(address . bug-guix@gnu.org)
86v9ev2ypw.fsf@gmail.com
Dear,
Let’s take the example:
Toggle snippet (51 lines)
$ guix import cran -a bioconductor diffcyt -r
Starting download of /tmp/guix-file.qJmqja
From https://bioconductor.org/packages/release/bioc/src/contrib/diffcyt_1.8.8.tar.gz...
…8.8.tar.gz 776KiB 585KiB/s 00:01 [##################] 100.0%
Starting download of /tmp/guix-file.qAoQ59
From https://bioconductor.org/packages/release/bioc/src/contrib/diffcyt_1.8.8.tar.gz...
…8.8.tar.gz 776KiB 565KiB/s 00:01 [##################] 100.0%
(define-public r-diffcyt
(package
(name "r-diffcyt")
(version "1.8.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "diffcyt" version))
(sha256
(base32
"1kq3zisgvi6kfra2sm17d01vw3rg0nz0vz5031jp2a96j7dryp98"))))
(properties `((upstream-name . "diffcyt")))
(build-system r-build-system)
(propagated-inputs
`(("r-circlize" ,r-circlize)
("r-complexheatmap" ,r-complexheatmap)
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-flowcore" ,r-flowcore)
("r-flowsom" ,r-flowsom)
("r-limma" ,r-limma)
("r-lme4" ,r-lme4)
("r-magrittr" ,r-magrittr)
("r-multcomp" ,r-multcomp)
("r-reshape2" ,r-reshape2)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment"
,r-summarizedexperiment)
("r-tidyr" ,r-tidyr)))
(native-inputs `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/lmweber/diffcyt")
(synopsis
"Differential discovery in high-dimensional cytometry via high-resolution clustering")
(description
"Statistical methods for differential discovery analyses in
high-dimensional cytometry data (including flow cytometry, mass
cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on
a combination of high-resolution clustering and empirical Bayes
moderated tests adapted from transcriptomics.")
(license expat)))
Well, added to gnu/packages/bioconductor.scm. Then the usual
“./pre-inst-env guix build r-diffcyt” where the relevant parts are:
Toggle snippet (54 lines)
starting phase `unpack'
[...]
diffcyt/inst/NEWS
diffcyt/inst/doc/
diffcyt/inst/doc/diffcyt_workflow.R
diffcyt/inst/doc/diffcyt_workflow.Rmd
diffcyt/inst/doc/diffcyt_workflow.html
[...]
starting phase `install'
* installing *source* package ‘diffcyt’ ...
** using staged installation
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (diffcyt)
[...]
starting phase `check'
Testing examples for package ‘diffcyt’
Running specific tests for package ‘diffcyt’
Running ‘testthat.R’
Running vignettes for package ‘diffcyt’
Running ‘diffcyt_workflow.Rmd’
*** Source Errors ***
File diffcyt_workflow.R:
Cannot find the file(s): "diffcyt.png"
*** Weave Errors ***
File diffcyt_workflow.Rmd:
Cannot find the file(s): "diffcyt.png"
Warning message:
In engine$weave(path, quiet = TRUE, encoding = enc) :
The vignette engine knitr::rmarkdown is not available because the rmarkdown package is not available. Did you forget to add it to Suggests in DESCRIPTION? Please see https://github.com/yihui/knitr/issues/1864 for more information.
phase `check' succeeded after 61.9
[..]
Therefore, trying to address this error in the check phase, I am
puzzled. Initially, I thought it was a change in ’knitr’ [1,2], I
added:
Toggle snippet (10 lines)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'check 'patch-knitr-include_graphics
(lambda _
(substitute* "vignettes/diffcyt_workflow.Rmd"
(("knitr::include_graphics\\(\"diffcyt.png\"\\)")
"knitr::include_graphics(\"diffcyt.png\", error = FALSE)")
and even tried “after ’unpack” phase; idem.
Well, the error is about a missing file, however:
tar -xvf $(./pre-inst-env guix build r-diffcyt -S)
and tree returns:
├── inst
│ ├── doc
│ │ ├── diffcyt_workflow.html
│ │ ├── diffcyt_workflow.R
│ │ └── diffcyt_workflow.Rmd
│ └── NEWS
[...]
└── vignettes
├── diffcyt.png
└── diffcyt_workflow.Rmd
and “inst/doc/diff_workflow.html“ is correct, i.e., displaying the logo
(which is diffcyt.png).
The issue for this specific package is that the check is running
inst/doc/diff_workflow.Rmd instead of vignettes/diffcyt_workflow.Rmd;
which one story.
The other story is how “inst/doc/diff_workflow.html” is generated? I am
not sure it is locally generated. To be sure, let fetch the tarball
from upstream:
Toggle snippet (5 lines)
wget https://bioconductor.org/packages/release/bioc/src/contrib/diffcyt_1.8.8.tar.gz
tar xvf diffcyt_1.8.8.tar.gz
tree diffcyt
But it is not the case when cloning from upstream:
Do I miss something?
All the best,
simon