Hi, The latest build report for derfinderPlot (1.9.2) shows the following error:
Quitting from lines 188-190 (derfinderPlot.Rmd) Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics: could not find function "aes" I traced it down to biovizBase::parseArgsForAes() as shown below: ## evaluated code > library('biovizBase') > args <- alist(a = color, b = "b") > parseArgsForAes(args) Error in parseArgsForAes(args) : could not find function "aes" > traceback() 1: parseArgsForAes(args) > > library('ggplot2') > parseArgsForAes(args) * NULL -> > > library('devtools') > options(width = 120) > session_info() Session info ----------------------------------------------------------------------------------------------------------- setting value version R Under development (unstable) (2016-10-26 r71594) system x86_64, darwin13.4.0 ui AQUA language (EN) collate en_US.UTF-8 tz America/New_York date 2016-11-23 Packages --------------------------------------------------------------------------------------------------------------- package * version date source acepack 1.4.1 2016-10-29 CRAN (R 3.4.0) AnnotationDbi 1.37.0 2016-10-26 Bioconductor AnnotationHub 2.7.6 2016-11-19 Bioconductor assertthat 0.1 2013-12-06 CRAN (R 3.4.0) Biobase 2.35.0 2016-10-23 Bioconductor BiocGenerics 0.21.0 2016-10-23 Bioconductor BiocInstaller 1.25.2 2016-10-25 Bioconductor BiocParallel 1.9.2 2016-11-18 Bioconductor biomaRt 2.31.1 2016-10-23 Bioconductor Biostrings 2.43.1 2016-11-17 Bioconductor biovizBase * 1.23.1 2016-10-29 Bioconductor bitops 1.0-6 2013-08-17 CRAN (R 3.4.0) BSgenome 1.43.1 2016-11-11 Bioconductor chron 2.3-47 2015-06-24 CRAN (R 3.4.0) cluster 2.0.5 2016-10-08 CRAN (R 3.4.0) colorspace 1.3-1 2016-11-18 CRAN (R 3.4.0) data.table 1.9.6 2015-09-19 CRAN (R 3.4.0) DBI 0.5-1 2016-09-10 CRAN (R 3.4.0) devtools * 1.12.0 2016-06-24 CRAN (R 3.4.0) dichromat 2.0-0 2013-01-24 CRAN (R 3.4.0) digest 0.6.10 2016-08-02 CRAN (R 3.4.0) ensembldb 1.99.3 2016-11-15 Bioconductor foreign 0.8-67 2016-09-13 CRAN (R 3.4.0) Formula 1.2-1 2015-04-07 CRAN (R 3.4.0) GenomeInfoDb 1.11.6 2016-11-17 Bioconductor GenomicAlignments 1.11.3 2016-11-17 Bioconductor GenomicFeatures 1.27.2 2016-11-11 Bioconductor GenomicRanges 1.27.12 2016-11-17 Bioconductor ggplot2 * 2.2.0 2016-11-11 CRAN (R 3.4.0) gridExtra 2.2.1 2016-02-29 CRAN (R 3.4.0) gtable 0.2.0 2016-02-26 CRAN (R 3.4.0) Hmisc 4.0-0 2016-11-01 CRAN (R 3.4.0) htmlTable 1.7 2016-10-19 CRAN (R 3.4.0) htmltools 0.3.5 2016-03-21 CRAN (R 3.4.0) httpuv 1.3.3 2015-08-04 CRAN (R 3.4.0) httr 1.2.1 2016-07-03 CRAN (R 3.4.0) interactiveDisplayBase 1.13.0 2016-10-23 Bioconductor IRanges 2.9.8 2016-11-12 Bioconductor knitr 1.15.1 2016-11-22 CRAN (R 3.4.0) lattice 0.20-34 2016-09-06 CRAN (R 3.4.0) latticeExtra 0.6-28 2016-02-09 CRAN (R 3.4.0) lazyeval 0.2.0 2016-06-12 CRAN (R 3.4.0) magrittr 1.5 2014-11-22 CRAN (R 3.4.0) Matrix 1.2-7.1 2016-09-01 CRAN (R 3.4.0) memoise 1.0.0 2016-01-29 CRAN (R 3.4.0) mime 0.5 2016-07-07 CRAN (R 3.4.0) munsell 0.4.3 2016-02-13 CRAN (R 3.4.0) nnet 7.3-12 2016-02-02 CRAN (R 3.4.0) plyr 1.8.4 2016-06-08 CRAN (R 3.4.0) ProtGenerics 1.7.0 2016-10-23 Bioconductor R6 2.2.0 2016-10-05 CRAN (R 3.4.0) RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.0) Rcpp 0.12.8 2016-11-17 CRAN (R 3.4.0) RCurl 1.95-4.8 2016-03-01 CRAN (R 3.4.0) rpart 4.1-10 2015-06-29 CRAN (R 3.4.0) Rsamtools 1.27.2 2016-10-23 Bioconductor RSQLite 1.0.0 2014-10-25 CRAN (R 3.4.0) rtracklayer 1.35.1 2016-10-29 Bioconductor S4Vectors 0.13.2 2016-11-09 Bioconductor scales 0.4.1 2016-11-09 CRAN (R 3.4.0) shiny 0.14.2 2016-11-01 CRAN (R 3.4.0) stringi 1.1.2 2016-10-01 CRAN (R 3.4.0) stringr 1.1.0 2016-08-19 CRAN (R 3.4.0) SummarizedExperiment 1.5.3 2016-11-11 Bioconductor survival 2.40-1 2016-10-30 CRAN (R 3.4.0) tibble 1.2 2016-08-26 CRAN (R 3.4.0) VariantAnnotation 1.21.4 2016-11-19 Bioconductor withr 1.0.2 2016-06-20 CRAN (R 3.4.0) XML 3.98-1.5 2016-11-10 CRAN (R 3.4.0) xtable 1.8-2 2016-02-05 CRAN (R 3.4.0) XVector 0.15.0 2016-10-23 Bioconductor yaml 2.1.14 2016-11-12 CRAN (R 3.4.0) zlibbioc 1.21.0 2016-10-23 Bioconductor > ## clean code library('biovizBase') args <- alist(a = color, b = "b") parseArgsForAes(args) traceback() library('ggplot2') parseArgsForAes(args) library('devtools') options(width = 120) session_info() This issue is not getting picked up by the build reports for biovizBase because the parseArgsForAes() example is commented out. Anyhow, it seems like it's just a matter of importing the ggplot2::aes function in biovizBase so that https://github.com/Bioconductor-mirror/biovizBase/blob/a58520d1451d7e0648366ef1e95b2d1e0e600ab0/R/aes.R#L11 will work. Best, Leo _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel