We don't want biovizBase to depend on ggplot2, but I fixed this by creating
the object directly. Not very clean, but the real fix is probably to move
the aes stuff back up into ggbio, and I don't have time for that right now.
Thanks,
Michael
On Wed, Nov 23, 2016 at 8:53 AM, Leonardo Collado Torres <lcoll...@jhu.edu>
wrote:
> 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
>
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