Installation issue: glib #16214
Description
Hi all,
Sorry to bother you. I am trying a macOS-clang installation of py-jupyter and after having done some workarounds I find myself again a bit stuck on an issue that I don't understand how to fix.
Maybe the issue is similar to pybind/pybind11#595 and https://lists.apple.com/archives/xcode-users/2016/Dec/msg00102.html, but I don't know how to try what they changed.
So I was wondering if you had any suggestions or fixes that I could try.
Thank you for all your help.
Steps to reproduce the issue
$ spack install glib
==> Warning: [email protected] cannot build optimized binaries for "skylake". Using best target possible: "x86_64"
==> Warning: Missing a source id for [email protected]
==> [email protected] : externally installed in /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gettext-0.20.1-hzoq5l22mfztxm43le6elarw3spsldqy
==> [email protected] : already registered in DB
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gettext-0.20.1-hzoq5l22mfztxm43le6elarw3spsldqy
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/libffi-3.2.1-z5a645geugqdal6hdent6ncexra2ftci
==> [email protected] : externally installed in /usr
==> [email protected] : already registered in DB
[+] /usr
==> [email protected] : externally installed in /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/python-3.7.6-jf3fylzmkcammhce6oleqazwo4qfb7zl
==> [email protected] : already registered in DB
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/python-3.7.6-jf3fylzmkcammhce6oleqazwo4qfb7zl
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/pcre-8.43-rfttmpy3n4ichx3xsjksivk2w57kd53w
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/pkgconf-1.6.3-5eu2c6jojxkebrpsnkw4owpzvhkumz7d
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff37x
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/py-setuptools-41.4.0-licvt732h4opxowsk2j7jshgt2aqoqvy
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/ninja-1.10.0-ciqhnrsuipor4ep6otsxyp4e5bkomdpj
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/ncurses-6.2-cqw64pfhfhnycxlvncbgfbmnos2edzhv
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/meson-0.54.0-mu2x5z5fmrrn5fri4whpkvfkj6yz6a3t
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/readline-8.0-4jsebddi4vlbjvd6dzdoixuuwbuptbh3
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gdbm-1.18.1-6fk65ra2aoeep7cb7w45xdlppttr2vym
[+] /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/perl-5.30.1-eb7pj2tmpwgs4gnjmo3dfs366zn4gga4
==> 9982: Installing glib
==> Warning: microarchitecture specific optimizations are not supported yet on mixed compiler toolchains [check [email protected] for further details]
==> Fetching http://ftp.gnome.org/pub/gnome/sources/glib/2.64/glib-2.64.1.tar.xz
##################################################################################################################################################################### 100.0%##################################################################################################################################################################### 100.0%
==> Staging archive: /var/folders/5p/x7ftfty12yndrs3p6ntlk1jc0000gp/T/LDianaAmorim/spack-stage/spack-stage-glib-2.64.1-3qslb2e7otxja57e2p2b3r4q7fkdjpqf/glib-2.64.1.tar.xz
==> Created stage in /var/folders/5p/x7ftfty12yndrs3p6ntlk1jc0000gp/T/LDianaAmorim/spack-stage/spack-stage-glib-2.64.1-3qslb2e7otxja57e2p2b3r4q7fkdjpqf
==> Applied patch /Users/LDianaAmorim/Documents/opt/spack/var/spack/repos/builtin/packages/glib/meson-gettext.patch
==> 9982: glib: Building glib [Package]
==> 9982: glib: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
'ninja' '-j8' 'install'
1 error found in build log:
1517 Could not strip file.
1518
1519 Stdout:
1520
1521
1522 Stderr:
>> 1523 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip: error: symbols referenced by indirect symbol table entries that
can't be stripped in: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/glib-2.64.1-3qslb2e7otxja57e2p2b3r4q7fkdjpqf
/lib/libglib-2.0.0.dylib
1524 _NSSearchPathForDirectoriesInDomains
1525 _UCCompareTextDefault
1526 _UCCreateCollator
1527 _UCGetCollationKey
1528 __NSGetEnviron
1529 ____chkstk_darwin
See build log for details:
/var/folders/5p/x7ftfty12yndrs3p6ntlk1jc0000gp/T/LDianaAmorim/spack-stage/spack-stage-glib-2.64.1-3qslb2e7otxja57e2p2b3r4q7fkdjpqf/spack-build-out.txt
==> Error: Failed to install glib due to ChildError: ProcessError: Command exited with status 1:
'ninja' '-j8' 'install'
1 error found in build log:
