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macOS M1: Spack fails to bootstrap without Xcode #28190

@certik

Description

@certik

I started from a clean repository updated to the latest develop branch (c2e1a12).

$ spack compilers
==> Available compilers
-- apple-clang bigsur-arm64 -------------------------------------
[email protected]
~ $ spack spec qemu
Input spec
--------------------------------
qemu

Concretized
--------------------------------
==> Bootstrapping clingo from pre-built binaries
==> Bootstrapping clingo from sources
==> Installing gnuconfig-2021-08-14-gedovjnheiii5r4na5e3pjlekcergep6
==> No binary for gnuconfig-2021-08-14-gedovjnheiii5r4na5e3pjlekcergep6 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/69/69b6d2868e70167ba1bdb9030b49beeb20f00b37e30825e83fd04291d96bc5f7.tar.gz
==> No patches needed for gnuconfig
==> gnuconfig: Executing phase: 'install'
==> gnuconfig: Successfully installed gnuconfig-2021-08-14-gedovjnheiii5r4na5e3pjlekcergep6
  Fetch: 0.85s.  Build: 0.19s.  Total: 1.03s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/gnuconfig-2021-08-14-gedovjnheiii5r4na5e3pjlekcergep6
==> Installing zlib-1.2.11-a3p23rnymc7d6ens3mk7wj75r5sucdvr
==> No binary for zlib-1.2.11-a3p23rnymc7d6ens3mk7wj75r5sucdvr found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/c3/c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1.tar.gz
==> No patches needed for zlib
==> zlib: Executing phase: 'install'
==> zlib: Successfully installed zlib-1.2.11-a3p23rnymc7d6ens3mk7wj75r5sucdvr
  Fetch: 1.06s.  Build: 1.68s.  Total: 2.74s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/zlib-1.2.11-a3p23rnymc7d6ens3mk7wj75r5sucdvr
[+] /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8 (external python-3.8-yumcagn3zdktmhjepxgxvbokqdl24zaz)
==> Installing libiconv-1.16-fyaei4lfz3n7nzpna2vetg4a5uq7pdbk
==> No binary for libiconv-1.16-fyaei4lfz3n7nzpna2vetg4a5uq7pdbk found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/e6/e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04.tar.gz
==> No patches needed for libiconv
==> libiconv: Executing phase: 'autoreconf'
==> libiconv: Executing phase: 'configure'
==> libiconv: Executing phase: 'build'
==> libiconv: Executing phase: 'install'
==> libiconv: Successfully installed libiconv-1.16-fyaei4lfz3n7nzpna2vetg4a5uq7pdbk
  Fetch: 2.18s.  Build: 18.15s.  Total: 20.34s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/libiconv-1.16-fyaei4lfz3n7nzpna2vetg4a5uq7pdbk
==> Installing libsigsegv-2.13-jx46dmox6wtqotnsvvcrqwx6jfuj72pc
==> No binary for libsigsegv-2.13-jx46dmox6wtqotnsvvcrqwx6jfuj72pc found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/be/be78ee4176b05f7c75ff03298d84874db90f4b6c9d5503f0da1226b3a3c48119.tar.gz
==> No patches needed for libsigsegv
==> libsigsegv: Executing phase: 'autoreconf'
==> libsigsegv: Executing phase: 'configure'
==> libsigsegv: Executing phase: 'build'
==> libsigsegv: Executing phase: 'install'
==> libsigsegv: Successfully installed libsigsegv-2.13-jx46dmox6wtqotnsvvcrqwx6jfuj72pc
  Fetch: 0.96s.  Build: 4.42s.  Total: 5.38s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/libsigsegv-2.13-jx46dmox6wtqotnsvvcrqwx6jfuj72pc
==> Installing berkeley-db-18.1.40-7q4rqdl4vtulxj4jx56l2mac2d2embea
