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

Leonardo Collado Torres lcollado at jhu.edu
Wed Nov 23 17:53:48 CET 2016


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



More information about the Bioc-devel mailing list