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CHECK report for exomePeak2 on malbec2

This page was generated on 2020-10-17 11:54:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE exomePeak2 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 572/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
exomePeak2 1.0.0
Zhen Wei
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/exomePeak2
Branch: RELEASE_3_11
Last Commit: 0b57ebf
Last Changed Date: 2020-04-27 15:34:23 -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: exomePeak2
Version: 1.0.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings exomePeak2_1.0.0.tar.gz
StartedAt: 2020-10-17 01:14:45 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:22:55 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 490.2 seconds
RetCode: 0
Status:  OK 
CheckDir: exomePeak2.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:exomePeak2.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings exomePeak2_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/exomePeak2.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomePeak2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak2’ version ‘1.0.0’
* package encoding: UTF-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 ‘exomePeak2’ 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
Results,SummarizedExomePeak: no visible global function definition for
  ‘glm_M’
exomePeakCalling,MeripBamFileList: no visible global function
  definition for ‘metadata’
exomePeakCalling,MeripBamFileList: no visible global function
  definition for ‘%over%’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘GC_idx’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘Log2FC’
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  ‘Label’
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  ‘GC_cont’
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  ‘value’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘samples’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘size_factors’
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable ‘Estimation_Methods’
Undefined global functions or variables:
  %over% Estimation_Methods GC_cont GC_idx Label Log2FC glm_M metadata
  samples size_factors value
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
exomePeak2                67.976  0.116  68.115
exomePeakCalling-methods  36.112  0.024  36.136
SummarizedExomePeak-class 25.212  0.786  26.197
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/exomePeak2.Rcheck/00check.log’
for details.



Installation output

exomePeak2.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL exomePeak2
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘exomePeak2’ ...
** using staged installation
** R
** inst
** 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 (exomePeak2)

Tests output


Example timings

exomePeak2.Rcheck/exomePeak2-Ex.timings

nameusersystemelapsed
GCsizeFactors-methods0.0770.0000.087
LibraryType-methods0.2960.0000.296
MeripBamFileList-class0.3240.0080.332
Parameter-methods0.1130.0150.128
Results-methods0.9680.0361.005
SummarizedExomePeak-class25.212 0.78626.197
estimateSeqDepth-methods0.0700.0000.071
exomePeak267.976 0.11668.115
exomePeak2Results-methods0.0050.0030.009
exomePeakCalling-methods36.112 0.02436.136
exportResults-methods0.8490.0000.849
glmDM-methods3.5490.0003.566
glmM-methods3.9660.0003.978
normalizeGC-methods0.1340.0000.134
plotExonLength-methods1.1190.0001.119
plotLfcGC-methods0.1830.0000.184
plotReadsGC-methods1.2290.0041.232
plotSizeFactors-methods0.4170.0000.416
scanMeripBAM0.3850.0040.389