Re: [Bioc-devel] Error in Vignette of package
Hi everyone, I've followed the conversation about the errors in rebuilding the vignettes. Thanks a lot for your effort on fixing it. I get the following error on Windows / tokay2 which has not been fixed yet: http://bioconductor.org/checkResults/devel/bioc-LATEST/hierinf/tokay2-buildsrc.html -- re-building 'vignette-hierinf.Rnw' using knitr Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", : running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "vignette-hierinf.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.11-bioc/R/share/texmf/bibtex/bst"' had status 1 Error: processing vignette 'vignette-hierinf.Rnw' failed with diagnostics: running 'texi2dvi' on 'vignette-hierinf.tex' failed LaTeX errors: ! LaTeX Error: File `.def' not found. Type X to quit or to proceed, or enter new name. (Default extension: def) I haven't changed my vignette lately and no error occurs using the win builder (https://win-builder.r-project.org/). Do you have any hints what's the problem or if I need to change our vignette? Thanks a lot for your help. Best wishes, Claude [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
> >
> > > > > On Wed, Dec 4, 2019 at 2:31 PM Andrzej Oleś <
> > > > > andrzej.o...@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.o...@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 <
> > > > > > > b2tremb...@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 <
> > > > > > > > > iov...@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: ... inline_exec -> hook_eval -> withVisible
> > > > > > > > > ->
> > > >
> > > > eval
> > > > > > > > -> eval
> > > > > > > > > Execution halted
> > > > > > > > >
> > > > > > > > > Should I wait until BiocStyle is updated?
> > > > > > > > >
> > > > > > > > > Best,
> > > > > > > > > Ioannis
> > > > > > > > >
> > > > > > > > > Fra: Martin Morgan <
> > > > > > > > > mtmorgan.b...@gmail.com
> > > > > > > > > >
> > > > > > > > > Sendt: søndag 1. desember 2019 11:51
> > > > > > > > > Til: Benjamin Jean-Marie Tremblay <
> > > > > > > > > b2tremb...@uwaterloo.ca
> > > > > > > > > >;
> > > >
> > > > Ioannis
> > > > > > > > Vardaxis <
> > > > > > > > iov...@hotmail.com
> > > > > > > > >
> > > > > > > > > Kopi:
> > >
Re: [Bioc-devel] Error in Vignette of package
All the "VerbBar" LaTeX errors have cleared up in release and devel.
Thanks again Andrzej!
Cheers,
H.
On 12/6/19 12:17, Hervé Pagès 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
>> 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
>>> 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 <
>>>> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible ->
>>>>>> eval
>>>>> -> eval
>>>>>> Execution halted
>>>>>>
>>>>>> Should I wait until BiocStyle is updated?
>>>>>>
>>>>>> Best,
>>>>>> Ioannis
>>>>>>
>>>>>> Fra: Martin Morgan
>>>>>> Sendt: søndag 1. desember 2019 11:51
>>>>>> Til: Benjamin Jean-Marie Tremblay ; Ioannis
>>>>> Vardaxis
>>>>>> Kopi: bioc-devel@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" >>>> b2tremb...@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
>>>>>
Re: [Bioc-devel] Error in Vignette of package
gt;> >>>
> >> >>> On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
> >> >>> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible ->
> >> eval
> >> >>>> -> eval
> >> >>>>> Execution halted
> >> >>>>>
> >> >>>>> Should I wait until BiocStyle is updated?
> >> >>>>>
> >> >>>>> Best,
> >> >>>>> Ioannis
> >> >>>>>
> >> >>>>> Fra: Martin Morgan
> >> >>>>> Sendt: søndag 1. desember 2019 11:51
> >> >>>>> Til: Benjamin Jean-Marie Tremblay ;
> >> Ioannis
> >> >>>> Vardaxis
> >> >>>>> Kopi: bioc-devel@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" >> >>>> b2tremb...@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 <
> >> iov...@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.
> >> >>>>
Re: [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 Oleś
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 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 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
>> 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
>> >> 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 <
>> >>> b2tremb...@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.
Re: [Bioc-devel] Error in Vignette of package
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 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 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
>> 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
>> >> 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 <
>> >>> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible ->
>> eval
>> >>>> -> eval
>> >>>>> Execution halted
>> >>>>>
>> >>>>> Should I wait until BiocStyle is updated?
