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://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz>*
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://files.pythonhosted.org/packages/11/74/2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf/virtualenv-16.7.4.tar.gz>*
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://files.pythonhosted.org/packages/3a/20/c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e/numpy-1.15.0.zip>*
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://files.pythonhosted.org/packages/13/ea/c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3/mmtf-python-1.1.2.tar.gz>*
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://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz>*
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://files.pythonhosted.org/packages/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz>*
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://files.pythonhosted.org/packages/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz>*
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://files.pythonhosted.org/packages/e7/20/8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa/Pmw-2.0.1.tar.gz>*
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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