Package: guix;
Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Tue, 27 Oct 2020 20:37:02 UTC
Severity: normal
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bug-guix <at> gnu.org:bug#44264; Package guix.
(Tue, 27 Oct 2020 20:37:02 GMT) Full text and rfc822 format available.zimoun <zimon.toutoune <at> gmail.com>:bug-guix <at> gnu.org.
(Tue, 27 Oct 2020 20:37:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: bug-guix <at> gnu.org Subject: Doc and vignettes bundled from Bioconductor Date: Tue, 27 Oct 2020 21:36:11 +0100
Dear,
Let’s take the example:
--8<---------------cut here---------------start------------->8---
$ 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)))
--8<---------------cut here---------------end--------------->8---
Well, added to gnu/packages/bioconductor.scm. Then the usual
“./pre-inst-env guix build r-diffcyt” where the relevant parts are:
--8<---------------cut here---------------start------------->8---
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
[..]
--8<---------------cut here---------------end--------------->8---
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:
--8<---------------cut here---------------start------------->8---
(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)")
--8<---------------cut here---------------end--------------->8---
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:
--8<---------------cut here---------------start------------->8---
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
--8<---------------cut here---------------end--------------->8---
But it is not the case when cloning from upstream:
git clone https://git.bioconductor.org/packages/diffcyt
Do I miss something?
All the best,
simon
1: <https://github.com/yihui/knitr/blob/master/NEWS.md#changes-in-knitr-version-128>
2: <https://github.com/yihui/knitr/blob/master/NEWS.md#changes-in-knitr-version-129>
bug-guix <at> gnu.org:bug#44264; Package guix.
(Tue, 27 Oct 2020 23:19:02 GMT) Full text and rfc822 format available.Message #8 received at submit <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: bug-guix <at> gnu.org Subject: Re: Doc and vignettes bundled from Bioconductor Date: Wed, 28 Oct 2020 00:18:48 +0100
On Tue, 27 Oct 2020 at 21:36, zimoun <zimon.toutoune <at> gmail.com> wrote:
On part of the story,
> --8<---------------cut here---------------start------------->8---
> (define-public r-diffcyt
> (package
> (name "r-diffcyt")
[...]
> (native-inputs
`(("r-knitr" ,r-knitr)
("r-rmarkdown" ,r-rmarkdown)
("pandoc" ,pandoc)
("pandoc" ,pandoc-citeproc)
("r-biocstyle" ,r-biocstyle)))
[...]
> (license expat)))
> --8<---------------cut here---------------end--------------->8---
leads to:
--8<---------------cut here---------------start------------->8---
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"
--8<---------------cut here---------------end--------------->8---
and I have no clue what I am missing.
The other part of the story is:
--8<---------------cut here---------------start------------->8---
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'delete
(lambda _
(delete-file-recursively "inst")
#t)))))
--8<---------------cut here---------------end--------------->8---
leads to:
--8<---------------cut here---------------start------------->8---
starting phase `install'
* installing *source* package ‘diffcyt’ ...
** using staged installation
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file '/gnu/store/nqymkk1g0zsmf2wwrq5zd6rh7sdhvpjm-r-diffcyt-1.8.8/site-library/00LOCK-diffcyt/00new/diffcyt/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing ‘/gnu/store/nqymkk1g0zsmf2wwrq5zd6rh7sdhvpjm-r-diffcyt-1.8.8/site-library/diffcyt’
command "R" "CMD" "INSTALL" "--install-tests" "--library=/gnu/store/nqymkk1g0zsmf2wwrq5zd6rh7sdhvpjm-r-diffcyt-1.8.8/site-library/" "--built-timestamp=1970-01-01" "." failed with status 1
builder for `/gnu/store/9dwqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv' failed with exit code 1
build of /gnu/store/9dwqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv failed
View build log at '/var/log/guix/drvs/9d/wqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv.bz2'.
guix build: error: build of `/gnu/store/9dwqj8vfn2rd8amprrqw2db511c65az4-r-diffcyt-1.8.8.drv' failed
--8<---------------cut here---------------end--------------->8---
and the addition of ’(mkdir-p "inst/doc")’ makes the build pass, but:
file:///gnu/store/…-r-diffcyt-1.8.8/site-library/diffcyt/doc/index.html
shows one HTML link pointing to:
file:///gnu/store/…-r-diffcyt-1.8.8/library/diffcyt/doc/diffcyt_workflow.html
which does not exist.
Another random example is ’r-ebimage’,
--8<---------------cut here---------------start------------->8---
$ tar xvf $(guix build r-ebimage -S) | grep "inst/doc"
EBImage/inst/doc/
EBImage/inst/doc/EBImage-introduction.R
EBImage/inst/doc/EBImage-introduction.Rmd
EBImage/inst/doc/EBImage-introduction.html
$ md5sum EBImage/inst/doc/EBImage-introduction.html $(guix build r-ebimage)/site-library/EBImage/doc/EBImage-introduction.html
4dabd489660ff7909e4787cb23fe89d7 EBImage/inst/doc/EBImage-introduction.html
4dabd489660ff7909e4787cb23fe89d7 /gnu/store/9lmzhb0palxsm8ynacy2nnh5w8gvbn6j-r-ebimage-4.30.0/site-library/EBImage/doc/EBImage-introduction.html
--8<---------------cut here---------------end--------------->8---
Well bit-to-bit identical HTML as upstream… strong evidence that the
documentation is not locally generated. And the upstream-upstream
https://github.com/aoles/EBImage/tree/master/inst
does not contains this HTML, AFAICT.
BTW, going via the Source Repository
git clone https://git.bioconductor.org/packages/EBImage
i.e., ’git-fetch’ instead of ’url-fetch’ seems the right direction to
fix. Because:
1. it is the “real” source and this source is easily verifiable; for
example it is easy to check the commit hash of the Bioconductor repo
against the one of the upstream GitHub repo.
2. the fallback to SWH works for git-fetch. The tarball is not ready
yet; and who knows when… :-)
All the best,
simon
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