==> No binary for berkeley-db-18.1.40-7q4rqdl4vtulxj4jx56l2mac2d2embea found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0c/0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8.tar.gz
==> Applied patch /Users/ondrej/repos/spack/var/spack/repos/builtin/packages/berkeley-db/drop-docs.patch
==> Ran patch() for berkeley-db
==> berkeley-db: Executing phase: 'autoreconf'
==> berkeley-db: Executing phase: 'configure'
==> berkeley-db: Executing phase: 'build'
==> berkeley-db: Executing phase: 'install'
==> berkeley-db: Successfully installed berkeley-db-18.1.40-7q4rqdl4vtulxj4jx56l2mac2d2embea
  Fetch: 9.03s.  Build: 26.26s.  Total: 35.30s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/berkeley-db-18.1.40-7q4rqdl4vtulxj4jx56l2mac2d2embea
==> Installing re2c-2.2-ahy7ntwn3wjqkphsppo2cixexk62gmau
==> No binary for re2c-2.2-ahy7ntwn3wjqkphsppo2cixexk62gmau found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0f/0fc45e4130a8a555d68e230d1795de0216dfe99096b61b28e67c86dfd7d86bda.tar.xz
==> No patches needed for re2c
==> re2c: Executing phase: 'autoreconf'
==> re2c: Executing phase: 'configure'
==> re2c: Executing phase: 'build'
==> re2c: Executing phase: 'install'
==> re2c: Successfully installed re2c-2.2-ahy7ntwn3wjqkphsppo2cixexk62gmau
  Fetch: 1.38s.  Build: 20.24s.  Total: 21.62s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/re2c-2.2-ahy7ntwn3wjqkphsppo2cixexk62gmau
==> Installing pkgconf-1.8.0-crd2i745cj5p6am2m5sajcycuvr3jonc
==> No binary for pkgconf-1.8.0-crd2i745cj5p6am2m5sajcycuvr3jonc found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/ef/ef9c7e61822b7cb8356e6e9e1dca58d9556f3200d78acab35e4347e9d4c2bbaf.tar.xz
==> No patches needed for pkgconf
==> pkgconf: Executing phase: 'autoreconf'
==> pkgconf: Executing phase: 'configure'
==> pkgconf: Executing phase: 'build'
==> pkgconf: Executing phase: 'install'
==> pkgconf: Successfully installed pkgconf-1.8.0-crd2i745cj5p6am2m5sajcycuvr3jonc
  Fetch: 1.07s.  Build: 5.01s.  Total: 6.08s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/pkgconf-1.8.0-crd2i745cj5p6am2m5sajcycuvr3jonc
==> Installing diffutils-3.8-tps25qichnyhdskh2yoimpoeersmou27
==> No binary for diffutils-3.8-tps25qichnyhdskh2yoimpoeersmou27 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/a6/a6bdd7d1b31266d11c4f4de6c1b748d4607ab0231af5188fc2533d0ae2438fec.tar.xz
==> No patches needed for diffutils
==> diffutils: Executing phase: 'autoreconf'
==> diffutils: Executing phase: 'configure'
==> diffutils: Executing phase: 'build'
==> diffutils: Executing phase: 'install'
==> diffutils: Successfully installed diffutils-3.8-tps25qichnyhdskh2yoimpoeersmou27
  Fetch: 1.41s.  Build: 32.46s.  Total: 33.87s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/diffutils-3.8-tps25qichnyhdskh2yoimpoeersmou27
==> Installing m4-1.4.19-ghuewuay4dqfxf35fzbqknakd5juhl7a
==> No binary for m4-1.4.19-ghuewuay4dqfxf35fzbqknakd5juhl7a found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/3b/3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70.tar.gz
==> Fetching https://mirror.spack.io/_source-cache/archive/bf/bfdffa7c2eb01021d5849b36972c069693654ad826c1a20b53534009a4ec7a89
==> Fetching https://mirror.spack.io/_source-cache/archive/9d/9dc5fbd0d5cb1037ab1e6d0ecc74a30df218d0a94bdd5a02759a97f62daca573
==> Applied patch http://git.savannah.gnu.org/cgit/m4.git/patch/?id=a1354086
