Opened 11 months ago

Closed 11 months ago

Last modified 11 months ago

#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 11 months ago by g5pw (Aljaž Srebrnič)

Hmm.. that file should be in the files/ subdirectory. Could you do a port -d selfupdate and retry the pymol install?

comment:2 Changed 11 months ago by g5pw (Aljaž Srebrnič)

Owner: changed from admin@… to g5pw
Status: newassigned

comment:3 Changed 11 months ago by carlosfamilia (Carlos Familia)

Tried that, didn't work. Any additional that I can do or check?

comment:4 Changed 11 months ago by jmroot (Joshua Root)

Cc: howarth.at.macports@… removed
Component: server/hostingports
Owner: changed from g5pw to jwhowarth

comment:5 Changed 11 months ago by jmroot (Joshua Root)

Cc: g5pw added

comment:6 Changed 11 months 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 11 months 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 pymol@2.1.0_1, the command you told me to run pointed to the local portfile directory instead. Strange right?

Last edited 11 months ago by carlosfamilia (Carlos Familia) (previous) (diff)

comment:8 Changed 11 months ago by jmroot (Joshua Root)

Resolution: invalid
Status: assignedclosed

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 11 months ago by carlosfamilia (Carlos Familia)

Thanks for your help. Sorry that this was such a dumb problem.

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