Hi Sumudu,
Homebrew gave a clang++ error. This may be due a recent upgrade of Xcode
which replaced MacOSX10.14.sdk with MacOSX10.15.sdk inside the Xcode.app.
If this happened to you, do the following:
cd
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs
sudo ln -s MacOSX.sdk MacOSX10.14.sdk
I am not sure about the origins of the segmentation fault in
with the macports pymol. I install it last week successfully.
I had python3.7 already installed in macports.
I installed the py37 variant of PyMOL.
I had run the commands below a year earlier.
I am not sure if these ports are necessary anymore.
sudo port install tcl -corefoundation
sudo port install tk -quartz
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Sumudu Leelananda [sumudu.leelana...@gmail.com]
Sent: Friday, October 04, 2019 10:53 AM
To: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] [PyMOL] Mac installation error: clang++, segmentation fault
11
Hi,
I was trying to get open source pymol installed on my Mac but was unable to do
so. I tried brew and macports. I'm on Mojave 10.14.6. I attached the error I
get with brew. With Macports, when I try to open Pymol it returns a
segmentation fault 11 error.
Has anybody seen this before? Any suggestions?
Thank you!
brew install brewsci/bio/pymol
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 4 taps (homebrew/core, homebrew/cask, homebrew/services and
caskroom/cask).
==> Updated Formulae
cmake ✔ deno ffsend go@1.12 gspell
haproxy iso-codes node rke
roswell rust
==> Installing pymol from brewsci/bio
==> Downloading
https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_schrodinger_pymol-2Dopen-2Dsource_archive_v2.3.0.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=Um_WhO1_-dwQYFKunIbXRV4fqmJsW65fMLP6bqDbMfc&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/a51d46dea90ae24d275dac1d9efa7cf70025ab5fed71dc210ce3000d5d65219c--pymol-open-source-2.3.0.tar.gz
==> Downloading
https://files.pythonhosted.org/packages/11/74/2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf/virtualenv-16.7.4.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_11_74_2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf_virtualenv-2D16.7.4.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=a4dBdjqDiDnC10aVIUHN-v0TtjddjFC73iVBkKaHPO0&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/507d2087bf24df82641b681a5fe4da778ef50ebe819a86ea1b584f70788f0f63--virtualenv-16.7.4.tar.gz
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> Downloading
https://files.pythonhosted.org/packages/3a/20/c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e/numpy-1.15.0.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_3a_20_c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e_numpy-2D1.15.0.zip&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=g_9yGKFX3t1BaE8uAGJXLH3pC0Nm15JIF4-P-OTvkio&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/c3591902b12abd9354b52438f4e5aa07974b9e83cf502a778095fd0fd6a1cc46--numpy-1.15.0.zip
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> Downloading
https://files.pythonhosted.org/packages/13/ea/c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3/mmtf-python-1.1.2.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_13_ea_c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3_mmtf-2Dpython-2D1.1.2.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=ebk16SyRo7S3WRYtFn6A1gARpXPcseHuOSHU441C9bM&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/8184cd2975ddc6f5276f8aca6273b4b0e2e98a69ae60a94e8f087e2bf4f7fbc2--mmtf-python-1.1.2.tar.gz
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> Downloading
https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_81_9c_0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578_msgpack-2D0.6.1.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=cKfy9zqGkC2Htf63F3IsV9EbtrTyLLvFMxgtY32YfZo&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/432b50d5f899f052d91eb12c17bb4fe7686828cd77a7f5d3b6e4f646b09eabf6--msgpack-0.6.1.tar.gz
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> Downloading
https://files.pythonhosted.org/packages/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_8a_20_6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091_msgpack-2Dpython-2D0.5.6.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=AuTIyzeL2Z-Ti44j29R9ylqJsx-6SFwqLrLd45RnFmY&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/49c4120b43aa86620eaebc552b359f6d897f72f59d979634a803f54088ea44d8--msgpack-python-0.5.6.tar.gz
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> Downloading
https://files.pythonhosted.org/packages/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_73_0c_55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134_msgpack-2Dtool-2D0.0.1.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=4jQJkEos6NKgVpw1a5gpmVOvP4DNLVt57MqOZnlKMu0&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/cc8ecf250035cd7b706c464cf5a1be6cfdd1a92482350d209d6900918ec93b34--msgpack-tool-0.0.1.tar.gz
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> Downloading
https://files.pythonhosted.org/packages/e7/20/8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa/Pmw-2.0.1.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_e7_20_8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa_Pmw-2D2.0.1.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=utv0f3_bZL9Yh3JfGRTMmdoNiQMxDPrGljDOtC1DBn0&e=>
Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/50fbcfa2c8f747eb0d10f58fb92b1405935cdbeb84b675b4a28b0235409fa10b--Pmw-2.0.1.tar.gz
==> python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man
==> python3 setup.py install
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--install-lib=/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.7/site-packages
--glut --use-msgpackc=c++11
Last 15 lines from /Users/sumudu/Library/Logs/Homebrew/pymol/08.python3:
^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: unused
function 'whereami' [-Wunused-function]
static void whereami(FILE *file) {
^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: unused
function 'replace_wavefunction' [-Wunused-function]
static void replace_wavefunction(qm_timestep_t *ts, int n) {
^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: unused
function 'del_wavefunction' [-Wunused-function]
static void del_wavefunction(qm_timestep_t *ts) {
^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: unused
function 'print_matrix4' [-Wunused-function]
static void print_matrix4(const float mat[16]) {
^
12 warnings generated.
error: command 'clang++' failed with exit status 1
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