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Re: python313 dependency mismatch?




To: jperkin%pkgsrc.org@localhost

Subject: Re: python313 dependency mismatch?

From: Havard Eidnes <he%NetBSD.org@localhost>

Date: Tue, 27 Jan 2026 19:31:47 +0100 (CET)


> Please can you try this diff for your next attempt?
>
>   https://gist.github.com/jperkin/b9b84a178c1cc6ac56be26eab265def9
>
> Apply it to latest pkgsrc pkgin and use it directly for the upgrade.
> It should hopefully work correctly, though now the initial
> pkgtools-only upgrade may pull in a lot more packages, which kinda
> renders it pointless on such systems.  I'd be interested in the output
> for both the initial run and the subsequent catch-all run.
>
> It passes the test I've added for this based on your output:
>
>   https://github.com/TritonDataCenter/pkgin-test-suite/commit/cd92ef2fb203f785f094844a7a1bc1a90505f62b

Excellent!

I did

# cd /usr/pkgsrc/pkgtools/pkgin
# cvs -q update -A
# make patch
# cd work/pkgin-*
# patch -p1 </tmp/pkgin-upgrade-pkgtools.diff  : (from the gist above)
# cd ../..
# make
# make replace

and ended up with pkgin-25.10.0nb1 installed, and with that:

# pkgin up
processing remote summary (https://cdn.NetBSD.org/pub/pkgsrc/packages/NetBSD/amd64/10.0/All)...
database for https://cdn.NetBSD.org/pub/pkgsrc/packages/NetBSD/amd64/10.0/All is up-to-date
# pkgin fug

1 package to refresh:
  llvm-19.1.7

4 packages to upgrade:
  pkgin-25.10.0 python311-3.11.14 python312-3.12.12 sqlite3-3.51.1

2 packages to install:
  mpdecimal-4.0.1 python313-3.13.11

0 to remove, 1 to refresh, 4 to upgrade, 2 to install
158M to download, 156M of additional disk space will be used

proceed ? [Y/n] 

Looks much more promising.  Here both python313 and mpdecimal is
dragged along because a refresh of llvm is triggered.  I see I'll
have to re-replace pkgin from my local build afterwards...

So let's give our consent:

proceed ? [Y/n] y
[1/7] llvm-19.1.7.tgz                         100%   88MB   2.3MB/s   00:39    
[2/7] mpdecimal-4.0.1.tgz                     100%  114KB 114.0KB/s   00:00    
[3/7] pkgin-25.10.0.tgz                       100%   69KB  69.1KB/s   00:00    
[4/7] python311-3.11.14.tgz                   100%   23MB   2.5MB/s   00:09    
[5/7] python312-3.12.12.tgz                   100%   23MB   2.3MB/s   00:10    
[6/7] python313-3.13.11.tgz                   100%   23MB   2.6MB/s   00:09    
[7/7] sqlite3-3.51.1.tgz                      100% 1228KB   1.2MB/s   00:00    
[1/7] upgrading sqlite3-3.51.1...
[2/7] installing mpdecimal-4.0.1...
[3/7] upgrading pkgin-25.10.0...
[4/7] upgrading python311-3.11.14...
[5/7] upgrading python312-3.12.12...
[6/7] installing python313-3.13.11...
[7/7] refreshing llvm-19.1.7...
pkg_install warnings: 0, errors: 0
reading local summary...
processing local summary...
Package tools were upgraded.  Re-run "pkgin upgrade" to complete the upgrade.
#

and then re-building pkgin and "make replace" again:

# pkgin upgrade

1 package to refresh:
  pkg_install-20250417

1 package to upgrade:
  pkgin-25.10.0

0 to remove, 1 to refresh, 1 to upgrade, 0 to install
295K to download, 216B of disk space will be freed up

proceed ? [Y/n] y
[1/1] pkg_install-20250417.tgz                100%  295KB 294.7KB/s   00:00    
[1/2] refreshing pkg_install-20250417...
[2/2] upgrading pkgin-25.10.0...
pkg_install warnings: 0, errors: 0
reading local summary...
processing local summary...
Package tools were upgraded.  Re-run "pkgin upgrade" to complete the upgrade.
#

another re-replace, and then:

