[Bioc-devel] BrowserViz: curious but needs a small tweak to run example

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