Installation issue: hdf-eos2@2.20v1.00 build fails on maOS Ventura with apple-clang@14.0.3 after recent updates

[climbfuji]

Steps to reproduce the issue

These errors happen when updating my fork from spack develop, which contains somewhat recent changes (i.e. removal of h4cc compiler wrapper etc - I believe #41782, therefore mentioning @payerle here). Note that I can't use v3 because these are automated (CI) tests that need to auto-download the source files.

$ spack spec -l hdf-eos2
Input spec
--------------------------------
 -   hdf-eos2

Concretized
--------------------------------
 -   cuapts6  hdf-eos2@2.20v1.00%apple-clang@14.0.3+shared+static build_system=autotools arch=darwin-ventura-m1
 -   k44gpqp      ^gnuconfig@2022-09-17%apple-clang@14.0.3 build_system=generic arch=darwin-ventura-m1
 -   euboozh      ^hdf@4.2.15%apple-clang@14.0.3~external-xdr~fortran~java~netcdf+pic~shared~szip build_system=autotools patches=49733dd,5434f29,5cfe120,ce75518,d54592d,f7d67e8 arch=darwin-ventura-m1
 -   iw4rvcc          ^bison@3.8.2%apple-clang@14.0.3 build_system=autotools arch=darwin-ventura-m1
 -   xtzdiom              ^diffutils@3.9%apple-clang@14.0.3 build_system=autotools arch=darwin-ventura-m1
 -   vxpsofi                  ^libc@1.0%apple-clang@14.0.3+iconv~rpc build_system=bundle arch=darwin-ventura-m1
[e]  tyt4zl2              ^m4@1.4.6%apple-clang@14.0.3+sigsegv build_system=autotools arch=darwin-ventura-m1
[e]  2obhvhz              ^perl@5.34.0%apple-clang@14.0.3~cpanm+open+shared+threads build_system=generic arch=darwin-ventura-m1
[e]  n3v5aln          ^flex@2.6.4%apple-clang@14.0.3+lex~nls build_system=autotools patches=f8b85a0 arch=darwin-ventura-m1
 -   huxyasc      ^libjpeg-turbo@2.1.0%apple-clang@14.0.3~ipo~jpeg8+pic+shared+static build_system=cmake build_type=Release generator=make arch=darwin-ventura-m1
[e]  hqzzzab          ^cmake@3.27.6%apple-clang@14.0.3~doc+ncurses+ownlibs~qt build_system=generic build_type=Release arch=darwin-ventura-m1
[e]  yigrjmj          ^gmake@3.81%apple-clang@14.0.3~guile build_system=autotools patches=ca60bd9 arch=darwin-ventura-m1
 -   4tuh7eo          ^nasm@2.15.05%apple-clang@14.0.3 build_system=autotools arch=darwin-ventura-m1
 -   cuyji66      ^zlib@1.2.13%apple-clang@14.0.3+optimize+pic+shared build_system=makefile arch=darwin-ventura-m1

Error message

Error below. I will also note that it looks like reconfigure is failing, but then it continues silently?

==> hdf-eos2: Executing phase: 'autoreconf'
==> [2024-05-13-22:33:34.376614] Find (recursive): /Users/ec2-user/spack-stack/manual-testing/spstup/cache/build_stage/spack-stage-hdf-eos2-2.20v1.00-brkub54sgdo57puhermsyi3yo3tqk4j5 ['config.sub', 'config.guess']
==> [2024-05-13-22:33:34.380615] Find complete: /Users/ec2-user/spack-stack/manual-testing/spstup/cache/build_stage/spack-stage-hdf-eos2-2.20v1.00-brkub54sgdo57puhermsyi3yo3tqk4j5 ['config.sub', 'config.guess']
==> [2024-05-13-22:33:34.560975] CalledProcessError: Command '['/Users/ec2-user/spack-stack/manual-testing/spstup/cache/build_stage/spack-stage-hdf-eos2-2.20v1.00-brkub54sgdo57puhermsyi3yo3tqk4j5/spack-src/config/config.sub', 'aarch64']' returned non-zero exit status 1.
==> [2024-05-13-22:33:34.698999] Find (not recursive): /Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/gnuconfig-2022-09-17-bmsack4 ['config.sub']
==> [2024-05-13-22:33:34.699363] Find complete: /Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/gnuconfig-2022-09-17-bmsack4 ['config.sub']
==> [2024-05-13-22:33:34.732418] Copying /Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/gnuconfig-2022-09-17-bmsack4/config.sub to /Users/ec2-user/spack-stack/manual-testing/spstup/cache/build_stage/spack-stage-hdf-eos2-2.20v1.00-brkub54sgdo57puhermsyi3yo3tqk4j5/spack-src/config/config.sub
==> hdf-eos2: Executing phase: 'configure'

ERROR:

...
/Users/ec2-user/spack-stack/manual-testing/spstup/spack/lib/spack/env/clang/clang -dynamiclib  -o .libs/libhdfeos.0.0.0.dylib  .libs/EHapi.o .libs/GDapi.o .libs/PTapi.o .libs/SWapi.o  -lmfhdf -ldf -lz -ljpeg -lm -Wl,-single_module -install_name  /Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/hdf-eos2-2.20v1.00-brkub54/lib/libhdfeos.0.dylib -Wl,-compatibility_version -Wl,1 -Wl,-current_version -Wl,1.0
Undefined symbols for architecture arm64:
  "_for_init", referenced from:
      _GDgetdefaults in GDapi.o
      _GDll2ij in GDapi.o
      _GDij2ll in GDapi.o
      _GDll2mm_cea in GDapi.o
  "_inv_init", referenced from:
      _GDij2ll in GDapi.o
      _GDrs2ll in GDapi.o
      _GDmm2ll_cea in GDapi.o
ld: symbol(s) not found for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [libhdfeos.la] Error 1
make: *** [all-recursive] Error 1
==> Error: ProcessError: Command exited with status 2:
    'make' '-j8' 'V=1'

4 errors found in build log:
     3404    46 warnings generated.
     3405     /Users/ec2-user/spack-stack/manual-testing/spstup/spack/lib/spack/env/clang/clang -DHAVE_CONFIG_H -I. -I. -I../include -I../include/ -g -O2 -I/Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install
             /apple-clang/14.0.3/hdf-4.2.15-a433l3p/include -g -O2 -I/Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/hdf-4.2.15-a433l3p/include -MT GDapi.lo -MD -MP -MF .deps/GDapi.Tpo
              -c GDapi.c  -fno-common -DPIC -o GDapi.o >/dev/null 2>&1
     3406    47 warnings generated.
     3407     /Users/ec2-user/spack-stack/manual-testing/spstup/spack/lib/spack/env/clang/clang -DHAVE_CONFIG_H -I. -I. -I../include -I../include/ -g -O2 -I/Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install
             /apple-clang/14.0.3/hdf-4.2.15-a433l3p/include -g -O2 -I/Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/hdf-4.2.15-a433l3p/include -MT SWapi.lo -MD -MP -MF .deps/SWapi.Tpo
              -c SWapi.c  -fno-common -DPIC -o SWapi.o >/dev/null 2>&1
     3408    /bin/sh ../libtool --mode=link --tag=CC /Users/ec2-user/spack-stack/manual-testing/spstup/spack/lib/spack/env/clang/clang  -g -O2 -I/Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clan
             g/14.0.3/hdf-4.2.15-a433l3p/include  -Wl,-single_module -o libhdfeos.la -rpath /Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/hdf-eos2-2.20v1.00-brkub54/lib  EHapi.lo GDa
             pi.lo PTapi.lo SWapi.lo  -lmfhdf -ldf -lz -ljpeg -lm
     3409    /Users/ec2-user/spack-stack/manual-testing/spstup/spack/lib/spack/env/clang/clang -dynamiclib  -o .libs/libhdfeos.0.0.0.dylib  .libs/EHapi.o .libs/GDapi.o .libs/PTapi.o .libs/SWapi.o  -lmfhdf -ldf -lz -ljpeg -lm -Wl,-single_modul
             e -install_name  /Users/ec2-user/spack-stack/manual-testing/spstup/envs/ci-env.macos-ci-aarch64/install/apple-clang/14.0.3/hdf-eos2-2.20v1.00-brkub54/lib/libhdfeos.0.dylib -Wl,-compatibility_version -Wl,1 -Wl,-current_version -Wl
             ,1.0
  >> 3410    Undefined symbols for architecture arm64:
     3411      "_for_init", referenced from:
     3412          _GDgetdefaults in GDapi.o
     3413          _GDll2ij in GDapi.o
     3414          _GDij2ll in GDapi.o
     3415          _GDll2mm_cea in GDapi.o
     3416      "_inv_init", referenced from:
     3417          _GDij2ll in GDapi.o
     3418          _GDrs2ll in GDapi.o
     3419          _GDmm2ll_cea in GDapi.o
     3420    ld: symbol(s) not found for architecture arm64
  >> 3421    clang: error: linker command failed with exit code 1 (use -v to see invocation)
  >> 3422    make[1]: *** [libhdfeos.la] Error 1
  >> 3423    make: *** [all-recursive] Error 1

See build log for details:
  /Users/ec2-user/spack-stack/manual-testing/spstup/cache/build_stage/spack-stage-hdf-eos2-2.20v1.00-brkub54sgdo57puhermsyi3yo3tqk4j5/spack-build-out.txt

==> Warning: Skipping build of met-11.1.0-a4dndsdeszfv5kdbr4btatcnty4wkcc4 since hdf-eos2-2.20v1.00-brkub54sgdo57puhermsyi3yo3tqk4j5 failed
==> Warning: Skipping build of metplus-5.1.0-qdnaagppv2ra233e6uefevh7lxuexc2d since met-11.1.0-a4dndsdeszfv5kdbr4btatcnty4wkcc4 failed
==> Warning: Skipping build of ufs-srw-app-env-1.0.0-igkciifj6e3ynl22nndevblr3pvpo5ue since metplus-5.1.0-qdnaagppv2ra233e6uefevh7lxuexc2d failed
==> Warning: Skipping build of global-workflow-env-1.0.0-hg27wj3fdip3wp5koj4dzg4f6ugrj7iw since metplus-5.1.0-qdnaagppv2ra233e6uefevh7lxuexc2d failed
==> Error: Terminating after first install failure: ProcessError: Command exited with status 2:
    'make' '-j8' 'V=1'

Information on your system

* **Spack:** 0.22.0.dev0 (3f063d6cb79d05aa768789ab9d8f70ac4295a5c3)
* **Python:** 3.9.6
* **Platform:** darwin-ventura-m1
* **Concretizer:** clingo

Additional information

spack-build-01-autoreconf-out.txt
spack-build-02-configure-out.txt
spack-build-03-build-out.txt
spack-build-env-mods.txt
spack-build-env.txt
spack-build-out.txt
spack-configure-args.txt

General information

• I have run spack debug report and reported the version of Spack/Python/Platform
• I have run spack maintainers <name-of-the-package> and @mentioned any maintainers
• I have uploaded the build log and environment files
• I have searched the issues of this repo and believe this is not a duplicate