BioC 3.6: CHECK report for BatchQC on malbec1

Package: BatchQC

Version: 1.5.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.5.0.tar.gz

StartedAt: 2017-08-15 21:23:32 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:25:59 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 146.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BatchQC.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BatchQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.0’
* 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 ... NOTE
gls.series.C: no visible global function definition for ‘lm.fit’
Undefined global functions or variables:
  lm.fit
Consider adding
  importFrom("stats", "lm.fit")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘lmFitC’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
batchQC 4.392  0.156   5.829
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BatchQC.Rcheck/00check.log’
for details.

* 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	4.392	0.156	5.829
batchQC_analyze	0.300	0.024	0.328
batchQC_condition_adjusted	0.044	0.012	0.060
batchQC_filter_genes	0.092	0.004	0.096
batchQC_fsva_adjusted	0.412	0.000	0.410
batchQC_num.sv	0.100	0.000	0.102
batchQC_shapeVariation	0.280	0.004	0.286
batchQC_sva	0.196	0.000	0.199
batchQC_svregress_adjusted	0.200	0.008	0.210
batchqc_circosplot	0.292	0.000	0.288
batchqc_correlation	0.144	0.000	0.144
batchqc_corscatter	0.048	0.000	0.048
batchqc_explained_variation	0.028	0.004	0.033
batchqc_heatmap	0.120	0.000	0.121
batchqc_pc_explained_variation	0.056	0.000	0.055
batchqc_pca	0.024	0.000	0.023
batchqc_pca_svd	0.136	0.000	0.134
batchtest	0.060	0.000	0.061
combatPlot	0.204	0.000	0.203
getShinyInput	0.040	0.020	0.059
getShinyInputCombat	0	0	0
getShinyInputOrig	0.032	0.012	0.048
getShinyInputSVA	0	0	0
getShinyInputSVAf	0.000	0.000	0.001
getShinyInputSVAr	0.004	0.000	0.000
gnormalize	0.000	0.000	0.001
log2CPM	0.040	0.004	0.042
rnaseq_sim	0.124	0.016	0.141
setShinyInput	0	0	0
setShinyInputCombat	0.004	0.000	0.000
setShinyInputOrig	0.000	0.000	0.001
setShinyInputSVA	0.000	0.000	0.001
setShinyInputSVAf	0.000	0.000	0.001
setShinyInputSVAr	0	0	0