Forgot to add bioc-devel On Fri, Apr 3, 2015 at 4:55 PM, Leonardo Collado Torres <lcoll...@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
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel