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Tue, 27 Oct 2020 13:36:17 -0700 (PDT) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id 71sm3573320wrm.20.2020.10.27.13.36.11 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 27 Oct 2020 13:36:16 -0700 (PDT) From: zimoun Date: Tue, 27 Oct 2020 21:36:11 +0100 Message-ID: <86v9ev2ypw.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=2a00:1450:4864:20::32b; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32b.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.4 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -2.3 (--) X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=IvIpf8wo; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Spam-Score: 0.09 X-TUID: wvoD5HQIhK9b Dear, Let=E2=80=99s 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... =E2=80=A68.8.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... =E2=80=A68.8.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-resolu= tion 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 =E2=80=9C./pre-inst-env guix build r-diffcyt=E2=80=9D where the relevant pa= rts 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 =E2=80=98diffcyt=E2=80=99 ... ** 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 pa= th * DONE (diffcyt) [...] starting phase `check' Testing examples for package =E2=80=98diffcyt=E2=80=99 Running specific tests for package =E2=80=98diffcyt=E2=80=99 Running =E2=80=98testthat.R=E2=80=99 Running vignettes for package =E2=80=98diffcyt=E2=80=99 Running =E2=80=98diffcyt_workflow.Rmd=E2=80=99 *** 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 =3D TRUE, encoding =3D enc) : The vignette engine knitr::rmarkdown is not available because the rmarkdo= wn package is not available. Did you forget to add it to Suggests in DESCRI= PTION? Please see https://github.com/yihui/knitr/issues/1864 for more infor= mation. 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 =E2=80=99knitr=E2=80=99 [= 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 =3D FALSE)") --8<---------------cut here---------------end--------------->8--- and even tried =E2=80=9Cafter =E2=80=99unpack=E2=80=9D phase; idem. Well, the error is about a missing file, however: tar -xvf $(./pre-inst-env guix build r-diffcyt -S) and tree returns: =E2=94=9C=E2=94=80=E2=94=80 inst =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 doc =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2= =94=80 diffcyt_workflow.html =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2= =94=80 diffcyt_workflow.R =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2= =94=80 diffcyt_workflow.Rmd =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 NEWS [...] =E2=94=94=E2=94=80=E2=94=80 vignettes =E2=94=9C=E2=94=80=E2=94=80 diffcyt.png =E2=94=94=E2=94=80=E2=94=80 diffcyt_workflow.Rmd and =E2=80=9Cinst/doc/diff_workflow.html=E2=80=9C is correct, i.e., display= ing 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 =E2=80=9Cinst/doc/diff_workflow.html=E2=80=9D is gen= erated? 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: 2: