Installation issue: flint

[jagot]

Steps to reproduce the issue

Version 1

$ spack spec -I flint
 -   o4yjsqg  flint@3.4.0 build_system=autotools platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  qftzyfe      ^apple-clang@17.0.0 build_system=bundle platform=darwin os=tahoe target=aarch64
[+]  dwzpelv      ^compiler-wrapper@1.0 build_system=generic platform=darwin os=tahoe target=m3
[e]  y64bfyx      ^gmake@3.81~guile build_system=generic platform=darwin os=tahoe target=aarch64
[+]  xszt6ur      ^gmp@6.3.0+cxx build_system=autotools libs:=shared,static platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  amrnftu          ^autoconf@2.72 build_system=autotools platform=darwin os=tahoe target=aarch64
[e]  etrteq5          ^automake@1.18.1 build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  52m24cx          ^compiler-wrapper@1.0 build_system=generic platform=darwin os=tahoe target=m3
[e]  73c3hes          ^gmake@3.81~guile build_system=generic platform=darwin os=tahoe target=aarch64
[e]  ljtjo2o          ^libtool@2.5.4 build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  smz2tkk          ^m4@1.4.20+sigsegv build_system=autotools platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[-]  rulmyap              ^compiler-wrapper@1.0 build_system=generic platform=darwin os=tahoe target=m3
[-]  ec36fte              ^diffutils@3.10 build_system=autotools platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  elenvao                  ^libiconv@1.18 build_system=autotools libs:=shared,static platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  3d5zhqf              ^libsigsegv@2.14 build_system=autotools platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  pdklxby      ^gnuconfig@2024-07-27 build_system=generic platform=darwin os=tahoe target=m3
[e]  vp2wcaa      ^m4@1.4.6+sigsegv build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  t7jgpg4      ^mpfr@4.2.1 build_system=autotools libs:=shared,static patches:=3ec29a6 platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  hj2bo5x          ^autoconf-archive@2023.02.20 build_system=autotools platform=darwin os=tahoe target=m3
[+]  wodwqdi          ^texinfo@7.2~xs build_system=autotools platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  tb4q4fo              ^gettext@0.26+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  iha4f5e              ^ncurses@6.5~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  ihh35x5                  ^pkgconf@2.5.1 build_system=autotools platform=darwin os=tahoe target=aarch64
[e]  ppej6xj              ^perl@5.34.1~cpanm+opcode+open+shared+threads build_system=generic platform=darwin os=tahoe target=aarch64

Version 2

$ spack spec -l flint
 -   yicpwxe  flint@3.4.0 build_system=autotools platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  qftzyfe      ^apple-clang@17.0.0 build_system=bundle platform=darwin os=tahoe target=aarch64
[+]  dwzpelv      ^compiler-wrapper@1.0 build_system=generic platform=darwin os=tahoe target=m3
[e]  y64bfyx      ^gmake@3.81~guile build_system=generic platform=darwin os=tahoe target=aarch64
[+]  xszt6ur      ^gmp@6.3.0+cxx build_system=autotools libs:=shared,static platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  amrnftu          ^autoconf@2.72 build_system=autotools platform=darwin os=tahoe target=aarch64
[e]  etrteq5          ^automake@1.18.1 build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  52m24cx          ^compiler-wrapper@1.0 build_system=generic platform=darwin os=tahoe target=m3
[e]  73c3hes          ^gmake@3.81~guile build_system=generic platform=darwin os=tahoe target=aarch64
[e]  ljtjo2o          ^libtool@2.5.4 build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  smz2tkk          ^m4@1.4.20+sigsegv build_system=autotools platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[-]  rulmyap              ^compiler-wrapper@1.0 build_system=generic platform=darwin os=tahoe target=m3
[-]  ec36fte              ^diffutils@3.10 build_system=autotools platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  elenvao                  ^libiconv@1.18 build_system=autotools libs:=shared,static platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  3d5zhqf              ^libsigsegv@2.14 build_system=autotools platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  pdklxby      ^gnuconfig@2024-07-27 build_system=generic platform=darwin os=tahoe target=m3
[e]  d47ytek      ^m4@1.4.20+sigsegv build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  t7jgpg4      ^mpfr@4.2.1 build_system=autotools libs:=shared,static patches:=3ec29a6 platform=darwin os=tahoe target=m3 %c=apple-clang@17.0.0
[+]  hj2bo5x          ^autoconf-archive@2023.02.20 build_system=autotools platform=darwin os=tahoe target=m3
[+]  wodwqdi          ^texinfo@7.2~xs build_system=autotools platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  tb4q4fo              ^gettext@0.26+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools platform=darwin os=tahoe target=aarch64
[+]  iha4f5e              ^ncurses@6.5~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=darwin os=tahoe target=m3 %c,cxx=apple-clang@17.0.0
[e]  ihh35x5                  ^pkgconf@2.5.1 build_system=autotools platform=darwin os=tahoe target=aarch64
[e]  ppej6xj              ^perl@5.34.1~cpanm+opcode+open+shared+threads build_system=generic platform=darwin os=tahoe target=aarch64