==> Applied patch http://git.savannah.gnu.org/cgit/m4.git/patch/?id=cd7f4d15
==> Ran patch() for m4
==> m4: Executing phase: 'autoreconf'
==> m4: Executing phase: 'configure'
==> m4: Executing phase: 'build'
==> m4: Executing phase: 'install'
==> m4: Successfully installed m4-1.4.19-ghuewuay4dqfxf35fzbqknakd5juhl7a
  Fetch: 1.88s.  Build: 47.45s.  Total: 49.33s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/m4-1.4.19-ghuewuay4dqfxf35fzbqknakd5juhl7a
==> Installing ncurses-6.2-exubvurzson2t7xztjvlg7gayp65kg7p
==> No binary for ncurses-6.2-exubvurzson2t7xztjvlg7gayp65kg7p found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/30/30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d.tar.gz
==> No patches needed for ncurses
==> ncurses: Executing phase: 'autoreconf'
==> ncurses: Executing phase: 'configure'
==> ncurses: Executing phase: 'build'
==> ncurses: Executing phase: 'install'
==> ncurses: Successfully installed ncurses-6.2-exubvurzson2t7xztjvlg7gayp65kg7p
  Fetch: 2.19s.  Build: 55.02s.  Total: 57.21s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/ncurses-6.2-exubvurzson2t7xztjvlg7gayp65kg7p
==> Installing bzip2-1.0.8-xoi7soo72qnpkswxbdby3a4kmip2e3ro
==> No binary for bzip2-1.0.8-xoi7soo72qnpkswxbdby3a4kmip2e3ro found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/ab/ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269.tar.gz
==> Ran patch() for bzip2
==> bzip2: Executing phase: 'install'
==> bzip2: Successfully installed bzip2-1.0.8-xoi7soo72qnpkswxbdby3a4kmip2e3ro
  Fetch: 1.22s.  Build: 1.03s.  Total: 2.25s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/bzip2-1.0.8-xoi7soo72qnpkswxbdby3a4kmip2e3ro
==> Installing readline-8.1-odmkrknw6jd6bu2rdomd5ivloae6gwig
==> No binary for readline-8.1-odmkrknw6jd6bu2rdomd5ivloae6gwig found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/f8/f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02.tar.gz
==> Ran patch() for readline
==> readline: Executing phase: 'autoreconf'
==> readline: Executing phase: 'configure'
==> readline: Executing phase: 'build'
==> readline: Executing phase: 'install'
==> readline: Successfully installed readline-8.1-odmkrknw6jd6bu2rdomd5ivloae6gwig
  Fetch: 1.89s.  Build: 8.31s.  Total: 10.20s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/readline-8.1-odmkrknw6jd6bu2rdomd5ivloae6gwig
==> Installing gdbm-1.19-tcvwmvv2iq7slyhayv5wswqpt7oy3ynw
==> No binary for gdbm-1.19-tcvwmvv2iq7slyhayv5wswqpt7oy3ynw found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/37/37ed12214122b972e18a0d94995039e57748191939ef74115b1d41d8811364bc.tar.gz
==> No patches needed for gdbm
==> gdbm: Executing phase: 'autoreconf'
==> gdbm: Executing phase: 'configure'
==> gdbm: Executing phase: 'build'
==> gdbm: Executing phase: 'install'
==> gdbm: Successfully installed gdbm-1.19-tcvwmvv2iq7slyhayv5wswqpt7oy3ynw
  Fetch: 0.95s.  Build: 8.24s.  Total: 9.19s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/gdbm-1.19-tcvwmvv2iq7slyhayv5wswqpt7oy3ynw
==> Installing perl-5.34.0-xzib42oxhft2bgakyhhovjy5o3lvip4w
==> No binary for perl-5.34.0-xzib42oxhft2bgakyhhovjy5o3lvip4w found: installing from source
==> Warning: Failed to detect macOS command line tools version: No receipt for 'com.apple.pkg.CLTools_Executables' found at '/'.

