Dear Pablo, Sometimes when building a vignette the lines reported are a bit off (I usually check the code above and below those lines). I could reproduce the error on R 4.0.1, the error is triggered on lines 515-519 on the following code:
relationship_plot(qtl_file=out.qtls.filtered, x="Abbrev", y="Ref_ID", cex=1,gap=2.5,degree = 60, canvas.xlim = c(-5, 5), canvas.ylim = c(-3, 3), grid.col = color.grid) Hope you can solve it. Cheers, Lluís On Thu, 5 Nov 2020 at 22:00, Pablo Fonseca <pfons...@uoguelph.ca> wrote: > > Dear Lluís Revilla, > > Thank you very much for the comments and suggestions. I changed the vignette > format from the BiocStyle to a regular html. However, I am still getting an > error. Now, the error is "Input vector too short" and it is related with the > same code chunk lines 465-506. > > I can't figure out a possible reason for this issue. Any comment or > suggestion will be very welcome. > > Kind regards. > > > Pablo Augusto de Souza Fonseca, Ph.D. > Postdoctoral Fellow at University of Guelph > Centre for Genetic Improvement of Livestock > E pfons...@uoguelph.ca > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca > ________________________________ > From: Lluís Revilla <lluis.revi...@gmail.com> > Sent: Thursday, November 5, 2020 11:38 AM > To: Pablo Fonseca <pfons...@uoguelph.ca> > Cc: Duncan Murdoch <murdoch.dun...@gmail.com>; r-package-devel@r-project.org > <r-package-devel@r-project.org> > Subject: Re: [R-pkg-devel] Error during automatic check for vignette > re-building - The magick package is required to crop > > CAUTION: This email originated from outside of the University of Guelph. Do > not click links or open attachments unless you recognize the sender and know > the content is safe. If in doubt, forward suspicious emails to > ith...@uoguelph.ca > > > Hi Pablo, > > "The magick package is required to crop" is related to using > BiocStyle for your vignette. Not sure what causes it, but I reported > this error some time ago: > https://github.com/Bioconductor/BiocStyle/issues/77. > On related issues and on bioc-devel mailing list > (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html) it > is mentioned to use knitr::opts_chunk$set(crop = NULL) to solve it. > If the package is intended for CRAN I would recommend not using > BiocStyle template, which would also solve this. > > Best, > > Lluís > > On Thu, 5 Nov 2020 at 17:28, Pablo Fonseca <pfons...@uoguelph.ca> wrote: > > > > Dear Duncan Murdoch, > > > > Thank you for the quickly reply. Yes, the package is on Github. Any comment > > or suggestion will be very welcome. > > > > https://github.com/pablobio/GALLO > > > > Kind regards. > > > > Pablo Augusto de Souza Fonseca, Ph.D. > > Postdoctoral Fellow at University of Guelph > > Centre for Genetic Improvement of Livestock > > E pfons...@uoguelph.ca <mailto:pfons...@uoguelph.ca> > > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca > > <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca> > > ________________________________ > > From: Duncan Murdoch <murdoch.dun...@gmail.com> > > Sent: Thursday, November 5, 2020 11:22 AM > > To: Pablo Fonseca <pfons...@uoguelph.ca>; r-package-devel@r-project.org > > <r-package-devel@r-project.org> > > Subject: Re: [R-pkg-devel] Error during automatic check for vignette > > re-building - The magick package is required to crop > > > > CAUTION: This email originated from outside of the University of Guelph. Do > > not click links or open attachments unless you recognize the sender and > > know the content is safe. If in doubt, forward suspicious emails to > > ith...@uoguelph.ca > > > > > > On 05/11/2020 10:55 a.m., Pablo Fonseca wrote: > > > Dear all, > > > > > > Currently I am trying to update my package (GALLO) with some small edits > > > in the code. However, the package is not passing in the automatic check. > > > I am getting only two warnings: > > > > > > The first one is a warning related with the maintainer email (my email in > > > the case), which is correct. I really think that this is not the cause of > > > the package failure during the automatic checking. > > > > The first one is actually about your version number: you called it > > version 1.0, but CRAN already has 1.0. You need to increase the number. > > > > > > > > > > The second warning is a problem during the vignette rebuilding. The > > > warning is "The magick package is required to crop". In my first > > > submission I didn't experience this error. In the recent submissions for > > > updates, I included the magick package as a dependency of the package. > > > However, this didn't fixed the issue. Additionally, I can't reproduce the > > > errors in my machines, even when running R CMD check --as-cran. The error > > > seems to be related with the lines 465-495 from the vignette. I double > > > checked the code and introduced some small changes (such as reducing the > > > figure dimensions). > > > > I am not sure about this one; I'd need to look at the package to check. > > Is it on Github? > > > > Duncan Murdoch > > > > > > > > Have ever someone faced a similar issue? However, it seems ineffective. > > > Is there any possibility to be a false negative? > > > > > > I am sending bellow the links for the check logs. > > > > > > package GALLO_1.0.tar.gz does not pass the incoming checks automatically, > > > please see the following pre-tests: > > > Windows: > > > <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_20201105_154946/Windows/00check.log> > > > Status: 2 WARNINGs > > > Debian: > > > <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_20201105_154946/Debian/00check.log> > > > Status: 2 WARNINGs > > > > > > Last released version's CRAN status: ERROR: 1, WARN: 11 > > > See: <https://CRAN.R-project.org/web/checks/check_results_GALLO.html> > > > > > > > > > Kind regards. > > > > > > > > > Pablo Augusto de Souza Fonseca, Ph.D. > > > Postdoctoral Fellow at University of Guelph > > > Centre for Genetic Improvement of Livestock > > > E pfons...@uoguelph.ca <mailto:pfons...@uoguelph.ca> > > > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca > > > <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca> > > > > > > [[alternative HTML version deleted]] > > > > > > ______________________________________________ > > > R-package-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
