BioC 3.2: CHECK report for SigCheck on oaxaca

Package: SigCheck

Version: 2.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SigCheck_2.2.1.tar.gz

StartedAt: 2016-04-23 04:25:25 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:33:49 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 503.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SigCheck.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SigCheck_2.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SigCheck.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SigCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigCheck’ version ‘2.2.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SigCheck’ can be installed ... [19s/29s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/SigCheck.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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
sigCheckKnown: no visible binding for global variable ‘knownSignatures’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [296s/301s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
sigCheckAll      137.961 16.331 154.631
sigCheckKnown     57.215  7.320  65.635
sigCheckPermuted  17.462  2.232  19.734
sigCheckPlot      16.750  1.977  18.747
sigCheck          15.243  1.158  19.528
sigCheckRandom    11.922  1.351  13.303
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/SigCheck.Rcheck/00check.log’
for details.

* installing *source* package ‘SigCheck’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Creating a new generic function for ‘signature’ in package ‘SigCheck’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (SigCheck)

name	user	system	elapsed
SigCheckObject-class	0.005	0.000	0.006
classifyResults	0.026	0.003	0.042
knownSignatures	0.037	0.002	0.040
nkiResults	0.024	0.003	0.027
sigCheck	15.243	1.158	19.528
sigCheckAll	137.961	16.331	154.631
sigCheckKnown	57.215	7.320	65.635
sigCheckPermuted	17.462	2.232	19.734
sigCheckPlot	16.750	1.977	18.747
sigCheckRandom	11.922	1.351	13.303