ERROR: could not find function "windowsFonts"

[AngieHinrichs]

Hi! I'm on Mac OS X 10.9.5; installed R 3.2.2, Cairo (1.14.2_1) and PostgreSQL (9.4.4) using homebrew; installed the required R packages as described in the "Required Software" section of README.md; and ran 'library(shiny)' and 'runGitHub("LocusExplorer", "oncogenetics")' as described.

Unfortunately when I visit the URL mentioned in the output (http://127.0.0.1:7074/) I get only the text:

ERROR: could not find function "windowsFonts"'

And I see the same error at the end of the output in R.

I'm not very familiar with R so I'm not sure how to proceed debugging this, but please let me know if there are diagnostic commands I could run or if you need more info.

Here is the R session from 'library shiny' onward:

> library(shiny)  
> runGitHub("LocusExplorer", "oncogenetics")
Downloading https://github.com/oncogenetics/LocusExplorer/archive/master.tar.gz

Listening on http://127.0.0.1:7074
data.table 1.9.6  For help type ?data.table or https://github.com/Rdatatable/data.table/wiki
The fastest way to learn (by data.table authors): https://www.datacamp.com/courses/data-analysis-the-data-table-way

Attaching package: ‘dplyr’

The following objects are masked from ‘package:data.table’:

    between, last

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:dplyr’:

    combine, intersect, setdiff, union

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist, unsplit

Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: ‘ggbio’

The following objects are masked from ‘package:ggplot2’:

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:dplyr’:

    rename

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:tidyr’:

    expand

The following objects are masked from ‘package:dplyr’:

    collapse, desc, slice

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:

    select

Loading required package: DBI

Error in eval(expr, envir, enclos) : 
  could not find function "windowsFonts"
Error in eval(expr, envir, enclos) : 
  could not find function "windowsFonts"

[zx8754]

I haven't tested the app in OSX, I suggest you "Download as ZIP" locally, and comment out as below in ui.R file. Open ui.R in RStudio, and runApp().

Change below:

windowsFonts(Courier=windowsFont("TT Courier New"))

to:

# windowsFonts(Courier=windowsFont("TT Courier New"))

I will test it on OSX, and will let you know more, in this thread.

[zx8754]

@AngieHinrichs Please let me know, if this doesn't resolve your issue.

[AngieHinrichs]

It gets past the windowsFonts, thank you very much for the quick fix!

Unfortunately it now fails on the next line:

ERROR: could not find function "setInternet2"

[zx8754]

@AngieHinrichs Please try again. Sorry, I don't have OSX here, will have to test this tomorrow properly.

[AngieHinrichs]

It works now! Thanks.

[zx8754]

@AngieHinrichs Great! Please, do let me know if you get stuck. Time to bed for me, 22:30 UK time...