[Bioc-devel] Error in Vignette of package
Sergio Picart Armada
@erg|@p|c@rt @end|ng |rom upc@edu
Mon Dec 9 23:25:51 CET 2019
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 Oleś <andrzej.oles using 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 using 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 using 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 Oleś 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 Oleś <andrzej.oles using 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 Oleś <andrzej.oles using 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 using 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 déc. 2019 à 10:47, Ioannis Vardaxis <iova89 using hotmail.com> a
>> écrit
>> >>>> :
>> >>>>>
>> >>>>> 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 using gmail.com>
>> >>>>> Sendt: søndag 1. desember 2019 11:51
>> >>>>> Til: Benjamin Jean-Marie Tremblay <b2tremblay using uwaterloo.ca>;
>> Ioannis
>> >>>> Vardaxis <iova89 using hotmail.com>
>> >>>>> Kopi: bioc-devel using r-project.org <bioc-devel using 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 using r-project.org on behalf of
>> >>>> b2tremblay using 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 à 10:25, Ioannis Vardaxis <
>> iova89 using hotmail.com>
>> >>>> a écrit :
>> >>>>> >
>> >>>>> > 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]]
>> >>>>> >
>> >>>>> > _______________________________________________
>> >>>>> > Bioc-devel using r-project.org mailing list
>> >>>>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> Bioc-devel using r-project.org mailing list
>> >>>>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=
>> >>>>
>> >>>> _______________________________________________
>> >>>> Bioc-devel using r-project.org mailing list
>> >>>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=
>> >>>>
>> >>>
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel using r-project.org mailing list
>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k&s=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54&e=
>> >
>>
>> --
>> Hervé Pagès
>>
>> 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 using fredhutch.org
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> 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/
>
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list