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

5 messages · Christian Mertes, Alvaro Cuadros, Martin Morgan +2 more

Christian Mertes
# 
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 assume this is rather a build system problem then a package problem 
or? If not, we would need to dive into why this happens.

Best regards,

Christian

--
Dr. Christian Mertes
Workflow Coordinator @ GHGA
GHGA at Munich / Gagneur lab / MDSI

Computational Molecular Medicine
Technical University of Munich
Boltzmannstra?e 3
85748 Garching, Germany

Mail:mertes at in.tum.de
https://www.ghga.de
https://www.cs.cit.tum.de/cmm
https://www.mdsi.tum.de
1 day later
Alvaro Cuadros
#
On Fri, Jun 7, 2024 at 10:23?PM Christian Mertes <mertes at in.tum.de> wrote:
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.
Martin Morgan
# 
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 at r-project.org> on behalf of Alvaro Cuadros <acuadros+bioc-devel at gmail.com>
Date: Sunday, June 9, 2024 at 5:00?AM
To: bioc-devel at r-project.org <bioc-devel at 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 at in.tum.de> wrote:
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.

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https://stat.ethz.ch/mailman/listinfo/bioc-devel
1 day later
Xiangyu Luo
# 
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 at gmail.com>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Mike Smith
    

    

      
      #
    

  


  

      
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 at gmail.com> wrote: