GNU bug report logs - #77442
[PATCH 0/2] Remove a deprecated R package and a depending package

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

From: Andreas Enge <andreas <at> enge.fr>
To: guix-patches <at> gnu.org
Cc: Andreas Enge <andreas <at> enge.fr>
Subject: [PATCH 0/2] Remove a deprecated R package and a depending package
Date: Wed,  2 Apr 2025 00:48:42 +0200

Rationale in the two following packages.
I suggest to remove them on or after May 2nd.

Andreas Enge (2):
  gnu: Remove r-velocyto.
  gnu: Remove r-h5.

 gnu/packages/bioinformatics.scm | 44 ---------------------------------
 gnu/packages/cran.scm           | 29 ----------------------
 2 files changed, 73 deletions(-)


base-commit: 486caf5751543d760d94accd7ddc1789512438b0
-- 
2.49.0

Message #8 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77442 <at> debbugs.gnu.org
Cc: Andreas Enge <andreas <at> enge.fr>
Subject: [PATCH 1/2] gnu: Remove r-velocyto.
Date: Wed,  2 Apr 2025 00:51:39 +0200

The package has not been updated since 2019 and depends on the
deprecated r-h5.

* gnu/packages/bioinformatics.scm (r-velocyto): Delete variable.

Change-Id: I9783c67c92b5351647b964364c281a0d40319949
---
 gnu/packages/bioinformatics.scm | 44 ---------------------------------
 1 file changed, 44 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8fd7789028..226594d8ed 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22632,50 +22632,6 @@ (define-public r-imagearray
       (description "@code{DelayedArray} based image operations.")
       (license license:expat))))
 
-(define-public r-velocyto
-  (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
-        (revision "1"))
-    (package
-      (name "r-velocyto")
-      (version (git-version "0.6" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/velocyto-team/velocyto.R")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n"))))
-      (build-system r-build-system)
-      (inputs
-       (list boost))
-      (propagated-inputs
-       (list r-hdf5r
-             r-mass
-             r-mgcv
-             r-pcamethods
-             r-rcpp
-             r-rcpparmadillo
-             ;; Suggested packages
-             r-rtsne
-             r-cluster
-             r-abind
-             r-h5
-             r-biocgenerics
-             r-genomicalignments
-             r-rsamtools
-             r-edger
-             r-igraph))
-      (home-page "https://velocyto.org")
-      (synopsis "RNA velocity estimation in R")
-      (description
-       "This package provides basic routines for estimation of gene-specific
-transcriptional derivatives and visualization of the resulting velocity
-patterns.")
-      (license license:gpl3))))
-
 (define-public r-voltron
   (let ((commit "21886d82292dc46521da2a03d978d78f3bd7210b")
         (revision "5"))
-- 
2.49.0

Message #11 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: 77442 <at> debbugs.gnu.org
Cc: Andreas Enge <andreas <at> enge.fr>
Subject: [PATCH 2/2] gnu: Remove r-h5.
Date: Wed,  2 Apr 2025 00:51:40 +0200

The package has been deprecated by its author in 2017 in favor of r-hdf5r.
It does not build with current hdf5 <at> 1.14.

* gnu/packages/cran.scm (r-h5): Delete variable.

Change-Id: Iaceb59b31af870a1aea1630d74bb5c03932808b0
---
 gnu/packages/cran.scm | 29 -----------------------------
 1 file changed, 29 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4e96d70849..8d80bc2091 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14921,35 +14921,6 @@ (define-public r-heatmaply
     ;; Either version of the license.
     (license (list license:gpl2 license:gpl3))))
 
-(define-public r-h5
-  (package
-    (name "r-h5")
-    (version "0.9.9")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "h5" version))
-       (sha256
-        (base32
-         "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
-    (build-system r-build-system)
-    (inputs
-     (list zlib hdf5-1.10))
-    (native-inputs
-     (list r-knitr r-testthat which))
-    (propagated-inputs
-     (list r-rcpp))
-    (home-page "https://github.com/mannau/h5")
-    (synopsis "Interface to the HDF5 Library")
-    (description
-     "This package provides an S4 interface to the HDF5 library supporting
-fast storage and retrieval of R-objects like vectors, matrices and arrays to
-binary files in a language independent format.  The HDF5 format can therefore
-be used as an alternative to R's save/load mechanism.  Since h5 is able to
-access only subsets of stored data it can also handle data sets which do not
-fit into memory.")
-    (license license:bsd-2)))
-
 (define-public r-cgdsr
   (package
     (name "r-cgdsr")
-- 
2.49.0

