BioC 3.4: CHECK report for BatchQC on malbec1

Package: BatchQC

Version: 1.2.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.2.1.tar.gz

StartedAt: 2017-04-14 21:06:21 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:08:25 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 124.4 seconds

RetCode: 0

Status:  OK

CheckDir: BatchQC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BatchQC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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	2.620	0.076	2.718
batchQC_analyze	0.252	0.012	0.264
batchQC_condition_adjusted	0.036	0.000	0.037
batchQC_filter_genes	0.048	0.000	0.045
batchQC_fsva_adjusted	0.128	0.012	0.142
batchQC_num.sv	0.080	0.000	0.079
batchQC_shapeVariation	0.076	0.000	0.076
batchQC_sva	0.136	0.000	0.135
batchQC_svregress_adjusted	0.148	0.004	0.151
batchqc_circosplot	0.160	0.000	0.161
batchqc_correlation	0.156	0.000	0.159
batchqc_corscatter	0.044	0.000	0.044
batchqc_explained_variation	0.020	0.008	0.029
batchqc_heatmap	0.144	0.000	0.145
batchqc_pc_explained_variation	0.04	0.00	0.04
batchqc_pca	0.028	0.008	0.036
batchqc_pca_svd	0.192	0.000	0.192
batchtest	0.060	0.000	0.059
combatPlot	0.044	0.000	0.046
getShinyInput	0.048	0.012	0.058
getShinyInputCombat	0.000	0.000	0.001
getShinyInputOrig	0.060	0.008	0.068
getShinyInputSVA	0	0	0
getShinyInputSVAf	0	0	0
getShinyInputSVAr	0	0	0
gnormalize	0.000	0.000	0.002
log2CPM	0.060	0.008	0.066
rnaseq_sim	0.252	0.024	0.274
setShinyInput	0.000	0.000	0.001
setShinyInputCombat	0.004	0.000	0.001
setShinyInputOrig	0.000	0.000	0.001
setShinyInputSVA	0	0	0
setShinyInputSVAf	0	0	0
setShinyInputSVAr	0.000	0.000	0.001