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

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