Hi Andreas,
The URL's were updated in upstream some time ago. The debian version of
libcifpp (and all dependent tools) are a bit out of date.
The problem I have is that development of libcifpp is a bit too fast.
Whenever I break the ABI I have to ask for someone to upload a newer
version. And last time this apparently did not went well and so the
update stalled. I don't remember who I asked to update, but since that
didn't happen I forgot about it.
Anyway, so I had an upload ready for version 5.2 and libcifpp is now at
version 6.1. I will thus have to prepare yet another update and then
upload all depending packages. I'll see what I can do.
regards, -maarten
Op 13-02-2024 om 08:28 schreef Andreas Tille:
Hi Maarten,
since last September there is a new upstream version in Git which was
not uploaded. I see less instances of ftp.wwpdb.org in this code but
there are some remainings. It would be great if you could upload your
preparation after checking that the bug below is fixed.
Kind regards
Andreas.
Am Mon, Feb 05, 2024 at 11:27:36AM -0500 schrieb Rick Bernard:
Package: libcifpp-data
Version: 5.0.7.1-3
Severity: important
Tags: patch
Dear Maintainer,
*** Reporter, please consider answering these questions, where appropriate ***
* What led up to the situation?
Installing libcifpp-data via "apt install". The incorrect URL causes apt to
hang for a long period of time before returrning to a prompt. As a result, the
file supposed to be loaced in /var/cache/libcifpp/components.cif fails to
download. The Stable version of this package was showing timeout errors when
attempting to connect to https://ftp.wwpdb.org. The correct URL that is
published by wwpdb.org is https://files.wwpdb.org for downloading via HTTP.
This will happen durring install via apt when you are prompted Package
configuration about setting up weekly downloads of these data files from
wwpdb.org.
* What exactly did you do (or not do) that was effective (or
ineffective)?
Editing the file /etc/cron.weekly/update-libcifpp-data and changing the URL
for the components.cif download from https://ftp.wwpdb.org to
https://files.wwpdb.org leaving all subpaths the same resolves the issue. This
also helps with the stable version of this package and fixes dpkg and apt when
running "dpkg --configure -a"
* What was the outcome of this action?
Resolves the package install and fixes apt/dpkg package management system.
* What outcome did you expect instead?
The expected outcome is that "apt install" will successfully install the
package and be able to run the download scripts successfully.
*** End of the template - remove these template lines ***
-- System Information:
Debian Release: 12.4
APT prefers stable
APT policy: (990, 'stable'), (500, 'stable-security'), (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.1.0-17-amd64 (SMP w/12 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages libcifpp-data depends on:
ii debconf [debconf-2.0] 1.5.82
libcifpp-data recommends no packages.
libcifpp-data suggests no packages.
-- debconf information:
* libcifpp/update: true
--- update-libcifpp-data.orig 2024-02-05 11:13:15.964579981 -0500
+++ update-libcifpp-data 2024-02-05 11:24:35.219320601 -0500
@@ -60,7 +60,7 @@
# Update the dictionaries
-update_dictionary "/var/cache/libcifpp/components.cif" "https://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz";
+update_dictionary "/var/cache/libcifpp/components.cif"
"https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz";
update_dictionary "/var/cache/libcifpp/mmcif_pdbx.dic"
"https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz";
update_dictionary "/var/cache/libcifpp/mmcif_ma.dic"
"https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic";
_______________________________________________
Debian-med-packaging mailing list
debian-med-packag...@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
--
Maarten L. Hekkelman
http://www.hekkelman.com/
