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>
