GNU bug report logs - #78105
r-posterior: Update to 1.6.1.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
To: guix-patches <at> gnu.org
Subject: r-posterior: Update to 1.6.1.
Date: Mon, 28 Apr 2025 09:46:57 +0300

[Message part 1 (text/plain, inline)]

Hi!

This patch updates r-posterior to 1.6.1. This fixes building, where
1.6.0 fails in testing.

I have checked the generated package, it does not bundle any new
javascript. I have not built all dependencies. 

Cheers,
Tor-björn

[0001-gnu-r-posterior-update-to-1.6.1.patch (text/x-patch, attachment)]

Message #8 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
To: 78105 <at> debbugs.gnu.org
Subject: Further patches
Date: Mon, 28 Apr 2025 12:11:31 +0300

[Message part 1 (text/plain, inline)]

Here is a patch series, which allows r-cardx to be built
successfully :-)

All patches in this series are point release package updates, fixing
build failiures due to failing tests already addressed by the respective
upstream projects.

Cheers,
Tor-björn Claesson

[0002-gnu-r-rhub-Update-to-2.0.1.patch (text/x-patch, attachment)]

[0003-gnu-r-datawizard-Update-to-1.0.2.patch (text/x-patch, attachment)]

[0004-gnu-r-cardx-Update-to-0.2.4.patch (text/x-patch, attachment)]

Message #11 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Tue, 29 Apr 2025 18:53:09 +0200

Hello Tor-björn,
(and cc to our R specialist),

thanks for your patches!

Unfortunately mixing different patches in this way confuses QA.
Could you please follow the description in
   https://guix.gnu.org/manual/devel/en/html_node/Submitting-Patches.html
for future patches?

Unrelated changes (like r-posterior and r-cardx) should be sent to
separate issues, and related changes can be grouped into one issue,
but then they should be sent using "git send-email", which will
create one mail per patch and send it to the same address.
When sending a new version of a patch or a series, make sure to use the
"-v2", "-v3", ... flags to "git send-email".

In this case, QA has only built one package, r-cardx:
   https://qa.guix.gnu.org/issue/78105
I suppose it has applied only the last patch, which is confirmed
following the "View Git branch" or "View series on Patchwork" link
on the previous page.

So apparently r-cardx is a leaf package and can be updated independently
of all the other packages. Hm, it depends on r-posterior, which fails to
build, so maybe this is a series after all :)  Strangely QA seems to
have built it, but locally it fails.

Concerning r-posterior, I tried to build its immediate dependencies
using the command
   ./pre-inst-env guix build -P 1 r-posterior
after applying your first patch (I would recommend to do so whenever you
submit patches, and to mention this in your cover letter), but this
results in a failure:
...
build of /gnu/store/cbh0lsf80gkv8g1y0zlrx5j0dmrm7lzs-r-delayedmatrixstats-1.28.1.drv failed
View build log at '/var/log/guix/drvs/cb/h0lsf80gkv8g1y0zlrx5j0dmrm7lzs-r-delayedmatrixstats-1.28.1.drv.gz'.
cannot build derivation `/gnu/store/41ffhwrdk1x692wzgbcsv2wiqb5k5icp-r-scran-1.34.0.drv': 1 dependencies couldn't be built
cannot build derivation `/gnu/store/3bbi85p6nd2d7n8hfm0z0fbxq7fmj9cs-r-scuttle-1.16.0.drv': 1 dependencies couldn't be built
cannot build derivation `/gnu/store/isy948jcij3d4ri4v5ynvdbkdhv7xpib-r-basics-2.18.0.drv': 1 dependencies couldn't be built
guix build: error: build of `/gnu/store/isy948jcij3d4ri4v5ynvdbkdhv7xpib-r-basics-2.18.0.drv' failed

So for now, I am not going to apply any of your patches; if you could
investigate further, this would be useful.

Please keep me in cc when you send updated patches (as a "-v2"), since
our current issue tracker does not keep people updated.

Thanks!

Andreas

Message #14 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: tor-bjorn <at> claesson.fi
To: Andreas Enge <andreas <at> enge.fr>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Wed, 30 Apr 2025 11:02:30 +0300 (EEST)

Hi Andreas,

thank you for taking the time to look at these patches!

I am sorry that I caused a bit of a mess. This is because of inexperience on my part. Thank you for explaining the proper way to submit patches.

My intention was to submit a series of changes that allow r-cardx to be built. The first of those was updating r-posterior. When fixing r-cardx turned out to be easier than I expected, I got enthusiastic and decided to mail the whole series (which I understand was a mistake.) Sorry about this.

The failure in building r-delayedmatrixstats is unrelated to updating r-posterior. The build segfaults in testing while calling .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges").

Updating r-delayedmatricstats, r-iranges, and multiple other dependencies of r-delayedmatrixstats and r-iranges) to the latest versions available on bioconductor fixes this. I will report separate issues for those changes, and submit the patches there. Slowly :-)

After these fixes, it is possible to build the immediate dependents of r-posterior, r-rhub, r-datawizard, and r-cardx, as updated with the attached patches.

