BioC 3.5: CHECK report for Rcade on malbec2

Package: Rcade

Version: 1.18.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.18.0.tar.gz

StartedAt: 2017-10-18 01:51:04 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:54:13 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 189.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rcade.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Rcade.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcade’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/home/biocbuild/bbs-3.5-bioc/meat/Rcade.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
constructRcadeTable: no visible binding for global variable ‘p.DE’
constructRcadeTable: no visible binding for global variable ‘p.ChIP’
plotBBB,Rcade: no visible global function definition for ‘decorate3d’
Undefined global functions or variables:
  decorate3d p.ChIP p.DE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RcadeAnalysis    6.016  0.028   6.048
diffCountsBaySeq 5.716  0.004   5.725
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/Rcade.Rcheck/00check.log’
for details.

* installing *source* package ‘Rcade’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (Rcade)

name	user	system	elapsed
Rcade-class	0.820	0.080	0.906
RcadeAnalysis	6.016	0.028	6.048
RcadeSTAT1	0.012	0.000	0.010
constructRcadeTable	0.112	0.000	0.111
countReads	1.976	0.008	1.988
defineBins	0.008	0.000	0.011
diffCountsBaySeq	5.716	0.004	5.725
exportRcade-methods	0.004	0.000	0.002