BioC 3.5: CHECK report for piano on veracruz2

Package: piano

Version: 1.16.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings piano_1.16.2.tar.gz

StartedAt: 2017-08-16 06:30:05 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:31:40 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 95.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: piano.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings piano_1.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/piano.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘piano/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘piano’ version ‘1.16.2’
* 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 ‘piano’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘piano’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/piano.Rcheck/00install.out’ for details.
* 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 ... NOTE
'library' or 'require' call to ‘snowfall’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
networkPlot     5.126  0.073   5.386
GSAheatmap      4.858  0.099   5.110
GSAsummaryTable 4.768  0.093   5.008
* 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/piano.Rcheck/00check.log’
for details.

* installing *source* package ‘piano’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘piano’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘piano’
* DONE (piano)

name	user	system	elapsed
GSAheatmap	4.858	0.099	5.110
GSAsummaryTable	4.768	0.093	5.008
consensusHeatmap	1.645	0.044	1.740
consensusScores	0.121	0.013	0.136
diffExp	3.462	0.126	3.993
extractFactors	0.426	0.009	0.442
geneSetSummary	3.982	0.071	4.147
loadGSC	0.013	0.000	0.014
loadMAdata	0.249	0.007	0.264
networkPlot	5.126	0.073	5.386
polarPlot	1.682	0.028	1.758
runGSA	3.546	0.053	3.697
runGSAhyper	0.310	0.005	0.320
runQC	1.072	0.032	1.161
writeFilesForKiwi	0.150	0.004	0.155