BioC 3.5: CHECK report for BatchQC on oaxaca

Package: BatchQC

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.3.2.tar.gz

StartedAt: 2017-03-03 23:24:38 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:27:39 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 180.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BatchQC.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BatchQC_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BatchQC.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.3.2’
* 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 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 7.13  0.305    7.63
* 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
  ‘/Users/biocbuild/bbs-3.5-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	7.130	0.305	7.630
batchQC_analyze	0.363	0.014	0.396
batchQC_condition_adjusted	0.066	0.009	0.075
batchQC_filter_genes	0.113	0.002	0.115
batchQC_fsva_adjusted	0.396	0.018	0.433
batchQC_num.sv	0.137	0.004	0.141
batchQC_shapeVariation	0.308	0.001	0.309
batchQC_sva	0.275	0.009	0.285
batchQC_svregress_adjusted	0.221	0.016	0.237
batchqc_circosplot	0.374	0.004	0.378
batchqc_correlation	0.264	0.003	0.267
batchqc_corscatter	0.097	0.001	0.099
batchqc_explained_variation	0.067	0.001	0.069
batchqc_heatmap	0.252	0.003	0.256
batchqc_pc_explained_variation	0.086	0.003	0.090
batchqc_pca	0.059	0.008	0.068
batchqc_pca_svd	0.247	0.002	0.250
batchtest	0.116	0.006	0.122
combatPlot	0.207	0.006	0.216
getShinyInput	0.073	0.043	0.117
getShinyInputCombat	0.000	0.000	0.001
getShinyInputOrig	0.059	0.033	0.093
getShinyInputSVA	0.000	0.000	0.001
getShinyInputSVAf	0.001	0.000	0.000
getShinyInputSVAr	0.000	0.000	0.001
gnormalize	0.001	0.000	0.001
log2CPM	0.051	0.009	0.060
rnaseq_sim	0.223	0.054	0.277
setShinyInput	0.001	0.000	0.001
setShinyInputCombat	0	0	0
setShinyInputOrig	0.000	0.000	0.001
setShinyInputSVA	0	0	0
setShinyInputSVAf	0.001	0.000	0.000
setShinyInputSVAr	0.000	0.000	0.001