>> >>>>>
>> >>>>> Best,
>> >>>>> Ioannis
>> >>>>>
>> >>>>> Fra: Martin Morgan
>> >>>>> Sendt: søndag 1. desember 2019 11:51
>> >>>>> Til: Benjamin Jean-Marie Tremblay ;
>> Ioannis
>> >>>> Vardaxis
>> >>>>> Kopi: bioc-devel@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.
>>
Re: [Bioc-devel] Error in Vignette of package
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 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
> 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
> >> 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 <
> >>> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible ->
> eval
> >>>> -> eval
> >>>>> Execution halted
> >>>>>
> >>>>> Should I wait until BiocStyle is updated?
> >>>>>
> >>>>> Best,
> >>>>> Ioannis
> >>>>>
> >>>>> Fra: Martin Morgan
> >>>>> Sendt: søndag 1. desember 2019 11:51
> >>>>> Til: Benjamin Jean-Marie Tremblay ; Ioannis
> >>>> Vardaxis
> >>>>> Kopi: bioc-devel@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" >>>> b2tremb...@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:
Re: [Bioc-devel] Error in Vignette of package
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 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
>> 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 <
>>> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible -> eval
>>>> -> eval
>>>>> Execution halted
>>>>>
>>>>> Should I wait until BiocStyle is updated?
>>>>>
>>>>> Best,
>>>>> Ioannis
>>>>>
>>>>> Fra: Martin Morgan
>>>>> Sendt: søndag 1. desember 2019 11:51
>>>>> Til: Benjamin Jean-Marie Tremblay ; Ioannis
>>>> Vardaxis
>>>>> Kopi: bioc-devel@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" >>> b2tremb...@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
>>>> 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.
>>>>> >
>>>&g
Re: [Bioc-devel] Error in Vignette of package
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 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
> 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 <
>> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible -> eval
>>> -> eval
>>> > Execution halted
>>> >
>>> > Should I wait until BiocStyle is updated?
>>> >
>>> > Best,
>>> > Ioannis
>>> >
>>> > Fra: Martin Morgan
>>> > Sendt: søndag 1. desember 2019 11:51
>>> > Til: Benjamin Jean-Marie Tremblay ; Ioannis
>>> Vardaxis
>>> > Kopi: bioc-devel@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" >> b2tremb...@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
>>> 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@r-project.org mailing list
>>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >
>>> > ___
>>> > Bioc-devel@r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
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 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 <
> b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible -> eval
>> -> eval
>> > Execution halted
>> >
>> > Should I wait until BiocStyle is updated?
>> >
>> > Best,
>> > Ioannis
>> >
>> > Fra: Martin Morgan
>> > Sendt: søndag 1. desember 2019 11:51
>> > Til: Benjamin Jean-Marie Tremblay ; Ioannis
>> Vardaxis
>> > Kopi: bioc-devel@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" > b2tremb...@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 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@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
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 <
b2tremb...@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 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: ... inline_exec -> hook_eval -> withVisible -> eval
> -> eval
> > Execution halted
> >
> > Should I wait until BiocStyle is updated?
> >
> > Best,
> > Ioannis
> >
> > Fra: Martin Morgan
> > Sendt: søndag 1. desember 2019 11:51
> > Til: Benjamin Jean-Marie Tremblay ; Ioannis
> Vardaxis
> > Kopi: bioc-devel@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" b2tremb...@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 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@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
___
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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" 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 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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
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 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: ... inline_exec -> hook_eval -> withVisible -> eval -> eval
> Execution halted
>
> Should I wait until BiocStyle is updated?
>
> Best,
> Ioannis
>
> Fra: Martin Morgan
> Sendt: søndag 1. desember 2019 11:51
> Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis
>
> Kopi: bioc-devel@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"
> 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 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@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
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: ... inline_exec -> hook_eval -> withVisible -> eval -> eval Execution halted Should I wait until BiocStyle is updated? Best, Ioannis Fra: Martin Morgan Sendt: søndag 1. desember 2019 11:51 Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis Kopi: bioc-devel@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" 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 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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
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 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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