# pkgin upgrade

1 package to upgrade:
  pkgin-25.10.0

0 to remove, 0 to refresh, 1 to upgrade, 0 to install
0B to download, 0B of additional disk space will be used

proceed ? [Y/n] n
#

Hm, stuck in a loop, apparently; it REALLY wants to use the
upstream pkgin.  Oh, well, let's see how that goes:

# pkgin upgrade

1 package to upgrade:
  pkgin-25.10.0

0 to remove, 0 to refresh, 1 to upgrade, 0 to install
0B to download, 0B of additional disk space will be used

proceed ? [Y/n] y
[1/1] upgrading pkgin-25.10.0...
pkg_install warnings: 0, errors: 0
reading local summary...
processing local summary...
Package tools were upgraded.  Re-run "pkgin upgrade" to complete the upgrade.
# pkgin upgrade
calculating dependencies...done.

23 packages to refresh:
  autoconf-2.72 automake-1.18 bonnie++-1.98nb2 collectd-5.12.0nb3
  cwrappers-20220403 digest-20220214 help2man-1.49.3 ipmitool-1.8.19nb1
  libcbor-0.13.0 libfido2-1.16.0 libtool-base-2.4.7nb1 libunistring-1.2
  libunwind-19.1.7nb1 libuuid-2.40.2 mktools-20250213 opendkim-2.10.3nb12
  openssh-10.2p1 p5-gettext-1.07nb10 pkgdiff-1.12 readline-8.3nb1 rsync-3.4.1
  xmlcatmgr-2.2nb1 xxhash-0.8.3

11 packages to upgrade:
  bash-5.3.9 cmake-4.1.2 curl-8.17.0 git-base-2.52.0 libfetch-2.40nb2
  nghttp2-1.68.0 pcre2-10.47 perl-5.42.0nb1 routinator-0.15.1 rust-1.90.0
  zabbix-agent-6.0.24nb9

0 to remove, 23 to refresh, 11 to upgrade, 0 to install
127M to download, 15M of additional disk space will be used