Error message

Error message, version 1

duplicate symbol '__fmpz_init_readonly_mpz' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_clear_readonly_mpz' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_new_mpz' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_clear_mpz' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_cleanup_mpz_content' in:
    build/fmpz/fmpz.lo
duplicate symbol '_mpz_free_arr' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_cleanup' in:
    build/fmpz/fmpz.lo
duplicate symbol '_mpz_free_num' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_promote_val' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_demote_val' in:
    build/fmpz/fmpz.lo
duplicate symbol '__fmpz_promote' in:
    build/fmpz/fmpz.lo
duplicate symbol '_mpz_free_alloc' in:
    build/fmpz/fmpz.lo
ld: 12 duplicate symbols for architecture arm64
make: *** [build/fmpz_merged.lo] Error 1
make: *** Waiting for unfinished jobs....
Traceback (most recent call last):
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/new_installer.py", line 316, in worker_function
    phase_fn.execute()
    ~~~~~~~~~~~~~~~~^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 379, in execute
    self.phase_fn(pkg, pkg.spec, pkg.prefix)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 251, in _adapter
    return phase_fn(spec, prefix)
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 156, in __forward
    return self.__getattr__(fn_name)(*args, **kwargs)
           ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 68, in __call__
    return self.phase_fn(self.builder.pkg, spec, prefix)
           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/jagot/.spack/package_repos/fncqgg4/repos/spack_repo/builtin/build_systems/autotools.py", line 633, in build
    pkg.module.make(*params)
    ~~~~~~~~~~~~~~~^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/build_environment.py", line 278, in __call__
    return super().__call__(*args, **kwargs)
           ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/util/executable.py", line 305, in __call__
    raise ProcessError("Command exited with status %d:" % proc.returncode, long_msg)
spack.util.executable.ProcessError: Command exited with status 2:
    '/usr/bin/make' 'V=1'

