GNU bug report logs - #55120
“guix import cran” fails for some git repositories

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

From: Ricardo Wurmus <rekado <at> elephly.net>
To: bug-guix <at> gnu.org
Subject: “guix import cran” fails
 for some git repositories
Date: Tue, 26 Apr 2022 08:42:01 +0200

Importing an R package from Git fails:

--8<---------------cut here---------------start------------->8---
$ guix import cran -a git -r https://github.com/RubD/Giotto/
Backtrace:
In guix/ui.scm:
   1347:6 19 (guix-import-cran . _)
In ice-9/boot-9.scm:
  1752:10 18 (with-exception-handler _ _ #:unwind? _ #:unwind-for-type _)
In guix/scripts/import/cran.scm:
   108:31 17 (_)
In guix/import/utils.scm:
   507:27 16 (recursive-import _ #:repo->guix-package _ #:guix-name _ #:version _ #:repo _)
   497:33 15 (lookup-node "https://github.com/RubD/Giotto/" #f)
In guix/memoization.scm:
     98:0 14 (mproc "https://github.com/RubD/Giotto/" #:version #f #:repo git)
In unknown file:
          13 (_ #<procedure 7ff8772e9aa0 at guix/memoization.scm:179:32 ()> #<procedure list _> (this is nothing))
In guix/import/cran.scm:
   596:24 12 (_ "https://github.com/RubD/Giotto/" #:repo _ #:version _)
   296:25 11 (fetch-description _ "https://github.com/RubD/Giotto/" _)
In guix/memoization.scm:
     98:0 10 (mproc "https://github.com/RubD/Giotto/" #:method git)
In unknown file:
           9 (_ #<procedure 7ff8772e9a00 at guix/memoization.scm:179:32 ()> #<procedure list _> (this is nothing))
In ice-9/boot-9.scm:
  1752:10  8 (with-exception-handler _ _ #:unwind? _ #:unwind-for-type _)
In guix/store.scm:
   658:37  7 (thunk)
In guix/git.scm:
    550:8  6 (latest-repository-commit #<store-connection 256.99 7ff87cea8230> "https://github.com/RubD/Giotto/" #:recursive? _ #:log-port _ # …)
    279:4  5 (update-cached-checkout _ #:ref _ #:recursive? _ #:check-out? _ #:starting-commit _ #:log-port _ #:cache-directory _)
   232:18  4 (resolve _)
In git/reference.scm:
     60:8  3 (_ _ _)
In git/bindings.scm:
     77:2  2 (raise-git-error _)
In ice-9/boot-9.scm:
  1685:16  1 (raise-exception _ #:continuable? _)
  1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
Git error: reference 'refs/remotes/origin/HEAD' not found
--8<---------------cut here---------------end--------------->8---

-- 
Ricardo

Message #8 received at 55120 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 55120 <at> debbugs.gnu.org
Subject: Re: bug#55120: “guix import cran” fails for some git repositories
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

Message #13 received at 55120-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 55120-done <at> debbugs.gnu.org
Subject: “guix import cran” fails
 for some git repositories
Date: Wed, 28 Dec 2022 19:22:36 +0100

This has been fixed in the meantime.  If you still have this problem you
may need to remove your git checkout cache in ~/.cache/guix/checkouts.

-- 
Ricardo

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