[MacPorts] #66208: broken port with hdf5
MacPorts
noreply at macports.org
Wed Nov 9 13:34:09 UTC 2022
#66208: broken port with hdf5
-----------------------+--------------------
Reporter: massonseb | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 2.8.0
Keywords: | Port: hdf5
-----------------------+--------------------
I have an issue when installing "hdf5 +gcc12". All the installation goes
smoothly until the last step when it looks for broken port. Port find that
hdf5 itself is broken and try to reinstall hdf5 again and agin...
See bellow for all details.
Note that I don't have the problem when installing "hdf5 +gcc12 +mpich" or
"hdf5 +gcc12 +openmi".
I am using macOS 12.6.1 with ARM64 (Apple M1 Pro).
Thank you for your help,
Sébastien
{{{
bash-5.1$ sudo port install hdf5 +gcc12
Password:
---> Computing dependencies for hdf5
---> Fetching archive for hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2
from https://fra.de.packages.macports.org/hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2
from https://mse.uk.packages.macports.org/hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2
from https://packages.macports.org/hdf5
---> Fetching distfiles for hdf5
---> Attempting to fetch hdf5-1.12.2.tar.bz2 from
https://distfiles.macports.org/hdf5
---> Verifying checksums for hdf5
---> Extracting hdf5
---> Applying patches to hdf5
---> Configuring hdf5
---> Building hdf5
---> Staging hdf5 into destroot
---> Installing hdf5 @1.12.2_0+cxx+gcc12+hl
---> Activating hdf5 @1.12.2_0+cxx+gcc12+hl
---> Cleaning hdf5
---> Scanning binaries for linking errors
---> No broken files found.
---> Found 1 broken port, determining rebuild order
You can always run 'port rev-upgrade' again to fix errors.
The following ports will be rebuilt: hdf5 @1.12.2+cxx+gcc12+hl
Continue? [Y/n]:
---> Fetching archive for hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2
from https://fra.de.packages.macports.org/hdf5
---> Attempting to fetch hdf5-1.12.2_0+cxx+gcc12+hl.darwin_21.arm64.tbz2
from https://mse.uk.packages.macports.org/hdf5
...
---> Cleaning hdf5
---> Scanning binaries for linking errors
---> No broken files found.
Error: Port hdf5 is still broken (cxx_stdlib mismatch) after rebuilding it
more than 3 times.
Error: Please run port -d -y rev-upgrade and use the output to report a
bug.
Error: rev-upgrade failed: Port hdf5 still broken after rebuilding 3 times
Error: Follow https://guide.macports.org/#project.tickets if you believe
there is a bug.
---> Some of the ports you installed have notes:
hdf5 has the following notes:
Mac users may need to set the environment variable
"HDF5_USE_FILE_LOCKING" to the five-character string "FALSE" when
accessing
network mounted files. This is an application run-time setting, not a
configure or build setting. Otherwise errors such as
"unable to open file" or "HDF5 error" may be encountered.
}}}
{{{
bash-5.1$ sudo port -d -y rev-upgrade
Password:
DEBUG: Copying /Users/smasson/Library/Preferences/com.apple.dt.Xcode.plist
to /opt/local/var/macports/home/Library/Preferences
---> Scanning binaries for linking errors
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/lib/libgcc/libgfortran.5.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/lib/libgcc/libgfortran.5.dylib
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/libgcc
/libobjc-gnu.4.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/lib/libgcc/libstdc++.6.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/bugpoint
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/dsymutil
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llc
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/lli
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-ar
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-as
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-bcanalyzer
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-c-test
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cat
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cfi-verify
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cov
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cvtres
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cxxdump
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cxxfilt
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-cxxmap
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-debuginfod-find
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-diff
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-dis
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-dwarfdump
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-dwp
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-extract
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-gsymutil
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-ifs
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-jitlink
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-libtool-darwin
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-link
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-lipo
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-lto
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-lto2
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-mc
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-mca
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-ml
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-modextract
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-mt
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-nm
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-objcopy
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-objdump
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-opt-report
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-pdbutil
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-profdata
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-profgen
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-rc
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-readobj
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-reduce
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-rtdyld
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-sim
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-size
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-split
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-stress
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-strings
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-symbolizer
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-tapi-diff
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-tli-checker
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-undname
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/llvm-xray
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/opt
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/sancov
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/sanstats
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/split-file
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/verify-uselistorder
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/lib/libLTO.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/lib/libRemarks.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/c-index-test
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/c-index-test
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-apply-replacements
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-apply-replacements
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-change-namespace
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-change-namespace
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-check
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-check
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-doc
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-doc
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-extdef-mapping
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-extdef-mapping
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-format
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-format
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-include-fixer
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-include-fixer
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-linker-wrapper
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-move
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-move
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-nvlink-wrapper
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-offload-bundler
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-offload-bundler
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-offload-wrapper
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-offload-wrapper
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-query
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-query
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-refactor
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-refactor
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-rename
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-rename
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-reorder-fields
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-reorder-fields
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-repl
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-repl
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-scan-deps
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-scan-deps
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-tidy
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clang-tidy
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clangd
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clangd
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clangd-xpc-test-client
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/clangd-xpc-test-client
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/diagtool
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/diagtool
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/find-all-symbols
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/find-all-symbols
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/lld
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/modularize
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/modularize
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/pp-trace
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/bin/pp-trace
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/lib/libClangdXPCLib.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/lib/libclang-cpp.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/libexec/llvm-14/lib/libclang.dylib
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/bin/emacs-28.2
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-
gcc12/libmpi_cxx.40.dylib
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-
gcc12/libmpi_usempi_ignore_tkr.40.dylib
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-
gcc12/libmpi_usempi_ignore_tkr.40.dylib
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-
gcc12/libmpi_usempif08.40.dylib
DEBUG: Ignoring loadcommand containing @rpath in /opt/local/lib/openmpi-
gcc12/libmpi_usempif08.40.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/lib/libhdf5_cpp.200.dylib
DEBUG: Ignoring loadcommand containing @rpath in
/opt/local/lib/libhdf5_hl_cpp.200.dylib
---> No broken files found.
hdf5 is using libstdc++ (this installation is configured to use libc++)
---> Found 1 broken port, determining rebuild order
DEBUG: Broken: hdf5
DEBUG: Processing port hdf5 @0:1.12.2_0+cxx+gcc12+hl
You can always run 'port rev-upgrade' again to fix errors.
The following ports will be rebuilt: hdf5 @1.12.2+cxx+gcc12+hl
Continue? [Y/n]: n
DEBUG: Checking time since last reclaim run
}}}
--
Ticket URL: <https://trac.macports.org/ticket/66208>
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