Hi Javier,
Because this is an issue about open-source pymol,
open an issue on the open-source GitHub site and report the problem
https://github.com/schrodinger/pymol-open-source/issues
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: CCP4 bulletin board [[log in to unmask]] on behalf of Javier Gonzalez [[log in to unmask]]
Sent: Saturday, June 13, 2020 6:45 PM
To: [log in to unmask]
Subject: [EXTERNAL] [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina
Hello,
I'm attempting to build pymol on a laptop running MacOS Catalina 10.15.5,
Processor 2.8GHz Quad-Core Intel i7, Graphics Intel Iris Pro 1536 MB
I downloaded the latest version of Xcode 11.1
I tried from Fink (fink install pymol-py27) and Macports (sudo port install pymol), as indicated here: https://pymolwiki.org/index.php/MAC_Install<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_MAC-5FInstall&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kT3F0qPZ7hI98b3h0YTHyCwS8vQy7JKxTnlsVitdb1w&s=B8hC_f0PMlJxXkzo7QpqvmuTlvPFET9myuMD5mUpUbU&e=>
Both scripts run to download all dependencies but at the end fail with different messages (see below). Any ideas? Is it doable or am I just following outdated instructions?
Thanks in advance!
Javier
Fink: fails at compiling term-readkey-pm5184-2.37-1
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Failed: phase compiling: term-readkey-pm5184-2.37-1 failed
Before reporting any errors, please run "fink selfupdate" and try again.
Also try using "fink configure" to set your maximum build jobs to 1 and
attempt to build the package again.
If you continue to have issues, please check to see if the FAQ on Fink's
website solves the problem. If not, ask on one (not both, please) of
these mailing lists:
The Fink Users List <[log in to unmask]<mailto:[log in to unmask]>>
The Fink Beginners List <[log in to unmask]<mailto:[log in to unmask]>>,
with a carbon copy to the maintainer:
Christian Schaffner <[log in to unmask]<mailto:[log in to unmask]>>
Note that this is preferable to emailing just the maintainer directly,
since most fink package maintainers do not have access to all possible
hardware and software configurations.
Please try to include the complete error message in your report. This
generally consists of a compiler line starting with e.g. "gcc" or "g++"
followed by the actual error output from the compiler.
Also include the following system information:
Package manager version: 0.45.1
Distribution version: selfupdate-rsync Fri Jun 12 21:49:17 2020, 10.15, x86_64
Trees: local/main stable/main
Xcode.app<https://urldefense.proofpoint.com/v2/url?u=http-3A__Xcode.app&d=DwQFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kT3F0qPZ7hI98b3h0YTHyCwS8vQy7JKxTnlsVitdb1w&s=pJ2WMWnX2YbGmVykOgsCdk15IJcJiGHSbScNq2RIdqM&e=>: 11.5
Xcode command-line tools: 11.5.0.0.1.1588476445
Max. Fink build jobs: 8
-------------------------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------------------------
Macports: apparently there is an issue with py38-pyqt5
---> Computing dependencies for pymol
The following dependencies will be installed: py38-pyqt5
Continue? [Y/n]:
---> Fetching archive for py38-pyqt5
---> Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from https://packages.macports.org/py38-pyqt5<https://urldefense.proofpoint.com/v2/url?u=https-3A__packages.macports.org_py38-2Dpyqt5&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kT3F0qPZ7hI98b3h0YTHyCwS8vQy7JKxTnlsVitdb1w&s=HXzceoCE4NrXw7l9SeGxEVG84RWS0KqIElfV_kw0Grk&e=>
---> Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from http://aus.us.packages.macports.org/macports/packages/py38-pyqt5<https://urldefense.proofpoint.com/v2/url?u=http-3A__aus.us.packages.macports.org_macports_packages_py38-2Dpyqt5&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kT3F0qPZ7hI98b3h0YTHyCwS8vQy7JKxTnlsVitdb1w&s=EMr3UPpvA_kadqXDAsDvRVJJuzPCPswslDML4vft2SQ&e=>
---> Attempting to fetch py38-pyqt5-5.14.2_0.darwin_19.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/py38-pyqt5<https://urldefense.proofpoint.com/v2/url?u=https-3A__ywg.ca.packages.macports.org_mirror_macports_packages_py38-2Dpyqt5&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kT3F0qPZ7hI98b3h0YTHyCwS8vQy7JKxTnlsVitdb1w&s=yaYYRaM3fYH3_Zia6lzTJRWitV6Vvu9wh6Nc_rWYx5w&e=>
---> Building py38-pyqt5
Error: Failed to build py38-pyqt5: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-pyqt5/py38-pyqt5/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets<https://urldefense.proofpoint.com/v2/url?u=https-3A__guide.macports.org_-23project.tickets&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kT3F0qPZ7hI98b3h0YTHyCwS8vQy7JKxTnlsVitdb1w&s=4Zj_TqgWdM3vja9QwPoNkwxD-SCldOJlMCyr2iPHam0&e=> to report a bug.
Error: Processing of port pymol failed
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--
Dr. Javier M. González
Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET)
Universidad Nacional de Santiago del Estero (UNSE)
RN9, Km 1125. Villa El Zanjón. (G4206XCP)
Santiago del Estero. Argentina
Tel: +54-(0385)-4238352
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