py37-scipy @1.3.1_1+gcc9+openblas AND hdf5 @1.10.5_0+cxx+gcc9+hl: Port "still broken after rebuilding it more than 3 times"

[nhchan]

I have the following error:

Error: Port py37-scipy is still broken 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 py37-scipy still broken after rebuilding 3 times
Error: Follow https://guide.macports.org/#project.tickets to report a bug.

In addition to the py37-scipy port, the hdf5 port is also "still broken after rebuilding it more than 3 times".

The output from running port -d -y rev-upgrade is attached as a file.

Things I have tried:

• Uninstalling and reinstalling the affected port;
• Uninstalling and reinstalling all ports, including MacPorts base (restarting the computer in between, for good measure);
• Attempting everything I have tried (as a clean install from scratch) with gcc7.

Additional info: I am unsure if this is relevant/related, but I have recently encountered the problem related to Xcode 11 (see ticket ​#59113). I had since completely removed Xcode 11 and reinstalled Xcode 10.3 and its corresponding Command Line Tools. Here are some information that may or may not be useful:

xcodebuild -version

Xcode 10.3
Build version 10G8

xcrun --show-sdk-path

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk

xcrun --show-sdk-platform-path

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform

clang -v

Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

gcc -v

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin18/9.2.0/lto-wrapper
Target: x86_64-apple-darwin18
Configured with: /opt/local/var/macports/build/_opt_bblocal_var_buildworker_ports_build_ports_lang_gcc9/gcc9/work/gcc-9.2.0/configure --prefix=/opt/local --build=x86_64-apple-darwin18 --enable-languages=c,c++,objc,obj-c++,lto,fortran --libdir=/opt/local/lib/gcc9 --includedir=/opt/local/include/gcc9 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-9 --with-local-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-9 --with-gxx-include-dir=/opt/local/include/gcc9/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-isl=/opt/local --enable-stage1-checking --disable-multilib --enable-lto --enable-libstdcxx-time --with-build-config=bootstrap-debug --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --disable-tls --with-pkgversion='MacPorts gcc9 9.2.0_0' --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
Thread model: posix
gcc version 9.2.0 (MacPorts gcc9 9.2.0_0)

Last but not least, I am running macOS 10.14.6.

[nhchan]

Output from port -d -y rev-upgrade

[mamoll (Mark Moll)]

I can confirm that port -dv destroot hdf5 +gcc9 is failing for me too. What happens if you port install hdf5 -gcc9 first and then port install py37-scipy?

[nhchan]

Replying to mamoll:

I can confirm that port -dv destroot hdf5 +gcc9 is failing for me too. What happens if you port install hdf5 -gcc9 first and then port install py37-scipy?

Thank you!

Following your suggestion, I tried port install hdf5 -gcc9. hdf5 is no longer broken as a result.

This seems to have no effect on py37-scipy though; py37-scipy is still broken. I have attached the output of the subsequent port -dy rev-upgrade as rev-upgrade_output2.txt.

[nhchan]

Output from port -d -y rev-upgrade, after running port install hdf5 -gcc9.

[MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)]

In 0419e119aa8d74ee9834b1164ab8306073efeac5/macports-ports (master):

compilers PG: set c++ stdlib GCC compilers

Fixes #59199