Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:08 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 COCOA on tokay2


To the developers/maintainers of the COCOA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COCOA.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 364/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COCOA 2.8.0  (landing page)
John Lawson
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/COCOA
git_branch: RELEASE_3_14
git_last_commit: 30a31c3
git_last_commit_date: 2021-10-26 12:47:47 -0500 (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: COCOA
Version: 2.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COCOA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings COCOA_2.8.0.tar.gz
StartedAt: 2022-01-20 17:51:29 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 17:58:35 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 425.9 seconds
RetCode: 0
Status:   OK  
CheckDir: COCOA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:COCOA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings COCOA_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/COCOA.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.8.0'
* 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 10.71   0.56   11.27
runCOCOA      6.59   0.44    7.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
runCOCOAPerm 9.78   0.44   10.22
runCOCOA     4.95   0.14    5.09
* 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-3.14-bioc/meat/COCOA.Rcheck/00check.log'
for details.



Installation output

COCOA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/COCOA_2.8.0.tar.gz && rm -rf COCOA.buildbin-libdir && mkdir COCOA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=COCOA.buildbin-libdir COCOA_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL COCOA_2.8.0.zip && rm COCOA_2.8.0.tar.gz COCOA_2.8.0.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
  3 1694k    3 66025    0     0  27331      0  0:01:03  0:00:02  0:01:01 27339
 20 1694k   20  346k    0     0   133k      0  0:00:12  0:00:02  0:00:10  133k
100 1694k  100 1694k    0     0   509k      0  0:00:03  0:00:03 --:--:--  509k

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_2.8.0.zip
* DONE (COCOA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'COCOA' successfully unpacked and MD5 sums checked

Tests output

COCOA.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

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 
  14.00    1.25   15.26 

COCOA.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

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 
  16.65    0.64   17.29 

Example timings

COCOA.Rcheck/examples_i386/COCOA-Ex.timings

nameusersystemelapsed
aggregateSignal1.300.031.33
aggregateSignalGRList0.460.050.52
convertToFromNullDist0.020.000.02
getMetaRegionProfile2.250.372.62
getPermStat0.030.000.03
getTopRegions0.250.020.27
plotAnnoScoreDist0.390.050.44
regionQuantileByTargetVar0.290.060.36
rsRankingIndex0.000.010.01
rsScoreHeatmap0.020.020.03
runCOCOA6.590.447.03
runCOCOAPerm10.71 0.5611.27
signalAlongAxis0.250.030.28

COCOA.Rcheck/examples_x64/COCOA-Ex.timings

nameusersystemelapsed
aggregateSignal0.470.000.47
aggregateSignalGRList1.280.021.30
convertToFromNullDist000
getMetaRegionProfile2.410.122.53
getPermStat0.000.020.02
getTopRegions0.340.030.37
plotAnnoScoreDist0.470.010.49
regionQuantileByTargetVar0.360.000.36
rsRankingIndex0.010.000.01
rsScoreHeatmap0.020.000.02
runCOCOA4.950.145.09
runCOCOAPerm 9.78 0.4410.22
signalAlongAxis0.190.030.22