BioC 3.4: CHECK report for BatchQC on zin1

Package: BatchQC

Version: 1.1.22

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.1.22.tar.gz

StartedAt: 2016-09-20 03:28:58 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:30:56 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 117.8 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_1.1.22.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BatchQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.22’
* 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 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 ... 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	2.464	0.112	2.624
batchQC_analyze	0.200	0.020	0.221
batchQC_condition_adjusted	0.036	0.004	0.041
batchQC_filter_genes	0.048	0.000	0.049
batchQC_fsva_adjusted	0.192	0.008	0.197
batchQC_num.sv	0.108	0.000	0.111
batchQC_shapeVariation	0.072	0.000	0.071
batchQC_sva	0.164	0.004	0.167
batchQC_svregress_adjusted	0.184	0.004	0.188
batchqc_circosplot	0.112	0.000	0.113
batchqc_correlation	0.180	0.000	0.181
batchqc_corscatter	0.040	0.004	0.045
batchqc_explained_variation	0.036	0.000	0.034
batchqc_heatmap	0.160	0.004	0.165
batchqc_pc_explained_variation	0.044	0.000	0.046
batchqc_pca	0.044	0.004	0.044
batchqc_pca_svd	0.160	0.004	0.165
batchtest	0.052	0.008	0.058
combatPlot	0.052	0.000	0.051
getShinyInput	0.056	0.028	0.082
getShinyInputCombat	0	0	0
getShinyInputOrig	0.056	0.012	0.067
getShinyInputSVA	0	0	0
getShinyInputSVAf	0	0	0
getShinyInputSVAr	0.000	0.000	0.001
gnormalize	0	0	0
log2CPM	0.052	0.004	0.053
rnaseq_sim	0.180	0.052	0.233
setShinyInput	0	0	0
setShinyInputCombat	0.000	0.000	0.001
setShinyInputOrig	0	0	0
setShinyInputSVA	0	0	0
setShinyInputSVAf	0	0	0
setShinyInputSVAr	0	0	0