############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data 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 ‘/home/biocbuild/tmp/RtmpwwG00V/hgu95av2probe.Rcheck/00check.log’ for details. Warning in if (!is.character(x)) x <- structure(as.character(x), names = names(x)) : closing unused connection 4 (/home/biocbuild/tmp/Rtmp2OEObX/Rinst37c0b31d29e4d8/AnnotationForge/extdata/HG-U95Av2_probe_tab.gz) --- finished re-building ‘makeProbePackage.Rmd’ --- re-building ‘MakingNewAnnotationPackages.Rnw’ using knitr Quitting from MakingNewAnnotationPackages.Rnw:53-57 [Homo.sapiens] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! package 'GenomicFeatures' could not be loaded --- Backtrace: x 1. \-base::library(Homo.sapiens) 2. \-base::.getRequiredPackages2(...) 3. \-base::library(...) 4. \-base::.getRequiredPackages2(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'MakingNewAnnotationPackages.Rnw' failed with diagnostics: package 'GenomicFeatures' could not be loaded --- 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 --- finished re-building ‘SQLForge.Rnw’ SUMMARY: processing the following file failed: ‘MakingNewAnnotationPackages.Rnw’ Error: Vignette re-building failed. Execution halted