[Bioc-devel] Issue with biovizBase::parseArgsForAes(), likely just a namespace issue

Michael Lawrence lawrence.michael at gene.com
Thu Nov 24 16:05:52 CET 2016


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 <lcollado at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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