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 <xyluo1...@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 <grimbo...@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 <xyluo1...@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....@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-boun...@r-project.org> on behalf of >> Alvaro >> > > Cuadros <acuadros+bioc-de...@gmail.com> >> > > Date: Sunday, June 9, 2024 at 5:00 AM >> > > To: bioc-devel@r-project.org <bioc-devel@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 <mer...@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@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 >> > > >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
