Forgot to add bioc-devel On Fri, Apr 3, 2015 at 4:55 PM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:
Hi, From the April newsletter I got curious about BrowserViz but I couldn't run the simple example as-is. From http://bioconductor.org/checkResults/devel/bioc-LATEST/BrowserViz/ I can see that version 0.99.26 is passing all the checks in Linux/Mac OS X but I got errors as shown below.
library(BrowserViz)
Loading required package: httpuv
Loading required package: jsonlite
Attaching package: ?jsonlite?
The following object is masked from ?package:utils?:
View
Attaching package: ?BrowserViz?
The following object is masked from ?package:jsonlite?:
toJSON
bv <- BrowserViz(4000:4024)
Error: file.exists(browserFile) is not TRUE
traceback()
3: stop(sprintf(ngettext(length(r), "%s is not TRUE", "%s are not all TRUE"),
ch), call. = FALSE, domain = NA)
2: stopifnot(file.exists(browserFile))
1: BrowserViz(4000:4024)
devtools::session_info()
Session info------------------------------------------------------------------------------------------------------------------------ setting value version R Under development (unstable) (2014-11-01 r66923) system x86_64, darwin10.8.0 ui AQUA language (EN) collate en_US.UTF-8 tz America/New_York Packages---------------------------------------------------------------------------------------------------------------------------- package * version date source BiocGenerics 0.13.11 2015-04-03 Bioconductor BrowserViz * 0.99.26 2015-04-01 Bioconductor devtools 1.6.1 2014-10-07 CRAN (R 3.2.0) httpuv * 1.3.2 2014-10-23 CRAN (R 3.2.0) jsonlite * 0.9.13 2014-10-21 CRAN (R 3.2.0) Rcpp 0.11.5 2015-03-06 CRAN (R 3.2.0) rstudioapi 0.2 2014-12-31 CRAN (R 3.2.0) I can see that BrowserViz() by default uses browserFile = NA.
args(BrowserViz)
function (portRange, host = "localhost", title = "BrowserViz",
quiet = TRUE, browserFile = NA)
NULL
The man page states: "defaults to NA, which is interpreted as an
instruction to use viz.html in the inst directory of this package".
Looking at the code I noticed that BrowserViz() starts with:
if (is.na(browserFile))
browserFile <- browserVizBrowserFile
which is not working. However with
system.file('scripts', 'viz.html', package = 'BrowserViz')
[1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BrowserViz/scripts/viz.html" I can get it to work. See:
f <- system.file('scripts', 'viz.html', package = 'BrowserViz')
bv <- BrowserViz(4000:4024, browserFile = f)
Cheers, Leo