proceed ? [Y/n] y
[1/34] autoconf-2.72.tgz                      100%  600KB 600.4KB/s   00:01    
[2/34] automake-1.18.tgz                      100%  565KB 564.5KB/s   00:00    
[3/34] bash-5.3.9.tgz                         100% 1744KB   1.7MB/s   00:01    
[4/34] bonnie++-1.98nb2.tgz                   100%   52KB  51.6KB/s   00:00    
[5/34] cmake-4.1.2.tgz                        100%   12MB   2.4MB/s   00:05    
[6/34] collectd-5.12.0nb3.tgz                 100%  544KB 543.7KB/s   00:00    
[7/34] curl-8.17.0.tgz                        100%  975KB 974.8KB/s   00:00    
[8/34] cwrappers-20220403.tgz                 100%   26KB  26.4KB/s   00:00    
[9/34] digest-20220214.tgz                    100%   45KB  45.0KB/s   00:00    
[10/34] git-base-2.52.0.tgz                   100% 6858KB   1.7MB/s   00:04    
[11/34] help2man-1.49.3.tgz                   100%  116KB 116.1KB/s   00:00    
[12/34] ipmitool-1.8.19nb1.tgz                100%  388KB  97.0KB/s   00:04    
[13/34] libcbor-0.13.0.tgz                    100%   34KB  34.1KB/s   00:00    
[14/34] libfetch-2.40nb2.tgz                  100%   35KB  34.9KB/s   00:00    
[15/34] libfido2-1.16.0.tgz                   100%  190KB 190.3KB/s   00:00    
[16/34] libtool-base-2.4.7nb1.tgz             100%  284KB 284.2KB/s   00:00    
[17/34] libunistring-1.2.tgz                  100%  609KB 609.1KB/s   00:00    
[18/34] libunwind-19.1.7nb1.tgz               100%   47KB  46.6KB/s   00:00    
[19/34] libuuid-2.40.2.tgz                    100%   36KB  36.5KB/s   00:00    
[20/34] mktools-20250213.tgz                  100% 5228     5.1KB/s   00:00    
[21/34] nghttp2-1.68.0.tgz                    100%  156KB 156.4KB/s   00:00    
[22/34] opendkim-2.10.3nb12.tgz               100%  269KB 269.4KB/s   00:00    
[23/34] openssh-10.2p1.tgz                    100% 1042KB   1.0MB/s   00:01    
[24/34] p5-gettext-1.07nb10.tgz               100%   12KB  11.6KB/s   00:00    
[25/34] pcre2-10.47.tgz                       100%  846KB 845.6KB/s   00:01    
[26/34] perl-5.42.0nb1.tgz                    100%   12MB   2.5MB/s   00:05    
[27/34] pkgdiff-1.12.tgz                      100%   11KB  11.2KB/s   00:00    
[28/34] readline-8.3nb1.tgz                   100%  352KB 352.3KB/s   00:00    
[29/34] routinator-0.15.1.tgz                 100% 4096KB   1.3MB/s   00:03    
[30/34] rsync-3.4.1.tgz                       100%  285KB 285.3KB/s   00:00    
[31/34] rust-1.90.0.tgz                       100%   82MB   2.4MB/s   00:34    
[32/34] xmlcatmgr-2.2nb1.tgz                  100%   26KB  25.8KB/s   00:00    
[33/34] xxhash-0.8.3.tgz                      100%   84KB  84.4KB/s   00:00    
[34/34] zabbix-agent-6.0.24nb9.tgz            100%  275KB 274.9KB/s   00:00    
[1/34] refreshing libuuid-2.40.2...
[2/34] refreshing libunistring-1.2...
[3/34] refreshing readline-8.3nb1...
[4/34] refreshing libcbor-0.13.0...
[5/34] upgrading nghttp2-1.68.0...
[6/34] upgrading perl-5.42.0nb1...
[7/34] refreshing xmlcatmgr-2.2nb1...
[8/34] upgrading pcre2-10.47...
[9/34] upgrading bash-5.3.9...
[10/34] refreshing libunwind-19.1.7nb1...
[11/34] refreshing p5-gettext-1.07nb10...
[12/34] refreshing libfido2-1.16.0...
[13/34] upgrading curl-8.17.0...
[14/34] refreshing xxhash-0.8.3...
[15/34] refreshing libtool-base-2.4.7nb1...
[16/34] upgrading libfetch-2.40nb2...
[17/34] refreshing ipmitool-1.8.19nb1...
[18/34] upgrading routinator-0.15.1...
[19/34] refreshing pkgdiff-1.12...
[20/34] upgrading cmake-4.1.2...
[21/34] refreshing cwrappers-20220403...
[22/34] upgrading git-base-2.52.0...
[23/34] refreshing rsync-3.4.1...
[24/34] refreshing automake-1.18...
[25/34] refreshing help2man-1.49.3...
[26/34] refreshing digest-20220214...
[27/34] refreshing openssh-10.2p1...
[28/34] refreshing bonnie++-1.98nb2...
[29/34] upgrading zabbix-agent-6.0.24nb9...
[30/34] refreshing autoconf-2.72...
[31/34] upgrading rust-1.90.0...
[32/34] refreshing collectd-5.12.0nb3...
[33/34] refreshing mktools-20250213...
[34/34] refreshing opendkim-2.10.3nb12...
pkg_install warnings: 0, errors: 0
reading local summary...
processing local summary...
#

So...  I think we can conclude that your patch fixed the problem
I was observing.

Best regards,

- Håvard


Follow-Ups:

Re: python313 dependency mismatch?
From: Jonathan Perkin


References:

Re: python313 dependency mismatch?
From: Havard Eidnes

Re: python313 dependency mismatch?
From: Jonathan Perkin

Re: python313 dependency mismatch?
From: Jonathan Perkin




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