [options] target value 8 is obsolete and will be removed in a future release
| warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
| ../REXP.java:170: warning: [removal] finalize() in Object has been deprecated and marked for removal
| protected void finalize() throws Throwable {
| ^
| ../REXP.java:175: warning: [removal] finalize() in Object has been deprecated and marked for removal
| super.finalize();
| ^
| Note: Some input files use unchecked or unsafe operations.
| Note: Recompile with -Xlint:unchecked for details.
| 6 warnings
| if [ -n "" ]; then -d . -classpath . org.rosuda.JRI.Rengine; fi
| gcc -std=gnu23 -c -o Rengine.o Rengine.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -c -o jri.o jri.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -c -o Rcallbacks.o Rcallbacks.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -c -o Rinit.o Rinit.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -c -o globals.o globals.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -c -o rjava.o rjava.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -c -o rjstring.o rjstring.c -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -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 -std=gnu23 -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 -lzstd -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n
| /usr/bin/ld: cannot find -lzstd: No such file or directory

First rpy2, now rJava. Seems like we do need libzstd-dev exported / depended upon by r-base-dev.

Dirk

| 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: 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/202504/
|
| 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 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 add an affects on src:rjava, so that this is still
| visible in the BTS web page for this package.
|
| Thanks.

--
dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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