############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 AnnotationForge ### ############################################################################## ############################################################################## * checking for file ‘AnnotationForge/DESCRIPTION’ ... OK * preparing ‘AnnotationForge’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘makeProbePackage.Rmd’ using rmarkdown See ‘/tmp/Rtmp9Jopjs/hgu95av2probe.Rcheck/00check.log’ for details. Warning: closing unused connection 4 (/tmp/Rtmpg4h2uJ/Rinst1875ca5123c64d/AnnotationForge/extdata/HG-U95Av2_probe_tab.gz) --- finished re-building ‘makeProbePackage.Rmd’ --- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr trying URL 'http://rest.uniprot.org/uniprotkb/search?query=P13368%20OR%20Q6GZX4&format=xml' Content type 'application/xml' length 45246 bytes (44 KB) ================================================== downloaded 44 KB Error: processing vignette 'MakingNewAnnotationPackages.Rnw' failed with diagnostics: Running 'texi2dvi' on 'MakingNewAnnotationPackages.tex' failed. LaTeX errors: ! Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... ! Emergency stop. ... l.78 ...}{rgb}{0.941, 0.941, 0.941}\color{fgcolor} \begin{kframe} ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘MakingNewAnnotationPackages.Rnw’ --- re-building ‘MakingNewOrganismPackages.Rmd’ using knitr --- finished re-building ‘MakingNewOrganismPackages.Rmd’ --- re-building ‘SQLForge.Rnw’ using knitr Warning: call dbDisconnect() when finished working with a connection Error: processing vignette 'SQLForge.Rnw' failed with diagnostics: Running 'texi2dvi' on 'SQLForge.tex' failed. LaTeX errors: ! Package xcolor Error: Undefined color `fgcolor'. See the xcolor package documentation for explanation. Type H for immediate help. ... ! Emergency stop. ... l.67 ...}{rgb}{0.941, 0.941, 0.941}\color{fgcolor} \begin{kframe} ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘SQLForge.Rnw’ SUMMARY: processing the following files failed: ‘MakingNewAnnotationPackages.Rnw’ ‘SQLForge.Rnw’ Error: Vignette re-building failed. Execution halted