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: 2015-11-10 10:37:30 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 10:49:56 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 746.3 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_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 ... [16s/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 ... [419s/419s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
MAplot      122.773  5.952 128.730
XBSeq       118.849  6.640 125.495
XBSeqTest   114.531  6.068 120.603
plotSCVEsts   4.959  1.454   6.414
estimateSCV   4.468  1.283   5.752
dispTable     4.450  1.285   5.735
fitInfo       4.417  1.248   5.665
dispEst       4.388  1.253   5.642
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [156s/156s]
 [156s/156s] 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	122.773	5.952	128.730
XBSeq	118.849	6.640	125.495
XBSeqDataSet-class	0.210	0.026	0.236
XBSeqTest	114.531	6.068	120.603
XBplot	0.531	0.048	0.605
conditions	0.168	0.032	0.198
counts	0.160	0.021	0.182
dispEst	4.388	1.253	5.642
dispTable	4.450	1.285	5.735
estimateRealCount	0.179	0.030	0.209
estimateSCV	4.468	1.283	5.752
fitInfo	4.417	1.248	5.665
getSignalVars	3.550	1.119	4.670
plotSCVEsts	4.959	1.454	6.414