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This page was generated on 2022-01-14 13:06:02 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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 basecallQC on tokay2


To the developers/maintainers of the basecallQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basecallQC.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 115/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.18.0  (landing page)
Thomas Carroll
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: RELEASE_3_14
git_last_commit: 503470b
git_last_commit_date: 2021-10-26 12:34:33 -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: basecallQC
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:basecallQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings basecallQC_1.18.0.tar.gz
StartedAt: 2022-01-13 15:43:12 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 15:54:12 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 660.1 seconds
RetCode: 0
Status:   OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:basecallQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings basecallQC_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.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 'basecallQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'basecallQC' version '1.18.0'
* 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 'basecallQC' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
reportBCL         8.22   0.64   11.59
passFilterBoxplot 5.99   0.17    6.16
basecallQC        5.79   0.05    5.92
baseCallMetrics   4.97   0.78    6.58
demuxBarplot      5.38   0.08    5.45
makeFQTable       4.97   0.14    5.11
passFilterBar     4.98   0.11    5.09
demuxBoxplot      5.05   0.00    5.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
reportBCL             8.47   0.46   10.22
makeFQTable           5.95   0.00    5.95
summaryDemuxTable     5.93   0.00    5.93
baseCallMetrics       5.46   0.03    5.48
basecallQC            5.36   0.02    5.77
summaryConvStatsTable 5.25   0.01    5.27
demuxBoxplot          5.01   0.03    5.04
* 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

basecallQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/basecallQC_1.18.0.tar.gz && rm -rf basecallQC.buildbin-libdir && mkdir basecallQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=basecallQC.buildbin-libdir basecallQC_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL basecallQC_1.18.0.zip && rm basecallQC_1.18.0.tar.gz basecallQC_1.18.0.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  661k  100  661k    0     0  2771k      0 --:--:-- --:--:-- --:--:-- 2779k

install for i386

* installing *source* package 'basecallQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'basecallQC'
    finding HTML links ... done
    BCL2FastQparams                         html  
    baseCallMetrics                         html  
    basecallQC                              html  
    createBCLcommand                        html  
    createBasemasks                         html  
    demultiplexMetrics                      html  
    demuxBarplot                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/demuxBarplot+2CbasecallQC-method.html
    demuxBoxplot                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/demuxBoxplot+2CbasecallQC-method.html
    indexlengths                            html  
    interOpsReport                          html  
    makeFQTable                             html  
    passFilterBar                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/passFilterBar+2CbasecallQC-method.html
    passFilterBoxplot                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/passFilterBoxplot+2CbasecallQC-method.html
    passFilterTileplot                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/passFilterTilePlot+2CbasecallQC-method.html
    readlengths                             html  
    reportBCL                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/reportBCL+2CbasecallQC-method.html
    summaryConvStatsTable                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/summaryConvStatsTable+2CbasecallQC-method.html
    summaryDemuxTable                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/basecallQC.buildbin-libdir/00LOCK-basecallQC/00new/basecallQC/help/summaryDemuxTable+2CbasecallQC-method.html
    validateBCLSheet                        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 'basecallQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'basecallQC' as basecallQC_1.18.0.zip
* DONE (basecallQC)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'basecallQC' successfully unpacked and MD5 sums checked

Tests output

basecallQC.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(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
> 
> test_check("basecallQC")
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  19.68    1.93   21.60 

basecallQC.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(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
> 
> test_check("basecallQC")
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  23.00    0.57   23.56 

Example timings

basecallQC.Rcheck/examples_i386/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.310.000.31
baseCallMetrics4.970.786.58
basecallQC5.790.055.92
createBCLcommand0.40.00.4
createBasemasks0.460.000.46
demultiplexMetrics0.100.000.11
demuxBarplot5.380.085.45
demuxBoxplot5.050.005.05
indexlengths0.030.000.03
interOpsReport0.030.000.03
makeFQTable4.970.145.11
passFilterBar4.980.115.09
passFilterBoxplot5.990.176.16
passFilterTileplot4.780.004.78
readlengths0.030.000.03
reportBCL 8.22 0.6411.59
summaryConvStatsTable4.870.034.91
summaryDemuxTable4.420.004.42
validateBCLSheet0.110.000.11

basecallQC.Rcheck/examples_x64/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.200.000.21
baseCallMetrics5.460.035.48
basecallQC5.360.025.77
createBCLcommand0.40.00.4
createBasemasks0.390.000.39
demultiplexMetrics0.060.000.06
demuxBarplot4.930.034.96
demuxBoxplot5.010.035.04
indexlengths0.030.000.04
interOpsReport0.020.000.01
makeFQTable5.950.005.95
passFilterBar4.920.024.94
passFilterBoxplot4.850.014.86
passFilterTileplot4.860.004.86
readlengths0.030.000.03
reportBCL 8.47 0.4610.22
summaryConvStatsTable5.250.015.27
summaryDemuxTable5.930.005.93
validateBCLSheet0.080.020.10