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CHECK report for MAGeCKFlute on machv2

This page was generated on 2020-10-14 11:58:56 -0400 (Wed, 14 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MAGeCKFlute PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 976/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAGeCKFlute 1.8.0
Wubing Zhang
Snapshot Date: 2020-10-13 14:50:23 -0400 (Tue, 13 Oct 2020)
URL: https://git.bioconductor.org/packages/MAGeCKFlute
Branch: RELEASE_3_11
Last Commit: 3df188c
Last Changed Date: 2020-04-27 15:12:41 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MAGeCKFlute
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.8.0.tar.gz
StartedAt: 2020-10-14 04:02:18 -0400 (Wed, 14 Oct 2020)
EndedAt: 2020-10-14 04:10:15 -0400 (Wed, 14 Oct 2020)
EllapsedTime: 476.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MAGeCKFlute.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:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGeCKFlute’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAGeCKFlute’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.7Mb
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
enrich.ORT      17.180  0.801  17.995
arrangePathview  7.066  0.301   9.124
KeggPathwayView  4.545  0.153   7.299
* 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/MAGeCKFlute.Rcheck/00check.log’
for details.



Installation output

MAGeCKFlute.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MAGeCKFlute
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MAGeCKFlute’ ...
** 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 (MAGeCKFlute)

Tests output


Example timings

MAGeCKFlute.Rcheck/MAGeCKFlute-Ex.timings

nameusersystemelapsed
BarView0.8020.0080.810
BatchRemove1.5250.0221.551
ConsistencyView0.3970.0190.417
CutoffCalling0.0050.0010.005
DensityDiffView0.6230.0390.663
DensityView0.6050.0110.617
EnrichAnalyzer0.0160.0010.018
EnrichedFilter0.0170.0010.018
EnrichedGeneView0.0170.0010.018
EnrichedView0.0110.0010.011
FluteMLE0.0020.0010.002
FluteRRA0.0010.0010.002
HeatmapView0.1360.0040.140
IdentBarView0.1730.0020.175
IncorporateDepmap0.1370.0040.142
KeggPathwayView4.5450.1537.299
MAView4.4250.0474.475
MapRatesView0.4690.0060.476
NormalizeBeta0.3520.0050.358
OmitCommonEssential0.1230.0020.126
RankView0.9190.0340.953
ReadBeta0.1240.0020.126
ReadGMT0.8570.2201.092
ReadRRA0.1370.0020.145
ReadsgRRA0.7920.0200.825
ResembleDepmap0.1260.0020.129
ScatterView0.6860.0220.712
Selector0.4150.0030.421
SquareView0.8000.0200.822
TransGeneID2.2380.0222.260
ViolinView0.8960.0340.931
VolcanoView0.9950.0411.037
arrangePathview7.0660.3019.124
enrich.GSE0.0150.0010.016
enrich.HGT1.8360.0601.896
enrich.ORT17.180 0.80117.995
getCols0.0100.0010.011
getGeneAnn000
getOrg0.0010.0010.001
getOrtAnn0.0000.0010.000
gsGetter0.2560.0040.260
hclustView0.1550.0070.162
normalize.loess0.3510.0040.355
sgRankView2.0100.0872.099