BioC 3.3: CHECK report for BatchQC on morelia

Package: BatchQC

Version: 0.99.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_0.99.5.tar.gz

StartedAt: 2016-04-20 23:28:44 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 23:31:21 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 156.1 seconds

RetCode: 0

Status:  OK

CheckDir: BatchQC.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BatchQC.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.5’
* 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 ... [12s/12s] 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 ... 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 ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/11s]
 [11s/11s] 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	3.274	0.218	3.602
batchQC_analyze	0.512	0.013	0.527
batchQC_condition_adjusted	0.021	0.008	0.030
batchQC_fsva_adjusted	0.186	0.016	0.203
batchQC_num.sv	0.104	0.002	0.106
batchQC_shapeVariation	0.090	0.001	0.091
batchQC_sva	0.188	0.004	0.193
batchQC_svregress_adjusted	0.16	0.01	0.17
batchqc_circosplot	0.108	0.001	0.109
batchqc_correlation	0.217	0.002	0.221
batchqc_corscatter	0.046	0.001	0.114
batchqc_explained_variation	0.018	0.002	0.020
batchqc_heatmap	0.210	0.001	0.212
batchqc_pc_explained_variation	0.036	0.002	0.040
batchqc_pca	0.027	0.009	0.036
batchqc_pca_svd	0.207	0.001	0.208
batchtest	0.057	0.007	0.064
combatPlot	0.038	0.003	0.071
getShinyInput	0.077	0.051	0.128
getShinyInputCombat	0.000	0.000	0.001
getShinyInputOrig	0.063	0.034	0.096
getShinyInputSVA	0	0	0
getShinyInputSVAf	0.000	0.000	0.001
getShinyInputSVAr	0.001	0.000	0.001
log2CPM	0.038	0.009	0.047
rnaseq_sim	0.085	0.045	0.131
setShinyInput	0.000	0.000	0.001
setShinyInputCombat	0	0	0
setShinyInputOrig	0	0	0
setShinyInputSVA	0.001	0.000	0.001
setShinyInputSVAf	0.001	0.000	0.000
setShinyInputSVAr	0.000	0.000	0.001