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CHECK report for COCOA on tokay1

This page was generated on 2021-05-06 12:30:26 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the COCOA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 346/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COCOA 2.4.0  (landing page)
John Lawson
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/COCOA
Branch: RELEASE_3_12
Last Commit: 9a75d3f
Last Changed Date: 2020-10-27 11:40:00 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: COCOA
Version: 2.4.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COCOA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings COCOA_2.4.0.tar.gz
StartedAt: 2021-05-06 01:38:51 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:47:13 -0400 (Thu, 06 May 2021)
EllapsedTime: 502.3 seconds
RetCode: 0
Status:   OK   
CheckDir: COCOA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COCOA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings COCOA_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/COCOA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'COCOA/DESCRIPTION' ... OK
* this is package 'COCOA' version '2.4.0'
* 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 'COCOA' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
prepare_Rd: getGammaPVal.Rd:67-69: Dropping empty section \examples
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runCOCOAPerm 13.88   1.12   15.00
runCOCOA      9.37   0.27   10.51
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runCOCOAPerm 15.79   0.51   20.72
runCOCOA      9.83   0.25   10.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/COCOA.Rcheck/00check.log'
for details.



Installation output

COCOA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/COCOA_2.4.0.tar.gz && rm -rf COCOA.buildbin-libdir && mkdir COCOA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=COCOA.buildbin-libdir COCOA_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL COCOA_2.4.0.zip && rm COCOA_2.4.0.tar.gz COCOA_2.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1691k  100 1691k    0     0  26.5M      0 --:--:-- --:--:-- --:--:-- 27.0M

install for i386

* installing *source* package 'COCOA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'COCOA'
    finding HTML links ... done
    COCOA                                   html  
    aggregateSignal                         html  
    aggregateSignalGRList                   html  
    atf3_chr1                               html  
    brcaATACCoord1                          html  
    brcaATACData1                           html  
    brcaMCoord1                             html  
    brcaMetadata                            html  
    brcaMethylData1                         html  
    brcaPCScores                            html  
    brcaPCScores657                         html  
    convertToFromNullDist                   html  
    esr1_chr1                               html  
    gata3_chr1                              html  
    getGammaPVal                            html  
    getMetaRegionProfile                    html  
    getPermStat                             html  
    getTopRegions                           html  
    nrf1_chr1                               html  
    plotAnnoScoreDist                       html  
    regionQuantileByTargetVar               html  
    rsRankingIndex                          html  
    rsScoreHeatmap                          html  
    rsScores                                html  
    runCOCOA                                html  
    runCOCOAPerm                            html  
    signalAlongAxis                         html  
** 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

install for x64

* installing *source* package 'COCOA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COCOA' as COCOA_2.4.0.zip
* DONE (COCOA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'COCOA' successfully unpacked and MD5 sums checked

Tests output

COCOA.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(COCOA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("COCOA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  17.25    2.14   19.39 

COCOA.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(COCOA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("COCOA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  14.67    0.65   15.37 

Example timings

COCOA.Rcheck/examples_i386/COCOA-Ex.timings

nameusersystemelapsed
aggregateSignal0.510.030.54
aggregateSignalGRList0.740.080.81
convertToFromNullDist0.020.000.02
getMetaRegionProfile2.730.453.18
getPermStat0.030.050.08
getTopRegions0.360.050.50
plotAnnoScoreDist0.650.081.03
regionQuantileByTargetVar0.540.120.73
rsRankingIndex0.000.020.02
rsScoreHeatmap0.030.010.05
runCOCOA 9.37 0.2710.51
runCOCOAPerm13.88 1.1215.00
signalAlongAxis0.360.030.41

COCOA.Rcheck/examples_x64/COCOA-Ex.timings

nameusersystemelapsed
aggregateSignal0.400.020.43
aggregateSignalGRList0.490.030.51
convertToFromNullDist0.040.000.03
getMetaRegionProfile4.180.074.26
getPermStat0.050.000.05
getTopRegions0.310.020.33
plotAnnoScoreDist0.640.020.66
regionQuantileByTargetVar0.450.040.55
rsRankingIndex0.020.020.03
rsScoreHeatmap0.030.000.03
runCOCOA 9.83 0.2510.09
runCOCOAPerm15.79 0.5120.72
signalAlongAxis0.320.000.32