1517 Could not strip file.
1518
1519 Stdout:
1520
1521
1522 Stderr:
>> 1523 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strip: error: symbols referenced by indirect symbol table entries that
can't be stripped in: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/glib-2.64.1-3qslb2e7otxja57e2p2b3r4q7fkdjpqf
/lib/libglib-2.0.0.dylib
1524 _NSSearchPathForDirectoriesInDomains
1525 _UCCompareTextDefault
1526 _UCCreateCollator
1527 _UCGetCollationKey
1528 __NSGetEnviron
1529 ____chkstk_darwin
See build log for details:
/var/folders/5p/x7ftfty12yndrs3p6ntlk1jc0000gp/T/LDianaAmorim/spack-stage/spack-stage-glib-2.64.1-3qslb2e7otxja57e2p2b3r4q7fkdjpqf/spack-build-out.txt
Traceback (most recent call last):
File "/Users/LDianaAmorim/Documents/opt/spack/lib/spack/spack/build_environment.py", line 802, in child_process
return_value = function()
File "/Users/LDianaAmorim/Documents/opt/spack/lib/spack/spack/installer.py", line 1113, in build_process
phase(pkg.spec, pkg.prefix)
File "/Users/LDianaAmorim/Documents/opt/spack/lib/spack/spack/package.py", line 108, in phase_wrapper
phase(spec, prefix)
File "/Users/LDianaAmorim/Documents/opt/spack/lib/spack/spack/multimethod.py", line 133, in __call__
return spec_method(package_self, *args, **kwargs)
File "/Users/LDianaAmorim/Documents/opt/spack/var/spack/repos/builtin/packages/glib/package.py", line 127, in install
File "/Users/LDianaAmorim/Documents/opt/spack/lib/spack/spack/build_environment.py", line 131, in __call__
return super(MakeExecutable, self).__call__(*args, **kwargs)
File "/Users/LDianaAmorim/Documents/opt/spack/lib/spack/spack/util/executable.py", line 189, in __call__
proc.returncode, long_msg)
spack.util.executable.ProcessError: Command exited with status 1:
'ninja' '-j8' 'install'Information on your system
- Spack: 0.14.2-702-def1d5e63
- Python: 3.7.3
- Platform: darwin-catalina-skylake
My ~/.spack/darwin/packages.yaml is:
packages:
cmake:
buildable: False
paths:
cmake@3.17.0: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/cmake-3.17.0-6exaq5d4lp7sxf77nhk6kfkuajiy3qwm
llvm:
buildable: False
paths:
llvm@9.0.0: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/llvm-9.0.0-3qcfmwfcsffhy6t6abbz4v3ftoibvuzb
python:
buildable: False
paths:
python@3.7.6: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/python-3.7.6-jf3fylzmkcammhce6oleqazwo4qfb7zl
gettext:
buildable: False
paths:
gettext@0.20: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gettext-0.20.1-hzoq5l22mfztxm43le6elarw3spsldqy
libiconv:
buildable: False
paths:
libiconv: /usr
all:
providers:
mpi: [mpich, openmpi]And my ~/.spack/darwin/compilers.yaml is:
compilers:
- compiler:
spec: clang@11.0.3-apple
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gcc-9.3.0-fdh4ye65koilywzhjbza74sdjmklmnea/bin/gfortran
fc: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gcc-9.3.0-fdh4ye65koilywzhjbza74sdjmklmnea/bin/gfortran
flags: {}
operating_system: catalina
target: x86_64
modules: []
environment: {unset: []}
extra_rpaths: []
- compiler:
spec: gcc@9.3.0
paths:
cc: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gcc-9.3.0-fdh4ye65koilywzhjbza74sdjmklmnea/bin/gcc
cxx: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gcc-9.3.0-fdh4ye65koilywzhjbza74sdjmklmnea/bin/g++
f77: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gcc-9.3.0-fdh4ye65koilywzhjbza74sdjmklmnea/bin/gfortran
fc: /Users/LDianaAmorim/Documents/opt/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/gcc-9.3.0-fdh4ye65koilywzhjbza74sdjmklmnea/bin/gfortran
flags: {}
operating_system: catalina
target: x86_64
modules: []
environment: {}
extra_rpaths: []Additional information
spack-build-env.txt
spack-build-out.txt
General information
- I have run
spack debug reportand 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