[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
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