==> Fetching https://mirror.spack.io/_source-cache/archive/55/551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a.tar.gz
==> Fetching https://mirror.spack.io/_source-cache/archive/9d/9da50e155df72bce55cb69f51f1dbb4b62d23740fb99f6178bb27f22ebdf8a46.tar.gz
==> Moving resource stage
	source : /var/folders/wm/h8g03zb53_sgm6r8r8h9pmpw0000gp/T/ondrej/spack-stage/resource-cpanm-xzib42oxhft2bgakyhhovjy5o3lvip4w/spack-src/
	destination : /var/folders/wm/h8g03zb53_sgm6r8r8h9pmpw0000gp/T/ondrej/spack-stage/spack-stage-perl-5.34.0-xzib42oxhft2bgakyhhovjy5o3lvip4w/spack-src/cpanm/cpanm
==> Ran patch() for perl
==> perl: Executing phase: 'configure'
==> perl: Executing phase: 'build'
==> perl: Executing phase: 'install'
==> perl: Successfully installed perl-5.34.0-xzib42oxhft2bgakyhhovjy5o3lvip4w
  Fetch: 6.44s.  Build: 1m 30.54s.  Total: 1m 36.98s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/perl-5.34.0-xzib42oxhft2bgakyhhovjy5o3lvip4w
==> Installing bison-3.8.2-comfky2x72qyu32uakmlltap4sc5jfit
==> No binary for bison-3.8.2-comfky2x72qyu32uakmlltap4sc5jfit found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/06/06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb.tar.gz
==> No patches needed for bison
==> bison: Executing phase: 'autoreconf'
==> bison: Executing phase: 'configure'
==> bison: Executing phase: 'build'
==> bison: Executing phase: 'install'
==> bison: Successfully installed bison-3.8.2-comfky2x72qyu32uakmlltap4sc5jfit
  Fetch: 2.27s.  Build: 34.04s.  Total: 36.31s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/bison-3.8.2-comfky2x72qyu32uakmlltap4sc5jfit
==> Installing openssl-1.1.1l-xq4viuhggqsoqii6osjf5k25ugjizejv
==> No binary for openssl-1.1.1l-xq4viuhggqsoqii6osjf5k25ugjizejv found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0b/0b7a3e5e59c34827fe0c3a74b7ec8baef302b98fa80088d7f9153aa16fa76bd1.tar.gz
==> Ran patch() for openssl
==> openssl: Executing phase: 'install'
==> openssl: Successfully installed openssl-1.1.1l-xq4viuhggqsoqii6osjf5k25ugjizejv
  Fetch: 3.51s.  Build: 24.16s.  Total: 27.67s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/openssl-1.1.1l-xq4viuhggqsoqii6osjf5k25ugjizejv
==> Installing cmake-3.22.1-i4ydo5hgu5g5dzybpmqznbihusnz7hwq
==> No binary for cmake-3.22.1-i4ydo5hgu5g5dzybpmqznbihusnz7hwq found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0e/0e998229549d7b3f368703d20e248e7ee1f853910d42704aa87918c213ea82c0.tar.gz
==> No patches needed for cmake
==> cmake: Executing phase: 'bootstrap'
==> cmake: Executing phase: 'build'
==> cmake: Executing phase: 'install'
==> cmake: Successfully installed cmake-3.22.1-i4ydo5hgu5g5dzybpmqznbihusnz7hwq
  Fetch: 3.90s.  Build: 3m 22.81s.  Total: 3m 26.71s.
[+] /Users/ondrej/.spack/bootstrap/store/darwin-bigsur-aarch64/apple-clang-12.0.5/cmake-3.22.1-i4ydo5hgu5g5dzybpmqznbihusnz7hwq
==> Installing clingo-bootstrap-spack-7ctouvxrqj6vs2mw2txgl5jfsqfrnpuc
==> No binary for clingo-bootstrap-spack-7ctouvxrqj6vs2mw2txgl5jfsqfrnpuc found: installing from source
==> Error: RuntimeError: Unable to locate Python3.framework/Versions/3.8/Python3 libraries in /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib

/Users/ondrej/repos/spack/var/spack/repos/builtin/packages/python/package.py:828, in libs:
        825                return LibraryList(os.path.join(macos_developerdir, ldlibrary))
        826            else:
        827                msg = 'Unable to locate {0} libraries in {1}'
  >>    828                raise RuntimeError(msg.format(ldlibrary, libdir))
        829        else:
        830            library = self.config_vars['LIBRARY']
        831


==> Error: cannot bootstrap the "clingo" Python module from spec "clingo-bootstrap@spack+python %apple-clang target=aarch64" due to the following failures:
    'spack-install' raised InstallError: Terminating after first install failure: RuntimeError: Unable to locate Python3.framework/Versions/3.8/Python3 libraries in /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib
    Please run `spack -d spec zlib` for more verbose error messages

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