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CHECK report for MAGeCKFlute on merida1

This page was generated on 2019-04-16 12:04:05 -0400 (Tue, 16 Apr 2019).

Package 867/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAGeCKFlute 1.2.3
Wubing Zhang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MAGeCKFlute
Branch: RELEASE_3_8
Last Commit: 0df39fe
Last Changed Date: 2019-02-21 01:04:56 -0400 (Thu, 21 Feb 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: MAGeCKFlute
Version: 1.2.3
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_1.2.3.tar.gz
StartedAt: 2019-04-16 00:58:16 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:07:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 564.3 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_1.2.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MAGeCKFlute.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 ‘MAGeCKFlute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGeCKFlute’ version ‘1.2.3’
* 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 ... NOTE
Found the following non-portable file paths:
  MAGeCKFlute/vignettes/MAGeCKFlute_cache/html/CheckCountSummary_772d2f34111dd8efb7ea46fc8b46e5b8.RData
  MAGeCKFlute/vignettes/MAGeCKFlute_cache/html/EstimateCellCycle_2d76364f66438e955d3cbfef21e61b9d.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAGeCKFlute’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data      5.3Mb
    extdata   4.6Mb
* 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
BatchRemove: no visible binding for global variable ‘PC1’
BatchRemove: no visible binding for global variable ‘PC2’
BatchRemove: no visible binding for global variable ‘shape’
CellCycleView: no visible binding for global variable ‘x’
CellCycleView: no visible binding for global variable ‘y’
DensityDiffView: no visible binding for global variable ‘Diff’
DensityDiffView: no visible binding for global variable ‘..density..’
DensityDiffView: no visible binding for global variable ‘r’
DensityView: no visible binding for global variable ‘value’
DensityView: no visible binding for global variable ‘variable’
EnrichedGSEView: no visible binding for global variable ‘NES’
EnrichedGSEView: no visible binding for global variable ‘Description’
EnrichedGSEView: no visible binding for global variable ‘logP’
EnrichedGeneView: no visible binding for global variable ‘Gene’
EnrichedGeneView: no visible binding for global variable ‘Term’
EnrichedGeneView: no visible binding for global variable ‘Size’
EnrichedGeneView: no visible binding for global variable ‘GeneScore’
EnrichedView: no visible binding for global variable ‘logP’
EnrichedView: no visible binding for global variable ‘Description’
EnrichedView: no visible binding for global variable ‘Count’
FluteMLE: no visible binding for global variable ‘Zuber_Essential’
KeggPathwayView: no visible binding for global variable ‘bods’
KeggPathwayView: no visible global function definition for ‘keggConv’
KeggPathwayView: no visible binding for global variable ‘rn.list’
KeggPathwayView: no visible global function definition for
  ‘parseKGML2Graph2’
MapRatesView: no visible binding for global variable ‘count’
MapRatesView: no visible binding for global variable ‘category’
MapRatesView: no visible binding for global variable ‘pos’
MapRatesView: no visible binding for global variable ‘percent’
NormalizeBeta: no visible binding for global variable ‘Zuber_Essential’
RankView: no visible binding for global variable ‘Rank’
RankView: no visible binding for global variable ‘group’
RankView: no visible binding for global variable ‘Gene’
ScatterView: no visible binding for global variable ‘Control’
ScatterView: no visible binding for global variable ‘Treatment’
ScatterView: no visible binding for global variable ‘group’
Selector: no visible binding for global variable ‘GeneNum’
Selector: no visible binding for global variable ‘x’
Selector: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘Control’
SquareView: no visible binding for global variable ‘Treatment’
SquareView: no visible binding for global variable ‘group’
SquareView: no visible binding for global variable ‘Gene’
ViolinView: no visible binding for global variable ‘variable’
ViolinView: no visible binding for global variable ‘value’
VolcanoView: no visible binding for global variable ‘group’
getOrg: no visible binding for global variable ‘bods’
sgRankView: no visible binding for global variable ‘x’
sgRankView: no visible binding for global variable ‘y’
sgRankView: no visible binding for global variable ‘value’
sgRankView: no visible binding for global variable ‘id’
sgRankView: no visible binding for global variable ‘LFC’
sgRankView: no visible binding for global variable ‘yend’
Undefined global functions or variables:
  ..density.. Control Count Description Diff Gene GeneNum GeneScore LFC
  NES PC1 PC2 Rank Size Term Treatment Zuber_Essential bods category
  count group id keggConv logP parseKGML2Graph2 percent pos r rn.list
  shape value variable x y yend
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
arrangePathview     23.123  0.685  25.714
enrich.ORT          20.375  0.236  20.773
MAView              19.414  0.224  19.807
EnrichedGeneView    18.617  0.259  17.226
EnrichedView        13.776  0.363  14.216
DensityView         12.980  0.182  13.469
EnrichSquare        12.473  0.259  13.024
RankView            12.327  0.135  12.573
SquareView          12.251  0.189  12.563
EnrichAB            12.273  0.130  12.631
enrichment_analysis 12.029  0.190  12.332
enrich.HGT          11.798  0.246  12.154
ViolinView          11.658  0.211  12.025
VolcanoView         11.635  0.152  11.858
ReadRRA             11.476  0.120  11.756
normalize.loess     11.334  0.137  11.484
CellCycleView       11.227  0.233  11.538
ScatterView         11.271  0.171  11.561
DensityDiffView     11.284  0.142  11.526
ReadBeta            11.141  0.111  11.458
NormalizeBeta       10.502  0.146  10.722
getOrg              10.189  0.094  10.309
TransGeneID         10.131  0.146  25.907
HeatmapView          9.929  0.122  10.164
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-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/3.5/Resources/library’
* installing *source* package ‘MAGeCKFlute’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (MAGeCKFlute)

Tests output


Example timings

MAGeCKFlute.Rcheck/MAGeCKFlute-Ex.timings

nameusersystemelapsed
BatchRemove0.9050.0340.948
CellCycleView11.227 0.23311.538
CorrView0.7360.0100.754
CutoffCalling0.0030.0000.004
DensityDiffView11.284 0.14211.526
DensityView12.980 0.18213.469
EnrichAB12.273 0.13012.631
EnrichSquare12.473 0.25913.024
EnrichedGSEView0.0000.0010.000
EnrichedGeneView18.617 0.25917.226
EnrichedView13.776 0.36314.216
FluteMLE0.0010.0020.004
FluteRRA0.0020.0010.003
HeatmapView 9.929 0.12210.164
IdentBarView0.2140.0030.217
KeggPathwayView0.0210.0050.027
MAView19.414 0.22419.807
MapRatesView0.5460.0050.560
NormalizeBeta10.502 0.14610.722
RankView12.327 0.13512.573
ReadBeta11.141 0.11111.458
ReadRRA11.476 0.12011.756
ReadsgRRA0.8680.0490.925
ScatterView11.271 0.17111.561
Selector0.2770.0050.287
SquareView12.251 0.18912.563
TransGeneID10.131 0.14625.907
ViolinView11.658 0.21112.025
VolcanoView11.635 0.15211.858
arrangePathview23.123 0.68525.714
countsummary0.0070.0020.009
enrich.GSE0.0130.0000.013
enrich.HGT11.798 0.24612.154
enrich.ORT20.375 0.23620.773
enrichment_analysis12.029 0.19012.332
getOrg10.189 0.09410.309
mle.gene_summary0.0340.0060.040
normalize.loess11.334 0.13711.484
rra.gene_summary0.0280.0050.033
rra.sgrna_summary0.1550.0210.176
sgRankView0.5640.0370.602