[Bioc-devel] Build fail due to "undefined color `fgcolor`"

[Xiangyu Luo]

Dear Mike,

Build error messages for my packages still exist after a few days. I am
wondering how long the error will last. Thank you so much for your great
help!

Many thanks!

Xiangyu

On Sat, Jun 15, 2024 at 10:35 PM Xiangyu Luo <xyluo1991 using gmail.com> wrote:

> Dear Mike,
>
> Build error messages for my packages still exist after a few days. I am
> wondering how long the error will last. Thank you so much for your great
> help!
>
> Many thanks!
>
> Xiangyu
>
> On Tue, Jun 11, 2024 at 3:28 PM Mike Smith <grimbough using gmail.com> wrote:
>
>> This looks to be an issue introduced by changes in knitr 1.47.0, which
>> lead
>> to an incompatibility in the BiocStyle Rnw template.  We're working on a
>> patch to BiocStyle, which should be deployed on the build machines today,
>> and will hopefully fix the issue in the affected packages. The is nothing
>> package authors need to do at this time.
>>
>> I'll report back here on the status after the update has been rolled out.
>>
>> Best wishes,
>> Mike
>>
>> On Tue, 11 Jun 2024 at 04:09, Xiangyu Luo <xyluo1991 using gmail.com> wrote:
>>
>> > I also received the same error email for my packages BUScorrect and
>> > HIREewas. I don't know how to fix these "undefined color" issues.
>> >
>> > Thank you very much for all your help and replies!
>> >
>> > Best regards,
>> >
>> > Xiangyu
>> >
>> > On Sun, Jun 9, 2024 at 11:05 PM Martin Morgan <mtmorgan.xyz using gmail.com>
>> > wrote:
>> >
>> > > This seems to me like a change in the xcolor package, but I'm not
>> sure. I
>> > > opened an issue on the BiocStyle package at
>> > > https://github.com/Bioconductor/BiocStyle/issues/109.
>> > >
>> > > Martin
>> > >
>> > > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
>> Alvaro
>> > > Cuadros <acuadros+bioc-devel using gmail.com>
>> > > Date: Sunday, June 9, 2024 at 5:00 AM
>> > > To: bioc-devel using r-project.org <bioc-devel using r-project.org>
>> > > Subject: Re: [Bioc-devel] Build fail due to "undefined color
>> `fgcolor`"
>> > > On Fri, Jun 7, 2024 at 10:23 PM Christian Mertes <mertes using in.tum.de>
>> > wrote:
>> > > >
>> > > > Dear Bioc Team,
>> > > >
>> > > > I got today a build error from OUTRIDER and FRASER with:
>> > > >
>> > > > LaTeX errors:
>> > > > ! Package xcolor Error: Undefined color `fgcolor'.
>> > > >
>> > > > The same errror also pops up at other packages such as ggbio:
>> > > >
>> > > > output file: ggbio.tex
>> > > > ! Package xcolor Error: Undefined color `fgcolor'.
>> > >
>> > > I have the same error. I suppose there's an issue with BiocStyle.
>> > > After some debugging I found out that adding
>> > >
>> > > \definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
>> > > \newcommand{\hlsng}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
>> > > \newcommand{\hldef}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
>> > >
>> > > right after the `BiocStyle::latex()` chunk fixes the issue.
>> > >
>> > > _______________________________________________
>> > > Bioc-devel using r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
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>> > >
>> >
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