Updating mysql fails on my system due to a sandbox access violation: * ----------------------- SANDBOX ACCESS VIOLATION SUMMARY ----------------------- * LOG FILE: "/var/tmp/portage/dev-db/mysql-8.0.31-r2/temp/sandbox.log" * VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line F: unlink S: deny P: /var/lib/mysql/mysqld-auto.cnf.backup A: /var/lib/mysql/mysqld-auto.cnf.backup R: /var/lib/mysql/mysqld-auto.cnf.backup C: /var/tmp/portage/dev-db/mysql-8.0.31-r2/work/mysql_build/runtime_output_directory/mysqld --no-defaults --help * -------------------------------------------------------------------------------- /var/lib/mysql/mysqld-auto.cnf.backup does not exist after the failed update, but I do have a file /var/lib/mysql/mysqld-auto.cnf.
Please include the full build.log and emerge --info.
Change the status to UNCONFIRMED once the above has been provided.
Created attachment 859827 [details] Build log (compressed)
Created attachment 859828 [details] emerge --info
I was able to re-produce the problem on a fresh installation of gentoo. 1. install mysql: emerge --ask mysql 2. configure mysql: emerge --config dev-db/mysql 3. start mysql server: /etc/init.d/mysql start 4. start mysql shell: mysql -p 5. on mysql shell: set persist binlog_expire_logs_seconds = 259200; 6. re-emerge mysql: emerge --ask mysql
Thank you!
I was able to get mysql updated by adding a file /etc/sandbox.d/99mysql: > # cat /etc/sandbox.d/99mysql > SANDBOX_WRITE="/var/lib/mysql/mysqld-auto.cnf.backup" > # But I am not sure, why the filename in /etc/sandbox.d/ start with a number. In /etc/rc2.d, filenames starting with numbers were use to control the execution order, but I do not see the impact of ordering sandbox configurations. I also assume that tis exceptions allows all ebuilds to write to /var/lib/mysql/mysqld-auto.cnf.backup, not just only dev-db/mysql.
I confirm the bug and the fix given in comment 7. Originally, mysql emerged without any problems, and I have been installing mysql on multiple systems over the years without ever hitting that bug. But I just tried to emerge sci-libs/pytorch which for some reasons caused a mysql rebuild, and that is when I hit the current bug. In order to emerge pytorch, I had to make the following changes to my system: # cat /etc/portagepackage.accept_keywords/pytorch sci-libs/pytorch ~amd64 sci-libs/caffe2 ~amd64 dev-libs/cpuinfo ~amd64 dev-libs/pthreadpool ~amd64 sci-libs/onnx ~amd64 sci-libs/foxi ~amd64 dev-libs/psimd ~amd64 dev-libs/FP16 ~amd64 dev-libs/FXdiv ~amd64 dev-libs/pocketfft ~amd64 sci-libs/kineto ~amd64 dev-libs/dynolog ~amd64 dev-python/PeachPy ~amd64 dev-python/Opcodes ~amd64 # cat /etc/portage/package.use/pytorch sci-libs/caffe2 opencv Then: # emerge -a pytorch These are the packages that would be merged, in order: Calculating dependencies... done! Dependency resolution took 20.03 s (backtrack: 13/20). [ebuild N ~] dev-libs/pocketfft-2021.11.23 [ebuild N ] sys-libs/libunwind-1.7.2 USE="zlib -debug -debug-frame -doc -libatomic -lzma -static-libs -test" ABI_X86="(64) -32 (-x32)" [ebuild N ] dev-python/mpmath-1.3.0-r1 USE="-test" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)" [ebuild N ~] dev-python/Opcodes-0.3.14-r1 USE="-doc" PYTHON_TARGETS="python3_11 -python3_10 -python3_12" [ebuild N ] dev-python/pyyaml-6.0.1-r1 USE="-debug -examples -test" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)" [ebuild N ] dev-python/ptyprocess-0.7.0-r1 USE="-test" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)" [ebuild N ~] dev-python/PeachPy-2022.11.13-r2 USE="-doc" PYTHON_TARGETS="python3_11 -python3_10 -python3_12" [ebuild N ] dev-python/pexpect-4.9.0 USE="-doc -examples -test" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)" [ebuild N ] dev-cpp/gflags-2.2.2-r1 USE="-static-libs -test" ABI_X86="(64) -32 (-x32)" [ebuild N ] dev-cpp/glog-0.6.0 USE="libunwind -gflags -llvm-libunwind -test" ABI_X86="(64) -32 (-x32)" [ebuild N ~] dev-libs/psimd-2020.05.17 [ebuild N ~] dev-libs/FXdiv-2020.12.09-r1 USE="-test" [ebuild N ] dev-libs/flatbuffers-23.5.26 USE="-static-libs -test" [ebuild N ~] dev-libs/cpuinfo-2023.01.13 USE="-test" [ebuild N ] dev-libs/sleef-3.5.1-r1 USE="-test" [ebuild N ~] sci-libs/foxi-2021.05.27 [ebuild N ] dev-cpp/gtest-1.13.0 USE="-doc -examples -test" ABI_X86="(64) -32 (-x32)" [ebuild N ~] dev-libs/pthreadpool-2023.08.29 USE="-test" [ebuild N ~] dev-libs/FP16-2021.03.20-r4 USE="-test" PYTHON_TARGETS="python3_11 -python3_10 -python3_12" [ebuild N ~] dev-libs/dynolog-0.3.1_p20230126-r1 USE="-debug -test" [ebuild N ~] sci-libs/kineto-0.4.0_p20231127 USE="-test" [ebuild N ] dev-python/pyopengl-3.1.7-r1 USE="-test -tk" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)" [ebuild N ] dev-python/sympy-1.12-r1 USE="opengl pdf png -aesara -examples -imaging -ipython -latex -mathml -pyglet -symengine -test (-texmacs)" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)" [ebuild r UD ] dev-libs/protobuf-21.9 [21.12] USE="-static-libs%" [ebuild N ] dev-python/protobuf-python-4.21.9 USE="-debug -test" PYTHON_TARGETS="python3_11 -python3_10 (-python3_12)" [ebuild N ~] sci-libs/onnx-1.14.1-r2 USE="python -debug" PYTHON_TARGETS="python3_11 -python3_10 -python3_12" [ebuild N ] media-libs/opencv-4.8.1-r1 USE="contrib contribdnn eigen features2d ffmpeg jpeg opengl openmp png python qt5 tiff (-contribcvv) -contribfreetype (-contribhdf) (-contribovis) (-contribsfm) (-contribxfeatures2d) (-cuda) (-cudnn) -debug -dnnsamples -examples -gdal (-gflags) (-glog) -gphoto2 -gstreamer -gtk3 -ieee1394 -java -jpeg2k -lapack -non-free -opencl -opencvapps -openexr -qt6 -tbb (-tesseract) -testprograms -v4l -vaapi (-vtk) -webp -xine" ABI_X86="(64) -32 (-x32)" CPU_FLAGS_X86="avx avx2 avx512f f16c fma3 popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" PYTHON_TARGETS="python3_11 -python3_10 (-python3_12)" VIDEO_CARDS="-intel" [ebuild N ~] sci-libs/caffe2-2.1.2-r3 USE="ffmpeg numpy opencv openmp -cuda -distributed -fbgemm -gloo -mkl -mpi -nnpack -onednn -opencl -qnnpack -tensorpipe -xnnpack" PYTHON_SINGLE_TARGET="python3_11 -python3_10 -python3_12" [ebuild N ~] sci-libs/pytorch-2.1.2-r1 USE="-debug" PYTHON_SINGLE_TARGET="python3_11 -python3_10 -python3_12" [ebuild rR ] dev-db/mysql-8.0.32-r2 WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict: dev-libs/protobuf:0 (dev-libs/protobuf-21.12:0/3.21.12.0::gentoo, ebuild scheduled for merge) USE="zlib -emacs -examples -test" ABI_X86="(64) -32 (-x32)" conflicts with dev-libs/protobuf:0/32 required by (dev-python/protobuf-python-4.21.9:0/32::gentoo, ebuild scheduled for merge) USE="-debug -test" ABI_X86="(64)" PYTHON_TARGETS="python3_11 -python3_10 (-python3_12)" ^^^^^ The following packages are causing rebuilds: (dev-libs/protobuf-21.9:0/32::gentoo, ebuild scheduled for merge) causes rebuilds for: (dev-db/mysql-8.0.32-r2:8.0/8.0::gentoo, ebuild scheduled for merge) Would you like to merge these packages? [Yes/No] y Note that dev-libs/protobuf caused a rebuild of ev-db/mysql. Everything emerged successfully except mysqld: * ACCESS DENIED: unlink: /var/lib/mysql/mysqld-auto.cnf.backup * ----------------------- SANDBOX ACCESS VIOLATION SUMMARY ----------------------- * VERSION 1.0 FORMAT: F - Function called FORMAT: S - Access Status FORMAT: P - Path as passed to function FORMAT: A - Absolute Path (not canonical) FORMAT: R - Canonical Path FORMAT: C - Command Line F: unlink S: deny P: /var/lib/mysql/mysqld-auto.cnf.backup A: /var/lib/mysql/mysqld-auto.cnf.backup R: /var/lib/mysql/mysqld-auto.cnf.backup C: /var/tmp/portage/dev-db/mysql-8.0.32-r2/work/mysql_build/runtime_output_directory/ Comment 7 provided the fix. Thank you.
