Automatic update for R-4.2.2-2.fc38.
* Fri Nov 4 2022 Iñaki Úcar <iucar@fedoraproject.org> - 4.2.2-2
- Move Java configuration to the build phase
- Remove javareconf from posttrans scriptlets
- Remove noreplace from javaconf file
- Rename LTO flag to avoid conflicts with bcond
- Simplify default R_LIBS_SITE cleanup
- Update old _pkgdocdir specification
Updates may require up to 24 hours to propagate to mirrors. If the following command doesn't work, please retry later:
sudo dnf upgrade --refresh --advisory=FEDORA-2022-ef1f99b84fPlease log in to add feedback.
This update was automatically created
This update's test gating status has been changed to 'waiting'.
This update's test gating status has been changed to 'ignored'.
This update has been submitted for stable by bodhi
This update changed the linker flags used when building executable in R-packages.
With 4.2.2-1
gcc -o r -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include/R littler.c -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,--export-dynamic -fopenmp -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -L/usr/lib64/R/lib -lR -ltre -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n -lflexiblas -lflexiblas -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/java-17-openjdk-17.0.5.0.8-1.fc38.x86_64/lib/server -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/java-17-openjdk-17.0.5.0.8-1.fc38.x86_64/lib/server -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/java-17-openjdk-17.0.5.0.8-1.fc38.x86_64/lib/server
With 4.2.2-2:
gcc -o r -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include/R littler.c -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,--export-dynamic -fopenmp -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -L/usr/lib64/R/lib -lR -ltre -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n -lflexiblas -lflexiblas -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/jre/lib/amd64/server -Wl,-rpath,/usr/lib/jvm/jre/lib/amd64 -Wl,-rpath,/usr/lib/jvm/java/lib/amd64 -Wl,-rpath,/usr/lib/jvm/jre/lib/server -Wl,-rpath,/usr/java/packages/lib/amd64 -Wl,-rpath,/lib -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/jre/lib/amd64/server -Wl,-rpath,/usr/lib/jvm/jre/lib/amd64 -Wl,-rpath,/usr/lib/jvm/java/lib/amd64 -Wl,-rpath,/usr/lib/jvm/jre/lib/server -Wl,-rpath,/usr/java/packages/lib/amd64 -Wl,-rpath,/lib -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/jre/lib/amd64/server -Wl,-rpath,/usr/lib/jvm/jre/lib/amd64 -Wl,-rpath,/usr/lib/jvm/java/lib/amd64 -Wl,-rpath,/usr/lib/jvm/jre/lib/server -Wl,-rpath,/usr/java/packages/lib/amd64 -Wl,-rpath,/lib -Wl,-rpath,/usr/lib
The problem comes from:
-Wl,-rpath,/lib -Wl,-rpath,/usr/lib
This adds standard library paths to RPATH, which makes rpm builds fail:
* * WARNING: 'check-rpaths' detected a broken RPATH OR RUNPATH and will cause * 'rpmbuild' to fail. To ignore these errors, you can set the * '$QA_RPATHS' environment variable which is a bitmask allowing the * values below. The current value of QA_RPATHS is 0x0000. * * 0x0001 ... standard RPATHs (e.g. /usr/lib); such RPATHs are a minor * issue but are introducing redundant searchpaths without * providing a benefit. They can also cause errors in multilib * environments. * 0x0002 ... invalid RPATHs; these are RPATHs which are neither absolute * nor relative filenames and can therefore be a SECURITY risk * 0x0004 ... insecure RPATHs; these are relative RPATHs which are a * SECURITY risk * 0x0008 ... the special '$ORIGIN' RPATHs are appearing after other * RPATHs; this is just a minor issue but usually unwanted * 0x0010 ... the RPATH is empty; there is no reason for such RPATHs * and they cause unneeded work while loading libraries * 0x0020 ... an RPATH references '..' of an absolute path; this will break * the functionality when the path before '..' is a symlink *
* * Examples: * - to ignore standard and empty RPATHs, execute 'rpmbuild' like * $ QA_RPATHS=$(( 0x0001|0x0010 )) rpmbuild my-package.src.rpm * - to check existing files, set $RPM_BUILD_ROOT and execute check-rpaths like * $ RPM_BUILD_ROOT=<top-dir> /usr/lib/rpm/check-rpaths *
ERROR 0002: file '/usr/bin/r' contains an invalid runpath '/usr/java/packages/lib/amd64' in [/usr/lib64/R/lib:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/lib/jvm/jre/lib/server:/usr/java/packages/lib/amd64:/lib:/usr/lib] ERROR 0001: file '/usr/bin/r' contains a standard runpath '/lib' in [/usr/lib64/R/lib:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/lib/jvm/jre/lib/server:/usr/java/packages/lib/amd64:/lib:/usr/lib] ERROR 0001: file '/usr/bin/r' contains a standard runpath '/usr/lib' in [/usr/lib64/R/lib:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/lib/jvm/jre/lib/server:/usr/java/packages/lib/amd64:/lib:/usr/lib]
This build failure was detected by koschei:
https://koschei.fedoraproject.org/package/R-littler?collection=f38
[Facepalm] Rebuilding now, see the list.