BioC 3.2: CHECK report for XBSeq on perceval

Package: XBSeq

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XBSeq_1.0.0.tar.gz

StartedAt: 2015-10-27 13:22:13 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 10:34:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 751.8 seconds

RetCode: 0

Status:  OK

CheckDir: XBSeq.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 XBSeq_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/XBSeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XBSeq’ version ‘1.0.0’
* 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 ‘XBSeq’ can be installed ... [17s/17s] 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 ... NOTE
adjustScv: no visible binding for global variable
  ‘scvBiasCorrectionFits’
MAplot: no visible binding for global variable ‘baseMean’
MAplot: no visible binding for global variable ‘log2FoldChange’
XBplot: no visible binding for global variable ‘Sample’
XBplot: no visible binding for global variable ‘Group’
XBplot: no visible binding for global variable ‘..count..’
XBSeqDataSet: no visible global function definition for ‘DataFrame’
XBSeqDataSet: no visible global function definition for
  ‘SummarizedExperiment’
XBSeqTestForMatrices : <anonymous>: no visible binding for global
  variable ‘bgcounts’
counts,XBSeqDataSet : .local: no visible global function definition for
  ‘assays’
counts,XBSeqDataSet : .local: no visible global function definition for
  ‘assay’
estimateRealCount,XBSeqDataSet: no visible global function definition
  for ‘assay’
estimateRealCount,XBSeqDataSet: no visible global function definition
  for ‘assay<-’
* 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 ... [414s/414s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
MAplot      124.240  6.256 130.501
XBSeq       113.866  6.228 120.099
XBSeqTest   113.793  6.074 119.871
plotSCVEsts   4.899  1.415   6.314
dispTable     4.321  1.242   5.563
fitInfo       4.323  1.235   5.558
dispEst       4.317  1.228   5.546
estimateSCV   4.329  1.208   5.538
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [157s/157s]
 [157s/157s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/XBSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘XBSeq’ ...
** 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 (XBSeq)

name	user	system	elapsed
MAplot	124.240	6.256	130.501
XBSeq	113.866	6.228	120.099
XBSeqDataSet-class	0.207	0.025	0.232
XBSeqTest	113.793	6.074	119.871
XBplot	0.528	0.054	0.621
conditions	0.165	0.035	0.199
counts	0.160	0.023	0.184
dispEst	4.317	1.228	5.546
dispTable	4.321	1.242	5.563
estimateRealCount	0.175	0.027	0.202
estimateSCV	4.329	1.208	5.538
fitInfo	4.323	1.235	5.558
getSignalVars	3.465	1.126	4.591
plotSCVEsts	4.899	1.415	6.314