BioC 3.2: CHECK report for XBSeq on perceval

Package: XBSeq

Version: 0.99.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XBSeq_0.99.8.tar.gz

StartedAt: 2015-08-24 06:14:14 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 06:26:49 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 755.3 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_0.99.8.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 (2015-08-14 r69078)
* 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 ‘0.99.8’
* 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 ... [19s/19s] 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 ... [406s/407s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
MAplot      117.999  9.428 128.093
XBSeqTest   109.236  8.099 117.341
XBSeq       106.891  8.478 115.375
dispEst       4.270  1.870   6.139
plotSCVEsts   4.229  1.849   6.079
dispTable     3.979  1.836   5.815
fitInfo       3.952  1.834   5.786
estimateSCV   3.933  1.739   5.672
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [152s/152s]
 [152s/152s] 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	117.999	9.428	128.093
XBSeq	106.891	8.478	115.375
XBSeqDataSet-class	0.189	0.033	0.222
XBSeqTest	109.236	8.099	117.341
XBplot	0.548	0.082	0.651
conditions	0.198	0.063	0.262
counts	0.174	0.038	0.213
dispEst	4.270	1.870	6.139
dispTable	3.979	1.836	5.815
estimateRealCount	0.165	0.042	0.207
estimateSCV	3.933	1.739	5.672
fitInfo	3.952	1.834	5.786
getSignalVars	3.099	1.694	4.793
plotSCVEsts	4.229	1.849	6.079