#56452 closed defect (invalid)
Pymol installation fails
| Reported by: | carlosfamilia (Carlos Familia) | Owned by: | jwhowarth |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | 2.4.4 |
| Keywords: | Cc: | g5pw (Aljaž Srebrnič) | |
| Port: | Pymol |
Description
Hi,
Pymol installation fails in High Sierra with the following console output:
sudo port install pymol ---> Computing dependencies for pymol ---> Fetching distfiles for pymol ---> Attempting to fetch pymol_shell.diff from https://distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from http://lil.fr.distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from http://mse.uk.distfiles.macports.org/sites/distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from http://nue.de.distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from https://kent.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://freefr.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://netix.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://fco.it.distfiles.macports.org/mirrors/macports-distfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://netassist.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://superb-dca2.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://pilotfiber.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://iweb.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://ywg.ca.distfiles.macports.org/mirror/macports/distfiles/pymol ---> Attempting to fetch pymol_shell.diff from https://excellmedia.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://svwh.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://superb-sea2.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://cytranet.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://phoenixnap.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://sea.us.distfiles.macports.org/macports/distfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://liquidtelecom.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://ayera.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://tenet.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://ufpr.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://jnb.za.distfiles.macports.org/distfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://kmq.jp.distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from https://jaist.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from http://aarnet.au.distfiles.macports.org/pub/macports/distfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://jog.id.distfiles.macports.org/macports/distfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://cjj.kr.distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from http://nou.nc.distfiles.macports.org/pub/macports/distfiles.macports.org/pymol ---> Attempting to fetch pymol_shell.diff from https://pek.cn.distfiles.macports.org/macports/distfiles/pymol ---> Attempting to fetch pymol_shell.diff from http://nchc.dl.sourceforge.net/pymol ---> Attempting to fetch pymol_shell.diff from https://netcologne.dl.sourceforge.net/pymol Error: Failed to fetch pymol: The requested URL returned error: 404 Not Found Error: See /opt/local/var/macports/logs/_Users_myuser_.ports_science_pymol/pymol/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port pymol failed
I have checked on the http://distfiles.macports.org web page and some others in the above list, and there is no directory named pymol.
Change History (9)
comment:1 Changed 6 years ago by g5pw (Aljaž Srebrnič)
comment:2 Changed 6 years ago by g5pw (Aljaž Srebrnič)
| Owner: | changed from admin@… to g5pw |
|---|---|
| Status: | new → assigned |
comment:3 Changed 6 years ago by carlosfamilia (Carlos Familia)
Tried that, didn't work. Any additional that I can do or check?
comment:4 Changed 6 years ago by jmroot (Joshua Root)
| Cc: | howarth.at.macports@… removed |
|---|---|
| Component: | server/hosting → ports |
| Owner: | changed from g5pw to jwhowarth |
comment:5 Changed 6 years ago by jmroot (Joshua Root)
| Cc: | g5pw added |
|---|
comment:6 Changed 6 years ago by jmroot (Joshua Root)
Check if the file is there in your ports tree:
% ls -l `port dir pymol`/files
For me that shows
total 48 -rw-r--r-- 1 root 505 414 Aug 23 2017 apbs-psize.patch -rw-r--r-- 1 root 505 852 Apr 24 08:45 pdb2pqr.patch -rw-r--r-- 1 root 505 1874 Apr 24 08:45 pmg_tk_platform.patch -rw-r--r-- 1 root 505 3244 Aug 23 2017 pymol-use-glkit.diff -rw-r--r-- 1 root 505 768 Apr 24 08:45 pymol_shell.diff -rw-r--r-- 1 root 505 1045 Apr 29 19:23 setup.py.diff
comment:7 Changed 6 years ago by carlosfamilia (Carlos Familia)
I just found the problem, I had a local version of a portfile for pymol 1.8.6. Even though I was specifying to install pymol@2.1.0_1, the command you told me to run pointed to the local portfile directory instead. Strange right?
comment:8 Changed 6 years ago by jmroot (Joshua Root)
| Resolution: | → invalid |
|---|---|
| Status: | assigned → closed |
Sources are searched in the order they are listed in sources.conf. You can't specify a version when installing since a portfile only ever defines one version.
comment:9 Changed 6 years ago by carlosfamilia (Carlos Familia)
Thanks for your help. Sorry that this was such a dumb problem.
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Hmm.. that file should be in the files/ subdirectory. Could you do a
port -d selfupdateand retry the pymol install?