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CHECK report for subSeq on merida1

This page was generated on 2019-04-16 11:59:05 -0400 (Tue, 16 Apr 2019).

Package 1523/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
subSeq 1.12.1
Andrew J. Bass , John D. Storey
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/subSeq
Branch: RELEASE_3_8
Last Commit: fa7cd77
Last Changed Date: 2019-01-04 13:52:04 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: subSeq
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:subSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings subSeq_1.12.1.tar.gz
StartedAt: 2019-04-16 03:01:44 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:04:53 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 189.1 seconds
RetCode: 0
Status:  OK 
CheckDir: subSeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:subSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings subSeq_1.12.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/subSeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘subSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘subSeq’ version ‘1.12.1’
* 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 ‘subSeq’ 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
DESeq2: no visible global function definition for ‘selectMethod’
ccc: no visible global function definition for ‘cov’
ccc: no visible global function definition for ‘var’
generateSubsampledMatrix : <anonymous>: no visible global function
  definition for ‘rbinom’
plot.subsamples: no visible global function definition for ‘plot’
plot.summary.subsamples: no visible binding for global variable
  ‘metric’
plot.summary.subsamples: no visible binding for global variable ‘value’
plot.summary.subsamples: no visible binding for global variable
  ‘significant’
plot.summary.subsamples: no visible binding for global variable
  ‘percent’
plot.summary.subsamples: no visible binding for global variable
  ‘method’
plot.summary.subsamples: no visible binding for global variable ‘depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.depth’
plot.summary.subsamples: no visible binding for global variable
  ‘average.value’
subsample: no visible binding for global variable ‘proportion’
subsample: no visible binding for global variable ‘replication’
subsample: no visible binding for global variable ‘.’
subsample: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘count’
summary.subsamples: no visible binding for global variable ‘method’
summary.subsamples: no visible binding for global variable ‘depth’
summary.subsamples: no visible binding for global variable ‘pvalue’
summary.subsamples: no visible binding for global variable ‘proportion’
summary.subsamples: no visible binding for global variable
  ‘replication’
summary.subsamples: no visible global function definition for
  ‘p.adjust’
summary.subsamples: no visible binding for global variable ‘ID’
summary.subsamples: no visible binding for global variable ‘padj’
summary.subsamples: no visible binding for global variable
  ‘coefficient’
summary.subsamples: no visible binding for global variable
  ‘o.coefficient’
summary.subsamples: no visible global function definition for ‘cor’
summary.subsamples: no visible binding for global variable ‘valid’
summary.subsamples: no visible binding for global variable ‘o.lfdr’
summary.subsamples: no visible binding for global variable ‘o.padj’
summary.subsamples: no visible binding for global variable
  ‘significant’
summary.subsamples: no visible binding for global variable ‘estFDP’
summary.subsamples: no visible binding for global variable ‘rFDP’
summary.subsamples: no visible binding for global variable ‘metric’
summary.subsamples: no visible binding for global variable ‘value’
summary.subsamples: no visible binding for global variable ‘percent’
voomLimma: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  . ID average.depth average.value coefficient cor count cov depth
  estFDP method metric model.matrix o.coefficient o.lfdr o.padj
  p.adjust padj percent plot proportion pvalue rFDP rbinom replication
  selectMethod significant valid value var
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "selectMethod")
  importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom",
             "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
generateSubsampledMatrix 46.503  1.268  48.557
getSeed                  39.783  0.806  41.785
subsample                35.873  0.714  37.161
* 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-3.8-bioc/meat/subSeq.Rcheck/00check.log’
for details.



Installation output

subSeq.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL subSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘subSeq’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (subSeq)

Tests output


Example timings

subSeq.Rcheck/subSeq-Ex.timings

nameusersystemelapsed
combineSubsamples0.3480.0580.420
generateSubsampledMatrix46.503 1.26848.557
getSeed39.783 0.80641.785
plot.subsamples0.0010.0010.001
plot.summary.subsamples0.0000.0000.001
ss0.5210.0480.576
subsample35.873 0.71437.161
summary.subsamples0.4270.0580.487