Message #14 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Andreas Enge <andreas <at> enge.fr>, 77442 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado <at> elephly.net>, Andreas Enge <andreas <at> enge.fr>,
 Laurent Gatto <laurent.gatto <at> gmail.com>
Subject: Re: [bug#77442] [PATCH 2/2] gnu: Remove r-h5.
Date: Wed, 16 Apr 2025 18:31:19 +0200

Hi Andreas,

On Wed, 02 Apr 2025 at 00:51, Andreas Enge <andreas <at> enge.fr> wrote:

> The package has been deprecated by its author in 2017 in favor of r-hdf5r.
> It does not build with current hdf5 <at> 1.14.

[...]

> -    (inputs
> -     (list zlib hdf5-1.10))

Well, I have nothing against the removal of this package.  But please
note that we still have hdf5-1.8 and will keep hdf5-1.10 for some time.
Somehow, r-h5 does not need to upgrade its hdf5 input.

Somehow, I would be in favor to delay this removal.

Cheers,
simon

Message #17 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Andreas Enge <andreas <at> enge.fr>, 77442 <at> debbugs.gnu.org
Cc: Andreas Enge <andreas <at> enge.fr>
Subject: Re: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto.
Date: Wed, 16 Apr 2025 18:32:37 +0200

Hi Andreas,

On Wed, 02 Apr 2025 at 00:51, Andreas Enge <andreas <at> enge.fr> wrote:
> The package has not been updated since 2019 and depends on the
> deprecated r-h5.

This package builds with r-hdf5r, based on my small test.  Therefore, I
would be in favor to replace r-h5 by r-hdf5r.  WDYT?

Cheers,
simon

Message #20 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Simon Tournier <zimon.toutoune <at> gmail.com>
Cc: 77442 <at> debbugs.gnu.org
Subject: Re: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto.
Date: Wed, 16 Apr 2025 18:55:54 +0200

Am Wed, Apr 16, 2025 at 06:32:37PM +0200 schrieb Simon Tournier:
> This package builds with r-hdf5r, based on my small test.  Therefore, I
> would be in favor to replace r-h5 by r-hdf5r.  WDYT?

Sounds good!

Andreas

Message #23 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Simon Tournier <zimon.toutoune <at> gmail.com>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 77442 <at> debbugs.gnu.org,
 Laurent Gatto <laurent.gatto <at> gmail.com>
Subject: Re: [bug#77442] [PATCH 2/2] gnu: Remove r-h5.
Date: Wed, 16 Apr 2025 19:01:02 +0200

Am Wed, Apr 16, 2025 at 06:31:19PM +0200 schrieb Simon Tournier:
> > -    (inputs
> > -     (list zlib hdf5-1.10))
> Well, I have nothing against the removal of this package.  But please
> note that we still have hdf5-1.8 and will keep hdf5-1.10 for some time.
> Somehow, r-h5 does not need to upgrade its hdf5 input.
> Somehow, I would be in favor to delay this removal.

Well, we would like to get rid of hfd5-1.10, which is EOL and superseded
by 1.14 upstream. (This may not be possible immediately if some other
useful package depends on it, but we should not artificially delay the
transition.) This package itself has been deprecated upstream for more
than 7 years, with a suggested replacement, so I see no point in keeping it.
I think we have a tendency to accumulate cruft in Guix and am trying to get
rid of it...

Andreas

Message #26 received at 77442 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Andreas Enge <andreas <at> enge.fr>
Cc: Ricardo Wurmus <rekado <at> elephly.net>, 77442 <at> debbugs.gnu.org,
 Laurent Gatto <laurent.gatto <at> gmail.com>
Subject: Re: [bug#77442] [PATCH 2/2] gnu: Remove r-h5.
Date: Thu, 17 Apr 2025 12:40:15 +0200

Hi Andreas,

On Wed, 16 Apr 2025 at 19:01, Andreas Enge <andreas <at> enge.fr> wrote:

>                                   we should not artificially delay the
> transition.) This package itself has been deprecated upstream for more
> than 7 years, with a suggested replacement, so I see no point in keeping it.

OK, I agree.  Let remove r-h5 and replace r-h5 by r-hdf5r in r-velocyto.

Thanks for all this janitor work.

Cheers,
simon

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