I am having some trouble getting git send-mail working, but will resend the same patches (as -v2), one per email, with my usual email client, in the hope that the QA system understands them better=)

Thanks,
Tor-björn Claesson

> På 2025-04-29 19:53 EEST skrev Andreas Enge <andreas <at> enge.fr>:
> 
>  
> Hello Tor-björn,
> (and cc to our R specialist),
> 
> thanks for your patches!
> 
> Unfortunately mixing different patches in this way confuses QA.
> Could you please follow the description in
>    https://guix.gnu.org/manual/devel/en/html_node/Submitting-Patches.html
> for future patches?
> 
> Unrelated changes (like r-posterior and r-cardx) should be sent to
> separate issues, and related changes can be grouped into one issue,
> but then they should be sent using "git send-email", which will
> create one mail per patch and send it to the same address.
> When sending a new version of a patch or a series, make sure to use the
> "-v2", "-v3", ... flags to "git send-email".
> 
> In this case, QA has only built one package, r-cardx:
>    https://qa.guix.gnu.org/issue/78105
> I suppose it has applied only the last patch, which is confirmed
> following the "View Git branch" or "View series on Patchwork" link
> on the previous page.
> 
> So apparently r-cardx is a leaf package and can be updated independently
> of all the other packages. Hm, it depends on r-posterior, which fails to
> build, so maybe this is a series after all :)  Strangely QA seems to
> have built it, but locally it fails.
> 
> Concerning r-posterior, I tried to build its immediate dependencies
> using the command
>    ./pre-inst-env guix build -P 1 r-posterior
> after applying your first patch (I would recommend to do so whenever you
> submit patches, and to mention this in your cover letter), but this
> results in a failure:
> ...
> build of /gnu/store/cbh0lsf80gkv8g1y0zlrx5j0dmrm7lzs-r-delayedmatrixstats-1.28.1.drv failed
> View build log at '/var/log/guix/drvs/cb/h0lsf80gkv8g1y0zlrx5j0dmrm7lzs-r-delayedmatrixstats-1.28.1.drv.gz'.
> cannot build derivation `/gnu/store/41ffhwrdk1x692wzgbcsv2wiqb5k5icp-r-scran-1.34.0.drv': 1 dependencies couldn't be built
> cannot build derivation `/gnu/store/3bbi85p6nd2d7n8hfm0z0fbxq7fmj9cs-r-scuttle-1.16.0.drv': 1 dependencies couldn't be built
> cannot build derivation `/gnu/store/isy948jcij3d4ri4v5ynvdbkdhv7xpib-r-basics-2.18.0.drv': 1 dependencies couldn't be built
> guix build: error: build of `/gnu/store/isy948jcij3d4ri4v5ynvdbkdhv7xpib-r-basics-2.18.0.drv' failed
> 
> So for now, I am not going to apply any of your patches; if you could
> investigate further, this would be useful.
> 
> Please keep me in cc when you send updated patches (as a "-v2"), since
> our current issue tracker does not keep people updated.
> 
> Thanks!
> 
> Andreas

Message #17 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
To: 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Wed, 30 Apr 2025 11:05:19 +0300

[v2-0001-gnu-r-posterior-update-to-1.6.1.patch (text/x-patch, attachment)]

From ee5c464b1e235f7fb4f9d2b803c05bec0ff639ff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <tor-bjorn <at> claesson.fi>
Date: Mon, 28 Apr 2025 09:38:19 +0300
Subject: [PATCH v2 1/4] gnu: r-posterior: update to 1.6.1.

* gnu/packages/cran.scm (r-posterior): Update to 1.6.1.

Change-Id: I4cd5597feaa0a0fabb3d576c1eaa70ba4ac7082f
---
 gnu/packages/cran.scm | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 194133777e..38f6a3864b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -45588,28 +45588,25 @@ (define-public r-distributional
 (define-public r-posterior
   (package
     (name "r-posterior")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "posterior" version))
        (sha256
-        (base32
-         "037l1cav2vglcd2pgp8n89apfpsb3822mhzmdsxf7a0mzcwjlq9l"))))
+        (base32 "16d7gfg8mfx89gz365a6cjc5zl0vs0wbr2gcn8n597sc7yyxf1z5"))))
     (properties `((upstream-name . "posterior")))
     (build-system r-build-system)
-    (propagated-inputs
-     (list r-abind
-           r-checkmate
-           r-distributional
-           r-matrixstats
-           r-pillar
-           r-rlang
-           r-tensora
-           r-tibble
-           r-vctrs))
-    (native-inputs
-     (list r-knitr r-testthat))
+    (propagated-inputs (list r-abind
+                             r-checkmate
+                             r-distributional
+                             r-matrixstats
+                             r-pillar
+                             r-rlang
+                             r-tensora
+                             r-tibble
+                             r-vctrs))
+    (native-inputs (list r-knitr r-testthat))
     (home-page "https://mc-stan.org/posterior/")
     (synopsis "Tools for working with posterior distributions")
     (description
-- 
2.49.0

Message #20 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
To: 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Wed, 30 Apr 2025 11:06:05 +0300

[v2-0002-gnu-r-rhub-Update-to-2.0.1.patch (text/x-patch, attachment)]

From 7280fbe0dca6af51a32578d279e9092be53fda23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <tor-bjorn <at> claesson.fi>
Date: Mon, 28 Apr 2025 10:15:39 +0300
Subject: [PATCH v2 2/4] gnu: r-rhub: Update to 2.0.1.

