BioC 3.4: CHECK report for BatchQC on morelia

Package: BatchQC

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.2.1.tar.gz

StartedAt: 2017-04-14 22:56:00 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:58:53 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 172.8 seconds

RetCode: 0

Status:  OK

CheckDir: BatchQC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BatchQC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ version ‘1.2.1’
* 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 ‘BatchQC’ 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
batchQC 5.135  0.285   5.687
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

* installing *source* package ‘BatchQC’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BatchQC)

name	user	system	elapsed
batchQC	5.135	0.285	5.687
batchQC_analyze	0.296	0.014	0.311
batchQC_condition_adjusted	0.052	0.011	0.063
batchQC_filter_genes	0.069	0.002	0.071
batchQC_fsva_adjusted	0.227	0.012	0.264
batchQC_num.sv	0.147	0.001	0.148
batchQC_shapeVariation	0.113	0.001	0.115
batchQC_sva	0.212	0.002	0.215
batchQC_svregress_adjusted	0.205	0.015	0.222
batchqc_circosplot	0.175	0.001	0.176
batchqc_correlation	0.250	0.003	0.253
batchqc_corscatter	0.066	0.001	0.067
batchqc_explained_variation	0.047	0.004	0.051
batchqc_heatmap	0.261	0.002	0.264
batchqc_pc_explained_variation	0.058	0.004	0.064
batchqc_pca	0.053	0.009	0.062
batchqc_pca_svd	0.281	0.003	0.287
batchtest	0.094	0.006	0.099
combatPlot	0.060	0.002	0.064
getShinyInput	0.075	0.044	0.120
getShinyInputCombat	0.000	0.000	0.001
getShinyInputOrig	0.062	0.037	0.099
getShinyInputSVA	0.001	0.000	0.001
getShinyInputSVAf	0.000	0.000	0.001
getShinyInputSVAr	0.000	0.000	0.001
gnormalize	0.001	0.000	0.001
log2CPM	0.081	0.011	0.093
rnaseq_sim	0.278	0.058	0.335
setShinyInput	0	0	0
setShinyInputCombat	0.000	0.000	0.001
setShinyInputOrig	0.001	0.001	0.001
setShinyInputSVA	0.001	0.000	0.001
setShinyInputSVAf	0.001	0.000	0.000
setShinyInputSVAr	0.001	0.000	0.001