Subject: bug#55120: “guix import cran” fails for some git repositories

From: zimoun <[email-masked]>
Date: Tue, 26 Apr 2022 14:26:41 +0200

Hi Ricardo,

It works for me from my desktop machine behind the strong network of
the University.  And it also fails from my laptop at home.  Maybe it
comes from GitHub and our way to connect overthere.  I do not know.

--8<---------------cut here---------------start------------->8---
$  guix import cran -a git https://github.com/RubD/Giotto/ -r
Starting download of /tmp/guix-file.wKIOEz
>From http://cran.r-project.org/src/contrib/dbscan_1.1-10.tar.gz...
 …-10.tar.gz  2.2MiB                  3.6MiB/s 00:01 [##################] 100.0%

Starting download of /tmp/guix-file.zTh09D
>From https://bioconductor.org/packages/release/bioc/src/contrib/lfa_1.24.0.tar.gz...
 ….0.tar.gz  284KiB                  46.9MiB/s 00:00 [##################] 100.0%

Starting download of /tmp/guix-file.wx30kh
>From https://bioconductor.org/packages/release/bioc/src/contrib/lfa_1.24.0.tar.gz...
 ….0.tar.gz  284KiB                  55.6MiB/s 00:00 [##################] 100.0%
(define-public r-lfa
  (package
    (name "r-lfa")
    (version "1.24.0")
    (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lfa" version))
        (sha256
          (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr"))))
    (properties `((upstream-name . "lfa")))
    (build-system r-build-system)
    (propagated-inputs (list r-corpcor))
    (native-inputs (list r-knitr))
    (home-page "https://github.com/StoreyLab/lfa")
    (synopsis "Logistic Factor Analysis for Categorical Data")
    (description
      "LFA is a method for a PCA analogue on Binomial data via
estimation of latent
structure in the natural parameter.")
    (license gpl3)))

(define-public r-dbscan
  (package
    (name "r-dbscan")
    (version "1.1-10")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "dbscan" version))
        (sha256
          (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1"))))
    (properties `((upstream-name . "dbscan")))
    (build-system r-build-system)
    (propagated-inputs (list r-rcpp))
    (native-inputs (list r-knitr))
    (home-page "https://github.com/mhahsler/dbscan")
    (synopsis
      "Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms")
    (description
      "This package provides a fast reimplementation of several density-based
algorithms of the DBSCAN family.  Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and HDBSCAN
(hierarchical DBSCAN), the ordering algorithm OPTICS (ordering points to
identify the clustering structure), shared nearest neighbor clustering, and the
outlier detection algorithms LOF (local outlier factor) and GLOSH (global-local
outlier score from hierarchies).  The implementations use the kd-tree data
structure (from library ANN) for faster k-nearest neighbor search.  An R
interface to fast kNN and fixed-radius NN search is also provided.  Hahsler,
Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.")
    (license gpl2+)))

(define-public r-giotto
  (let ((commit "68d7390dce87223cac11d4d8f31705fe0144d011") (revision "1"))
    (package
      (name "r-giotto")
      (version (git-version "1.1.1" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://github.com/RubD/Giotto/")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32 "0mv60khc05wrxzr4ir6cirn7dpqvgwan5hm00lmafsyalr51nf5i"))))
      (properties `((upstream-name . "Giotto")))
      (build-system r-build-system)
      (propagated-inputs
        (list r-clusterr
              r-complexheatmap
              r-cowplot
              r-data-table
              r-dbscan
              r-deldir
              r-farver
              r-fitdistrplus
              r-ggdendro
              r-ggplot2
              r-ggraph
              r-ggrepel
              r-igraph
              r-irlba
              r-lfa
              r-limma
              r-magick
              r-magrittr
              r-matrix
              r-matrixstats
              r-plotly
              r-qvalue
              r-r-utils
              r-rcolorbrewer
              r-rcpp
              r-reshape2
              r-reticulate
              r-rfast
              r-rlang
              r-rtsne
              r-scales
              r-uwot))
      (native-inputs (list r-knitr))
      (home-page "https://github.com/RubD/Giotto/")
      (synopsis "Spatial Single-Cell Transcriptomics Toolbox")
      (description
        "Toolbox to process, analyze and visualize spatial single-cell
expression data.")
      (license #f))))
--8<---------------cut here---------------end--------------->8---

Cheers,
simon