Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:06 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 palomino4


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? 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 113/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
basecallQC 1.21.0  (landing page)
Thomas Carroll
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/basecallQC
git_branch: master
git_last_commit: 4bf056c
git_last_commit_date: 2022-04-26 11:40:14 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: basecallQC
Version: 1.21.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:basecallQC.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings basecallQC_1.21.0.tar.gz
StartedAt: 2022-06-23 23:20:50 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:27:18 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 387.3 seconds
RetCode: 0
Status:   OK  
CheckDir: basecallQC.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:basecallQC.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings basecallQC_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/basecallQC.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'basecallQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'basecallQC' version '1.21.0'
* 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
* 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
reportBCL             8.00   0.66    9.80
makeFQTable           6.08   0.12    6.20
demuxBoxplot          5.81   0.18    5.98
baseCallMetrics       5.62   0.29    5.92
passFilterBoxplot     5.49   0.14    5.63
demuxBarplot          5.33   0.06    5.39
summaryDemuxTable     5.20   0.05    5.25
summaryConvStatsTable 5.09   0.10    5.20
passFilterTileplot    4.95   0.12    5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/basecallQC_1.21.0.tar.gz && rm -rf basecallQC.buildbin-libdir && mkdir basecallQC.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=basecallQC.buildbin-libdir basecallQC_1.21.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL basecallQC_1.21.0.zip && rm basecallQC_1.21.0.tar.gz basecallQC_1.21.0.zip
###
##############################################################################
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  % 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  5868k      0 --:--:-- --:--:-- --:--:-- 5906k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'basecallQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'basecallQC' as basecallQC_1.21.0.zip
* DONE (basecallQC)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'basecallQC' successfully unpacked and MD5 sums checked

Tests output

basecallQC.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 15 | SKIP 0 | PASS 5 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  23.93    0.93   24.87 

Example timings

basecallQC.Rcheck/basecallQC-Ex.timings

nameusersystemelapsed
BCL2FastQparams0.190.000.21
baseCallMetrics5.620.295.92
basecallQC4.920.085.00
createBCLcommand0.610.000.61
createBasemasks0.580.000.58
demultiplexMetrics0.090.000.10
demuxBarplot5.330.065.39
demuxBoxplot5.810.185.98
indexlengths0.060.000.06
interOpsReport0.080.000.08
makeFQTable6.080.126.20
passFilterBar4.590.144.74
passFilterBoxplot5.490.145.63
passFilterTileplot4.950.125.08
readlengths0.050.000.04
reportBCL8.000.669.80
summaryConvStatsTable5.090.105.20
summaryDemuxTable5.200.055.25
validateBCLSheet0.130.000.13