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This page was generated on 2022-04-13 12:08:15 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MAGeCKFlute on machv2


To the developers/maintainers of the MAGeCKFlute package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/MAGeCKFlute.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1036/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAGeCKFlute 1.14.0  (landing page)
Wubing Zhang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MAGeCKFlute
git_branch: RELEASE_3_14
git_last_commit: e03a467
git_last_commit_date: 2021-10-26 12:40:34 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MAGeCKFlute
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGeCKFlute_1.14.0.tar.gz
StartedAt: 2022-04-12 14:56:05 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:00:50 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 285.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MAGeCKFlute.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGeCKFlute_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MAGeCKFlute.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.14.0’
* 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 13.9Mb
  sub-directories of 1Mb or more:
    extdata  13.5Mb
* 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 ... NOTE
'library' or 'require' call to ‘pathview’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
arrangePathview: no visible global function definition for ‘pathview’
Undefined global functions or variables:
  pathview
* 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  8.628  0.220   8.865
TransGeneID 6.026  0.108   6.138
ReadGMT     4.002  0.084   5.382
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MAGeCKFlute.Rcheck/00check.log’
for details.



Installation output

MAGeCKFlute.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAGeCKFlute
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
BarView0.2000.0220.222
BatchRemove2.6090.0672.681
ConsistencyView0.5680.0320.603
CutoffCalling0.0060.0010.007
DensityDiffView0.6500.0330.685
DensityView0.5470.0110.560
EnrichAnalyzer0.0180.0010.020
EnrichedFilter0.0130.0010.014
EnrichedGeneView0.0120.0010.013
EnrichedView0.0140.0000.014
FluteMLE0.0000.0000.002
FluteRRA0.0020.0000.002
HeatmapView0.1680.0040.174
IdentBarView0.2090.0030.213
IncorporateDepmap0.1310.0040.136
MAView4.3150.0514.371
MapRatesView0.5090.0060.558
NormalizeBeta0.3790.0100.390
OmitCommonEssential0.1230.0040.127
RankView0.5730.0190.593
ReadBeta0.1130.0040.117
ReadGMT4.0020.0845.382
ReadRRA0.2110.0060.217
ReadsgRRA1.0840.0201.105
ResembleDepmap0.9470.0110.959
ScatterView0.6960.0190.717
Selector0.4160.0050.422
SquareView0.9220.0520.976
TransGeneID6.0260.1086.138
ViolinView1.0240.0281.053
VolcanoView1.3070.0421.352
arrangePathview0.1110.0040.116
enrich.GSE0.0150.0020.016
enrich.HGT4.7130.0964.831
enrich.ORT8.6280.2208.865
getCols0.0110.0000.012
getGeneAnn0.0010.0000.000
getOrg0.0020.0000.001
getOrtAnn000
gsGetter0.3320.0040.337
hclustView0.3940.0090.403
normalize.loess0.3550.0030.358
sgRankView2.0540.0342.090