Package: Trendy

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Trendy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Trendy_1.5.6.tar.gz

StartedAt: 2019-04-09 04:12:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:15:24 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 191.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Trendy.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Trendy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Trendy_1.5.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Trendy.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Trendy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Trendy’ version ‘1.5.6’
* package encoding: UTF-8
* 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 ‘Trendy’ can be installed ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotFeature':
plotFeature
  Code: function(Data, tVectIn = NULL, featureNames, showFit = TRUE,
                 simple = FALSE, showLegend = TRUE, trendyOutData =
                 NULL, cexLegend = 1, legendLocation = "side", xlab =
                 "Time", ylab = "Normalized Expression", segColors =
                 c("chartreuse3", "coral1", "black", "cornflowerblue"),
                 customTitle = NULL, customLabels.x = NULL, spacing.x =
                 NULL)
  Docs: function(Data, tVectIn = NULL, featureNames, showFit = TRUE,
                 simple = FALSE, showLegend = TRUE, trendyOutData =
                 NULL, cexLegend = 1, legendLocation = "side", xlab =
                 "Time", ylab = "Normalized Expression", segColors =
                 c("chartreuse3", "coral1", "black", "cornflowerblue"),
                 customTitle = NULL, customLabels.x = NULL)
  Argument names in code not in docs:
    spacing.x

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
formatResults  7.655  4.701   1.292
extractPattern 4.119  1.763   3.059
plotFeature    4.982  0.286   5.322
* 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
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Trendy.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Trendy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Trendy’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Trendy)

name	user	system	elapsed
breakpointDist	0.291	0.087	3.646
extractPattern	4.119	1.763	3.059
formatResults	7.655	4.701	1.292
getCounts	1.537	0.606	0.069
plotFeature	4.982	0.286	5.322
results	0.091	0.036	1.141
topTrendy	1.594	0.689	2.804
trendHeatmap	2.962	0.791	2.824
trendy	3.010	0.769	2.707
trendyExampleData	0.001	0.002	0.004