[Bioc-devel] Error in Vignette of package
Hi all,? I've also followed this thread as the FELLA package has problems with the vignette as well.? I have two issues (link) First:Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-12-1.png"' execution failed with error code 4 Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "quickstart_files/figure-html/unnamed-chunk-13-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-13-1.png"' execution failed with error code 4 Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "quickstart_files/figure-html/unnamed-chunk-14-1.png" -trim "quickstart_files/figure-html/unnamed-chunk-14-1.png"' execution failed with error code 4 --- finished re-building 'quickstart.Rmd' (but I believe this one does not prevent the vignette from building) And the second: Error: processing vignette 'zebrafish.Rmd' failed with diagnostics: argument is of length zeroThis is the same one reported by Simina, in tokay2 too. I hope the new adjustement fixes at least the second one. Thank you Andrzej, Sergi ??????
On Monday, December 09, 2019 11:37 CET, Andrzej Ole? <andrzej.oles at gmail.com> wrote:
?Hi Simina, thank you for reporting the remaining problem on Windows builders. I have just made an adjustment to BiocStyle which should resolve the issue. Cheers, Andrzej
On Sun, Dec 8, 2019 at 4:18 PM Simina Boca <smb310 at georgetown.edu> wrote:
Hi all, I've been following this conversation as I was having the same issue for the swfdr package. Happy to see that it's now fixed on malbec and merida, though I now see a different error on tokay, also referring to the vignettes. I looked around a bit, and a bunch of other packages now have the tokay error, which is: * creating vignettes ... ERROR --- re-building 'swfdrQ.Rmd' using rmarkdown Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics: argument is of length zero --- failed re-building 'swfdrQ.Rmd' https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html Thanks! Cheers, Simina On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <hpages at fredhutch.org> wrote:
Great news Andrzej! We'll keep a close eye on the build reports in the next few days. Fingers crossed. Thanks! H. On 12/6/19 03:46, Andrzej Ole? wrote:
Dear Package Developers, An updated version of BiocStyle has been deployed to both the
development
and the release branch. The fix addresses vignette build errors
occurring
with rmarkdown v1.18, these should clear up within the next build cycle. Cheers, Andrzej On Wed, Dec 4, 2019 at 2:31 PM Andrzej Ole? <andrzej.oles at gmail.com>
wrote:
Dear Package Developers, BiocStyle will be patched within the next couple of days to address the observed errors. Until then please refrain from making any changes to
your
package, the issue should resolve itself once BiocStyle is updated. Cheers, Andrzej On Mon, Dec 2, 2019 at 11:20 AM Andrzej Ole? <andrzej.oles at gmail.com> wrote:
Hi, the error seems to be related to some recent changes in the upstream package rmarkdown v1.18. I will give you an update once I know more
details.
Cheers, Andrzej On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay < b2tremblay at uwaterloo.ca> wrote:
Not using BiocStyle::pdf_document means you can?t use the
helpers/macros.
Try this in a fresh interactive session:
library(BiocStyle)
rmarkdown::render("yourvignette.Rmd")
This should make the helpers/macros available. It won?t fix the issue
for passing R CMD check, but at least it?ll confirm what the issue
is and
thus you?ll know to wait for BiocStyle to update. BT
Le 1 d?c. 2019 ? 10:47, Ioannis Vardaxis <iova89 at hotmail.com> a
?crit
:
Thanks for the answer. However replacing it resulted in another
error
for me:
Quitting from lines 2-41 (MACPET.Rmd) Error in doc_date() : could not find function "doc_date" Calls: <Anonymous> ... inline_exec -> hook_eval -> withVisible ->
eval
-> eval
Execution halted Should I wait until BiocStyle is updated? Best, Ioannis Fra: Martin Morgan <mtmorgan.bioc at gmail.com> Sendt: s?ndag 1. desember 2019 11:51 Til: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>;
Ioannis
Vardaxis <iova89 at hotmail.com>
Kopi: bioc-devel at r-project.org <bioc-devel at r-project.org> Emne: Re: [Bioc-devel] Error in Vignette of package Thanks for that insight, we'll try to solve the issue with
BiocStyle.
Martin ?On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie
Tremblay" <bioc-devel-bounces at r-project.org on behalf of b2tremblay at uwaterloo.ca> wrote:
I?ve been getting the exact same error for compiling the
Rmarkdown
vignettes in my own package. Some partial testing before the
weekend
revealed that in my case the error could be circumvented
simply by
not
using output: BiocStyle::pdf_document but instead output: pdf_document in the yaml header. I?m not quite sure why, but when BiocStyle
is
used
some of the latex code for code highlighting is repeated,
leading
to the
'already defined' error. I?ve not updated my package since
before
this
error started. BT
Le 30 nov. 2019 ? 10:25, Ioannis Vardaxis <
iova89 at hotmail.com>
a ?crit :
Hey, I am trying to build my package Vegnette and I get the
following
error:
! LaTeX Error: Command \VerbBar already defined. Or name \end... illegal, see p.192 of the
manual.
I tried to find what this means with no luck. Best, Ioannis [[alternative HTML version deleted]]
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-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
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-- Simina M. Boca Assistant Professor Innovation Center for Biomedical Informatics (ICBI) Departments of Oncology and Biostatistics, Bioinformatics and Biomathematics | Georgetown University Medical Center Cancer Prevention and Control Program | Lombardi Comprehensive Cancer Center 2115 Wisconsin Ave NW, Suite 110, Washington, DC 20007 Phone: (202) 687-1545, Fax: (202) 687-5011 http://icbi.georgetown.edu/boca https://sites.google.com/georgetown.edu/siminaboca/
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