Version 1: spack-build-out.txt

Error message, version 2

/opt/homebrew/Cellar/spack/1.1.0/opt/spack/darwin-m3/compiler-wrapper-1.0-dwzpelvzyhien3sc5hteapzbdisieh4j/libexec/spack/clang/clang  -march=armv8-a -Wmissing-prototypes -Wno-stringop-overflow -Wno-stringop-overread -Werror=newline-eof -Werror=implicit-function-declaration -Wall -std=c11 -pedantic -O3 -g   -I/var/folders/3x/fs1m7b_d0458zrh1gt84s90c0000gn/T/jagot/spack-stage/spack-stage-flint-3.4.0-yicpwxepjhwgslxcb33ywn4i3tdwsenu/spack-src/src -Isrc  -I/opt/homebrew/Cellar/spack/1.1.0/opt/spack/darwin-m3/gmp-6.3.0-xszt6ureqy4itwsyjq6rb5wl4avszjhx/include -I/opt/homebrew/Cellar/spack/1.1.0/opt/spack/darwin-m3/mpfr-4.2.1-t7jgpg4sk7gqt4tffkgvx4vman53tyvp/include -DBUILDING_FLINT -DFLINT_NOSTDIO -DFLINT_NOSTDARG -c /var/folders/3x/fs1m7b_d0458zrh1gt84s90c0000gn/T/jagot/spack-stage/spack-stage-flint-3.4.0-yicpwxepjhwgslxcb33ywn4i3tdwsenu/spack-src/src/mpn_extras/sumdiff_n.c -o build/mpn_extras/sumdiff_n.lo -MMD -MP -MF build/mpn_extras/sumdiff_n.lo.d
warning: unknown warning option '-Wno-stringop-overflow'; did you mean '-Wno-shift-overflow'? [-Wunknown-warning-option]
warning: unknown warning option '-Wno-stringop-overread' [-Wunknown-warning-option]
2 warnings generated.
/bin/sh: /opt/homebrew/Cellar/spack/1.1.0/var/spack/environments/fiatlux/.spack-env/view/bin/m4: No such file or directory
warning: unknown warning option '-Wno-stringop-overflow'; did you mean '-Wno-shift-overflow'? [-Wunknown-warning-option]
make: *** [build/mpn_extras/arm64/mul_2_pic.s] Error 127
make: *** Waiting for unfinished jobs....
warning: unknown warning option '-Wno-stringop-overread' [-Wunknown-warning-option]
/bin/sh: /opt/homebrew/Cellar/spack/1.1.0/var/spack/environments/fiatlux/.spack-env/view/bin/m4: No such file or directory
2 warnings generated.
make: *** [build/mpn_extras/arm64/mul_hard_pic.s] Error 127
2 warnings generated.
clang: warning: overriding deployment version from '10.16' to '11.0' [-Woverriding-deployment-version]
clang: warning: overriding deployment version from '10.16' to '11.0' [-Woverriding-deployment-version]
2 warnings generated.
warning: warning: unknown warning option '-Wno-stringop-overflow'; did you mean '-Wno-shift-overflow'? [-Wunknown-warning-option]unknown warning option '-Wno-stringop-overflow'; did you mean '-Wno-shift-overflow'? [-Wunknown-warning-option]

warning: unknown warning option '-Wno-stringop-overread' [-Wunknown-warning-option]
warning: unknown warning option '-Wno-stringop-overread' [-Wunknown-warning-option]
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
clang: warning: overriding deployment version from '10.16' to '11.0' [-Woverriding-deployment-version]
warning: unknown warning option '-Wno-stringop-overflow'; did you mean '-Wno-shift-overflow'? [-Wunknown-warning-option]
warning: unknown warning option '-Wno-stringop-overread' [-Wunknown-warning-option]
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
Traceback (most recent call last):
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/new_installer.py", line 316, in worker_function
    phase_fn.execute()
    ~~~~~~~~~~~~~~~~^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 379, in execute
    self.phase_fn(pkg, pkg.spec, pkg.prefix)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 251, in _adapter
    return phase_fn(spec, prefix)
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 156, in __forward
    return self.__getattr__(fn_name)(*args, **kwargs)
           ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/builder.py", line 68, in __call__
    return self.phase_fn(self.builder.pkg, spec, prefix)
           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/jagot/.spack/package_repos/fncqgg4/repos/spack_repo/builtin/build_systems/autotools.py", line 633, in build
    pkg.module.make(*params)
    ~~~~~~~~~~~~~~~^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/build_environment.py", line 278, in __call__
    return super().__call__(*args, **kwargs)
           ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/spack/1.1.0/lib/spack/spack/util/executable.py", line 305, in __call__
    raise ProcessError("Command exited with status %d:" % proc.returncode, long_msg)
spack.util.executable.ProcessError: Command exited with status 2:
    '/usr/bin/make' 'V=1'

Version 2: spack-build-out.txt

Information on your system

$ gcc --version
Apple clang version 17.0.0 (clang-1700.6.3.2)
Target: arm64-apple-darwin25.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

$ uname -vm
Darwin Kernel Version 25.2.0: Tue Nov 18 21:09:41 PST 2025; root:xnu-12377.61.12~1/RELEASE_ARM64_T6031 arm64

$ spack debug report
* **Spack:** 1.1.0
* **Builtin repo:** https://github.com/spack/spack-packages/commit/9ead4b0e38f45f3f1e3ae3ec5416a69be51bab32
* **Python:** 3.14.2
* **Platform:** darwin-tahoe-m3

Additional information

The build works fine on Linux, but on macOS it fails, in two different ways as reported above, one in a clean environment, and one in my main development environment. Building manually using the default compiler works without issue, against GMP and MPFR libraries installed by either Homebrew or Spack. Homebrew has a working package as well.

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