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CHECK report for EBSeq on machv2

This page was generated on 2020-10-17 11:58:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE EBSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 523/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 1.28.0
Ning Leng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/EBSeq
Branch: RELEASE_3_11
Last Commit: 85f5918
Last Changed Date: 2020-04-27 14:34:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EBSeq
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EBSeq_1.28.0.tar.gz
StartedAt: 2020-10-17 00:46:46 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:48:33 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 107.1 seconds
RetCode: 0
Status:  OK 
CheckDir: EBSeq.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:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EBSeq_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/EBSeq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘1.28.0’
* 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 ‘EBSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
DenNHist: no visible global function definition for ‘hist’
DenNHist: no visible global function definition for ‘lines’
DenNHist: no visible global function definition for ‘dbeta’
DenNHist: no visible global function definition for ‘legend’
EBMultiTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBMultiTest: no visible global function definition for ‘quantile’
EBMultiTest : <anonymous>: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘var’
EBTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest: no visible global function definition for ‘quantile’
EBTest: no visible binding for global variable ‘var’
GetDEResults: no visible binding for global variable ‘median’
LogN: no visible global function definition for ‘optim’
LogNMulti: no visible global function definition for ‘optim’
MedianNorm : <anonymous>: no visible global function definition for
  ‘median’
MedianNorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
PlotPattern: no visible global function definition for ‘par’
PlotPattern: no visible global function definition for ‘rainbow’
PlotPattern: no visible global function definition for ‘heatmap’
PlotPostVsRawFC: no visible global function definition for ‘par’
PlotPostVsRawFC: no visible global function definition for ‘abline’
PlotPostVsRawFC: no visible global function definition for ‘rect’
PolyFitPlot: no visible global function definition for ‘lm’
PolyFitPlot: no visible global function definition for ‘smoothScatter’
PolyFitPlot: no visible global function definition for ‘axis’
PolyFitPlot: no visible global function definition for ‘lines’
QQP: no visible global function definition for ‘rbeta’
QQP: no visible global function definition for ‘qqplot’
QQP: no visible global function definition for ‘lm’
QQP: no visible global function definition for ‘abline’
QuantileNorm : <anonymous>: no visible global function definition for
  ‘quantile’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis dbeta heatmap hist legend lines lm median optim par
  qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "rect", "smoothScatter")
  importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
             "qqplot", "quantile", "rbeta", "var")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
             user system elapsed
EBMultiTest 7.760  0.031   7.800
GetMultiFC  7.225  0.022   7.258
GetMultiPP  7.209  0.016   7.256
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/EBSeq.Rcheck/00check.log’
for details.



Installation output

EBSeq.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EBSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘EBSeq’ ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EBSeq)

Tests output


Example timings

EBSeq.Rcheck/EBSeq-Ex.timings

nameusersystemelapsed
DenNHist2.1650.1732.340
EBMultiTest7.7600.0317.800
EBSeq_NingLeng-package0.4690.0260.495
EBTest0.5460.0300.576
GeneMat0.0040.0020.005
GetDEResults0.4120.0190.431
GetMultiFC7.2250.0227.258
GetMultiPP7.2090.0167.256
GetNg0.0100.0030.012
GetNormalizedMat0.0080.0010.009
GetPP0.5180.0140.532
GetPPMat0.6550.0110.667
GetPatterns0.0010.0010.001
IsoList0.0030.0010.004
IsoMultiList0.0010.0010.003
Likefun000
LikefunMulti000
LogN0.0000.0000.001
LogNMulti0.0000.0000.001
MedianNorm0.0040.0010.005
MultiGeneMat0.0010.0020.003
PlotPattern0.0100.0010.011
PlotPostVsRawFC0.8100.0270.839
PolyFitPlot0.0170.0020.020
PostFC0.6180.0080.628
QQP1.9070.1202.029
QuantileNorm0.0080.0020.010
RankNorm0.0100.0020.012
beta.mom0.0000.0000.001
crit_fun0.7220.0250.748
f00.0000.0000.001
f10.0000.0000.001