Package Details: coot 1.1.10-3

Git Clone URL: https://aur.archlinux.org/coot.git (read-only, click to copy)
Package Base: coot
Description: Crystallographic Object-Oriented Toolkit for model building, completion and validation
Upstream URL: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Keywords: science
Licenses: GPL
Replaces: coot-data
Submitter: Athemis
Maintainer: hgonomeg
Last Packager: hgonomeg
Votes: 2
Popularity: 0.000000
First Submitted: 2016-01-12 02:53 (UTC)
Last Updated: 2024-09-20 17:40 (UTC)

Pinned Comments

hgonomeg commented on 2024-09-10 21:15 (UTC)

Hi, I've adopted the package. Now it's the newest version (1.1.10).

If there's anything broken, let me know. Particularly, I don't know if Coot 1 supports Guile GUI at all.

At the time of posting this, there is just one dependency that fails to build and that is fftw2-float where openmpi is broken. The workaround is to edit the PKGBUILD and remove --with-openmpi in both places where it occurs.

All remaining dependencies should build just fine.

Athemis commented on 2018-07-10 19:44 (UTC)

Binary packages of coot and its dependencies can be found in my repo. Add these lines to your /etc/pacman.conf:

[home_Athemis_coot_Arch]
SigLevel = Never
Server = https://download.opensuse.org/repositories/home:/Athemis:/coot/Arch/$arch

And install coot via pacman -Syu & pacman -S coot

Latest Comments

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nmruser commented on 2018-07-31 20:56 (UTC)

@Athemis Thanks, works like charm!

Athemis commented on 2018-07-10 19:44 (UTC)

Binary packages of coot and its dependencies can be found in my repo. Add these lines to your /etc/pacman.conf:

[home_Athemis_coot_Arch]
SigLevel = Never
Server = https://download.opensuse.org/repositories/home:/Athemis:/coot/Arch/$arch

And install coot via pacman -Syu & pacman -S coot

Athemis commented on 2018-07-10 11:04 (UTC) (edited on 2018-07-10 19:56 (UTC) by Athemis)

@nmruser: haven't made any progress so far. I had it building successfully with rdkit-python2-2017_09_3 some time ago. Since then gcc version was bumped which is my best guess what's causing the problems with building against legacy rdkit.

I'll keep you updated on my progress.

UPDATE: The error in dynarama-main seems to be related to glibc-2.26: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=887632

UPDATE 2: The latest revision builds again (at least for me). Please test.

UPDATE 3: Binary packages available (see sticky comment)

nmruser commented on 2018-07-05 14:17 (UTC)

@Athemis, I cannot compile even if I revert to rdkit-python2_2017. Having trouble with dynarama, relevant lines seem to be:

... In file included from /usr/include/gtk-2.0/gtk/gtk.h:173, from dynarama-main.cc:36:

make[1]: [Makefile:1625: dynarama-main.o] Error 1 make: [Makefile:705: all-recursive] Error 1 ==> ERROR: A failure occurred in build(). Aborting...

Athemis commented on 2018-07-04 22:17 (UTC)

@nmruser: I'll look into that. We might have to wait for Paul to fix that upstream. Meanwhile, you may work around this by sticking to an older version of rdkit-python2

nmruser commented on 2018-07-04 18:06 (UTC)

Can you update the package for rdkit-python2_2018xx? Cannot compile with the latest rdkit-python2-2018_03_2-1.

jrdemasi commented on 2018-02-19 19:48 (UTC)

Worked like a charm! Thanks.

Athemis commented on 2018-02-15 12:25 (UTC) (edited on 2018-02-15 12:25 (UTC) by Athemis)

Btw, I added a package that builds libccp4-7.0 from the CCP4 VCS (they don't provide tarballs for the recent version). I don't know if there are any benefits from using that. Probably not, since official Coot binaries seem to be still built against libccp4-6.4. Anyhow, you may give it a try and replace libccp4 with libccp4-bzr.

Athemis commented on 2018-02-15 09:56 (UTC) (edited on 2018-02-15 11:41 (UTC) by Athemis)

Good catch. I updated the pyrogen patch to apply to the new release, but missed pushing the updated patch to git ;-)

jrdemasi commented on 2018-02-14 21:56 (UTC)

Actually, as it turns out the patching fails altogether.

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