FEDORA-2022-ef1f99b84f created by iucar 3 months ago for Fedora 38

Automatic update for R-4.2.2-2.fc38.

* Fri Nov  4 2022 Iñaki Úcar <> - 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

This update was automatically created

3 months ago

This update's test gating status has been changed to 'waiting'.

3 months ago

This update's test gating status has been changed to 'ignored'.

3 months ago

This update has been submitted for stable by bodhi

3 months ago
User Icon ellert commented & provided feedback 3 months ago

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- -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/java-17-openjdk- -Wl,-rpath,/usr/lib64/R/lib -Wl,-rpath,/usr/lib/jvm/java-17-openjdk-

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:

  • /usr/lib/rpm/check-rpaths

* 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:

[Facepalm] Rebuilding now, see the list.

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Content Type
Test Gating
Unstable by Karma
Stable by Karma
Stable by Time
0 days
3 months ago
in testing
3 months ago
in stable
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