Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:06:02 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 Chicago on tokay2


To the developers/maintainers of the Chicago package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Chicago.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 296/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.22.0  (landing page)
Mikhail Spivakov
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/Chicago
git_branch: RELEASE_3_14
git_last_commit: c377e14
git_last_commit_date: 2021-10-26 12:23:53 -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: Chicago
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Chicago.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Chicago_1.22.0.tar.gz
StartedAt: 2022-01-16 18:15:13 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 18:18:29 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 196.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Chicago.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Chicago_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Chicago.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 'Chicago/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Chicago' version '1.22.0'
* 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 'Chicago' 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 17.42   3.91   20.53
exportResults      11.91   0.89   12.80
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 16.92   3.58   18.79
exportResults      13.08   0.61   13.68
* 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: OK


Installation output

Chicago.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Chicago_1.22.0.tar.gz && rm -rf Chicago.buildbin-libdir && mkdir Chicago.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Chicago.buildbin-libdir Chicago_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Chicago_1.22.0.zip && rm Chicago_1.22.0.tar.gz Chicago_1.22.0.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  433k  100  433k    0     0  2330k      0 --:--:-- --:--:-- --:--:-- 2341k

install for i386

* installing *source* package 'Chicago' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Chicago'
    finding HTML links ... done
    Chicago-package                         html  
    cdUnitTest                              html  
    chicagoData                             html  
    chicagoPipeline                         html  
    copyCD                                  html  
    defaultSettings                         html  
    estimateBrownianComponent               html  
    estimateDistFun                         html  
    estimateTechnicalNoise                  html  
    exportResults                           html  
    getPvals                                html  
    getScores                               html  
    getSkOnly                               html  
    mergeSamples                            html  
    modifySettings                          html  
    normaliseBaits                          html  
    normaliseOtherEnds                      html  
    overlapFragWithFeatures                 html  
    finding level-2 HTML links ... done

    peakEnrichment4Features                 html  
    plotBaits                               html  
    plotDistFun                             html  
    readAndMerge                            html  
    readSample                              html  
    setExperiment                           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 'Chicago' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Chicago' as Chicago_1.22.0.zip
* DONE (Chicago)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Chicago' successfully unpacked and MD5 sums checked

Tests output

Chicago.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.

> library(testthat)
> library(Chicago)
Loading required package: data.table

Welcome to CHiCAGO - version 1.22.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
> 
> test_check("Chicago")
Read 4 items
Read 4 items
Read 4 items
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   4.09    0.51    4.43 

Chicago.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.

> library(testthat)
> library(Chicago)
Loading required package: data.table

Welcome to CHiCAGO - version 1.22.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
> 
> test_check("Chicago")
Read 4 items
Read 4 items
Read 4 items
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   4.32    0.35    4.53 

Example timings

Chicago.Rcheck/examples_i386/Chicago-Ex.timings

nameusersystemelapsed
cdUnitTest0.060.020.12
chicagoData000
chicagoPipeline0.040.030.08
copyCD0.020.000.01
defaultSettings000
estimateBrownianComponent0.330.010.38
estimateDistFun0.030.000.03
estimateTechnicalNoise0.110.020.13
exportResults11.91 0.8912.80
getPvals0.160.000.12
getScores0.110.010.13
getSkOnly0.180.110.32
mergeSamples1.160.051.21
modifySettings0.060.000.06
normaliseBaits0.110.000.11
normaliseOtherEnds17.42 3.9120.53
overlapFragWithFeatures0.030.040.08
peakEnrichment4Features0.850.501.34
plotBaits0.170.100.27
plotDistFun0.050.010.06
readAndMerge0.110.070.17
readSample0.000.070.08
setExperiment0.040.000.05

Chicago.Rcheck/examples_x64/Chicago-Ex.timings

nameusersystemelapsed
cdUnitTest0.060.000.07
chicagoData000
chicagoPipeline0.050.000.05
copyCD000
defaultSettings000
estimateBrownianComponent0.220.000.22
estimateDistFun0.010.000.01
estimateTechnicalNoise0.080.010.10
exportResults13.08 0.6113.68
getPvals0.140.000.18
getScores0.100.000.09
getSkOnly0.140.020.16
mergeSamples0.180.030.21
modifySettings0.070.000.07
normaliseBaits0.270.000.27
normaliseOtherEnds16.92 3.5818.79
overlapFragWithFeatures0.120.000.13
peakEnrichment4Features1.040.081.11
plotBaits0.180.030.22
plotDistFun0.070.000.06
readAndMerge0.070.030.11
readSample0.030.010.05
setExperiment0.020.020.03