Package: diffcyt

Version: 1.0.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffcyt_1.0.10.tar.gz

StartedAt: 2018-10-16 20:57:05 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:01:20 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 254.4 seconds

RetCode: 0

Status:  OK

CheckDir: diffcyt.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffcyt_1.0.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/diffcyt.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffcyt/DESCRIPTION’ ... OK
* this is package ‘diffcyt’ version ‘1.0.10’
* 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 ‘diffcyt’ 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 ... NOTE
calcCounts: no visible binding for global variable ‘cluster_id’
calcCounts: no visible binding for global variable ‘sample_id’
calcMedians: no visible binding for global variable ‘cluster_id’
calcMedians: no visible binding for global variable ‘sample_id’
calcMedians: no visible binding for global variable ‘value’
calcMediansByClusterMarker: no visible binding for global variable
  ‘cluster_id’
calcMediansByClusterMarker: no visible binding for global variable
  ‘marker’
calcMediansByClusterMarker: no visible binding for global variable
  ‘value’
calcMediansBySampleMarker: no visible binding for global variable
  ‘sample_id’
calcMediansBySampleMarker: no visible binding for global variable
  ‘marker’
calcMediansBySampleMarker: no visible binding for global variable
  ‘value’
Undefined global functions or variables:
  cluster_id marker sample_id value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
testDA_GLMM 10.926  0.045  11.058
diffcyt     10.382  0.077  10.568
plotHeatmap  8.829  0.231   9.158
topClusters  5.771  0.088   5.937
testDS_LMM   5.789  0.049   5.921
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/diffcyt.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘diffcyt’ ...
** R
** 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 (diffcyt)

name	user	system	elapsed
calcCounts	1.757	0.035	1.801
calcMedians	2.261	0.036	2.313
calcMediansByClusterMarker	1.469	0.019	1.500
calcMediansBySampleMarker	1.159	0.015	1.192
createContrast	0.001	0.000	0.002
createDesignMatrix	0.019	0.001	0.021
createFormula	0.008	0.001	0.008
diffcyt	10.382	0.077	10.568
generateClusters	1.189	0.012	1.214
plotHeatmap	8.829	0.231	9.158
prepareData	0.029	0.002	0.030
testDA_GLMM	10.926	0.045	11.058
testDA_edgeR	1.315	0.042	1.361
testDA_voom	1.291	0.017	1.317
testDS_LMM	5.789	0.049	5.921
testDS_limma	2.733	0.015	2.772
topClusters	5.771	0.088	5.937
transformData	0.061	0.004	0.066