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This page was generated on 2022-03-18 11:07:54 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


To the developers/maintainers of the MAGeCKFlute package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGeCKFlute.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1040/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAGeCKFlute 1.99.2  (landing page)
Wubing Zhang
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/MAGeCKFlute
git_branch: master
git_last_commit: 85fe2f2
git_last_commit_date: 2022-01-13 06:39:49 -0400 (Thu, 13 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MAGeCKFlute
Version: 1.99.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGeCKFlute.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.99.2.tar.gz
StartedAt: 2022-03-17 19:28:25 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:32:36 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 250.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MAGeCKFlute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGeCKFlute.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAGeCKFlute_1.99.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MAGeCKFlute.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAGeCKFlute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGeCKFlute' version '1.99.2'
* 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 whether package 'MAGeCKFlute' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.0Mb
  sub-directories of 1Mb or more:
    extdata  20.3Mb
* 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
MAView 7.75   0.17    7.92
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/MAGeCKFlute.Rcheck/00check.log'
for details.



Installation output

MAGeCKFlute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MAGeCKFlute' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2022-03-16
** help
*** installing help indices
  converting help for package 'MAGeCKFlute'
    finding HTML links ... done
    BarView                                 html  
    BatchRemove                             html  
    ConsistencyView                         html  
    CutoffCalling                           html  
    DensityDiffView                         html  
    DensityView                             html  
    EnrichAB                                html  
    EnrichAnalyzer                          html  
    EnrichSquare                            html  
    EnrichedFilter                          html  
    EnrichedGeneView                        html  
    EnrichedView                            html  
    FluteMLE                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/flutemle.html
    FluteRRA                                html  
    HeatmapView                             html  
    IdentBarView                            html  
    IncorporateDepmap                       html  
    MAView                                  html  
    MapRatesView                            html  
    NormalizeBeta                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/normalizebeta.html
    OmitCommonEssential                     html  
    RankView                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/rankview.html
    ReadBeta                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/readbeta.html
    ReadGMT                                 html  
    ReadRRA                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/readrra.html
    ReadsgRRA                               html  
    ResembleDepmap                          html  
    ScatterView                             html  
    Selector                                html  
    SquareView                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/squareview.html
    TransGeneID                             html  
    ViolinView                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/violinview.html
    VolcanoView                             html  
    arrangePathview                         html  
    enrich.GSE                              html  
    enrich.HGT                              html  
    enrich.ORT                              html  
    getCols                                 html  
    getGeneAnn                              html  
    getOrg                                  html  
    getOrtAnn                               html  
    gsGetter                                html  
    hclustView                              html  
    loadDepmap                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MAGeCKFlute/00new/MAGeCKFlute/help/LoadDepmap.html
    noEnrichPlot                            html  
    normalize.loess                         html  
    reexports                               html  
    retrieve_gs                             html  
    sgRankView                              html  
    writeGMT                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-03-16
** testing if installed package can be loaded from final location
snapshotDate(): 2022-03-16
** testing if installed package keeps a record of temporary installation path
* DONE (MAGeCKFlute)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'PanomiR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'recount3' is missing or broken
 done

Tests output


Example timings

MAGeCKFlute.Rcheck/MAGeCKFlute-Ex.timings

nameusersystemelapsed
BarView0.290.000.28
BatchRemove1.560.031.59
ConsistencyView0.720.130.84
CutoffCalling000
DensityDiffView0.890.010.91
DensityView0.820.000.81
EnrichAnalyzer0.010.000.00
EnrichedFilter0.020.000.01
EnrichedGeneView000
EnrichedView0.010.000.02
FluteMLE000
FluteRRA000
HeatmapView0.30.00.3
IdentBarView0.140.000.14
IncorporateDepmap0.160.000.15
MAView7.750.177.92
MapRatesView0.320.000.33
NormalizeBeta0.660.020.67
OmitCommonEssential000
RankView0.560.000.57
ReadBeta0.220.020.23
ReadRRA0.190.000.19
ReadsgRRA000
ResembleDepmap0.140.000.14
ScatterView2.640.072.72
Selector0.480.000.48
SquareView1.220.051.32
TransGeneID1.210.081.28
ViolinView0.860.080.93
VolcanoView1.400.061.47
arrangePathview0.240.000.24
enrich.GSE0.010.000.01
enrich.HGT1.530.111.64
enrich.ORT3.390.083.47
getCols0.020.000.01
getGeneAnn000
getOrg000
getOrtAnn000
gsGetter0.760.010.78
hclustView0.390.030.43
loadDepmap000
normalize.loess0.850.020.86
sgRankView0.100.000.11
writeGMT0.040.000.03