BioC 3.2: CHECK report for facopy on linux1.bioconductor.org

Package: facopy

Version: 1.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings facopy_1.4.0.tar.gz

StartedAt: 2015-10-27 03:22:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:26:11 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 199.1 seconds

RetCode: 0

Status:  OK

CheckDir: facopy.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings facopy_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/facopy.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘facopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘facopy’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘cgdsr’ ‘coin’ ‘ggplot2’ ‘gridExtra’ ‘facopy.annot’ ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘facopy’ can be installed ... [16s/16s] OK
* 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 ... NOTE
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.facopyPlotInt: no visible global function definition for ‘unit’
* 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 ... [22s/23s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
facopyPlot 5.748  0.004   5.752
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/facopy.Rcheck/00check.log’
for details.

* installing *source* package ‘facopy’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (facopy)

name	user	system	elapsed
addFeatures	1.934	0.031	1.967
addVariables	0.058	0.007	0.066
alterationSummary	0.635	0.003	0.640
calculateCor	1.217	0.004	2.177
facopy	1.888	0.008	1.897
facopyEnrichment	0.033	0.000	0.034
facopyInfo-class	0.001	0.000	0.001
facopyPlot	5.748	0.004	5.752
getFacopyInfo	0.004	0.000	0.004
myCalls	0.026	0.000	0.026
myStudy	0.033	0.000	0.033
myVariables	0.003	0.000	0.002
plotBar	0.683	0.004	0.687
plotHist	0.902	0.000	0.903
plotPCA	0.097	0.004	0.100
plotZoom	0.116	0.008	0.124
preview	1.014	0.000	1.014
readCNData	0	0	0
variableCor	0.041	0.004	0.045
variableSummary	0.080	0.000	0.083