* gnu/packages/cran.scm (r-rhub): Update to 2.0.1.

Change-Id: Id6a5130c0bea6174c7303f78bee9d9a8ce32e07f
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 38f6a3864b..cf9b5022a9 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -38286,13 +38286,13 @@ (define-public r-rhpcblasctl
 (define-public r-rhub
   (package
     (name "r-rhub")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rhub" version))
        (sha256
-        (base32 "05q1jv7c2l09ssb72d17hhcisvzqmcd3d1njc1j6w8lhvc5kqs47"))))
+        (base32 "0fc291gy7zpx6mcpfw5sjjmx4y7lxhzh6n61mwwmz96nn4qb2m1q"))))
     (properties
      '((upstream-name . "rhub")
        (updater-extra-native-inputs . ("r-knitr"))))
-- 
2.49.0

Message #23 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
To: 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Wed, 30 Apr 2025 11:06:26 +0300

[v2-0003-gnu-r-datawizard-Update-to-1.0.2.patch (text/x-patch, attachment)]

From c9ff77c73a67504f511eaa8aabf6ec1e8fe21ebd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <tor-bjorn <at> claesson.fi>
Date: Mon, 28 Apr 2025 11:10:10 +0300
Subject: [PATCH v2 3/4] gnu: r-datawizard: Update to 1.0.2.

* gnu/packages/cran.scm (r-datawizard): Update to 1.0.2.

Change-Id: Ia0430f526dadafb4fbcd9f79a53b02f227ef0e2d
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cf9b5022a9..a9791a4278 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2229,14 +2229,14 @@ (define-public r-data-table
 (define-public r-datawizard
   (package
     (name "r-datawizard")
-    (version "1.0.0")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "datawizard" version))
        (sha256
         (base32
-         "0477ldja6n4ar3hxrlxs5qwfggdbdfcsz7i1dgv3vjsxlvdjwgyd"))))
+         "1qwb1gw7rwjcdbjb721grm8qirnijzg8sipb922l85g85kf8gwvz"))))
     (properties
      `((upstream-name . "datawizard")
        (updater-ignored-native-inputs
-- 
2.49.0

Message #26 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Tor-björn Claesson <tor-bjorn <at> claesson.fi>
To: 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Wed, 30 Apr 2025 11:06:53 +0300

[v2-0004-gnu-r-cardx-Update-to-0.2.4.patch (text/x-patch, attachment)]

From 9964c45cdf2e7b86827ac233fbd8b06760b0010a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= <tor-bjorn <at> claesson.fi>
Date: Mon, 28 Apr 2025 11:59:38 +0300
Subject: [PATCH v2 4/4] gnu: r-cardx: Update to 0.2.4.

* gnu/packages/cran.scm (r-cardx): Update to 0.2.4.

Change-Id: Ifdda20fd5346389091829c70c07568b4e0ffb48e
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a9791a4278..85773061d5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1168,13 +1168,13 @@ (define-public r-cards
 (define-public r-cardx
   (package
     (name "r-cardx")
-    (version "0.2.2")
+    (version "0.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "cardx" version))
        (sha256
-        (base32 "0jsqldsmpfgm9hvsrb833l119xsmkm8nqwdbsl7p1vhn2km0f5dv"))))
+        (base32 "1qbfa2kbxbc7lnrajj79dgz2nkjf4616ngha1yk9fl6f10qmsk24"))))
     (properties `((upstream-name . "cardx")))
     (build-system r-build-system)
     (propagated-inputs (list r-cards
-- 
2.49.0

Message #29 received at 78105 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: tor-bjorn <at> claesson.fi
Cc: Andreas Enge <andreas <at> enge.fr>, 78105 <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: r-posterior: update to 1.6.1.
Date: Wed, 30 Apr 2025 15:49:29 +0200

Hi,

> Updating r-delayedmatricstats, r-iranges, and multiple other
> dependencies of r-delayedmatrixstats and r-iranges) to the 
> latest
> versions available on bioconductor fixes this. I will report 
> separate
> issues for those changes, and submit the patches there. Slowly 
> :-)

I've got a full Bioconductor upgrade on the r-team branch, which 
I'm hoping to merge as soon as it has been fully built on 
ci.guix.gnu.org.

Perhaps in the future we can coordinate these mass upgrades. 
Thank you for the effort you've put in your patches!

-- 
Ricardo

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