Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:05:57 -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 abseqR on tokay2


To the developers/maintainers of the abseqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/abseqR.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 9/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
abseqR 1.12.0  (landing page)
JiaHong Fong
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/abseqR
git_branch: RELEASE_3_14
git_last_commit: 2fdfd3e
git_last_commit_date: 2021-10-26 12:48:00 -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: abseqR
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:abseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings abseqR_1.12.0.tar.gz
StartedAt: 2022-01-13 15:12:29 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 15:17:01 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 271.9 seconds
RetCode: 0
Status:   OK  
CheckDir: abseqR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:abseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings abseqR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/abseqR.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 'abseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'abseqR' version '1.12.0'
* package encoding: UTF-8
* 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 'abseqR' 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 ... NOTE
.aminoAcidBar: no visible binding for global variable 'position'
.aminoAcidBar: no visible binding for global variable 'proportion'
.aminoAcidBar: no visible binding for global variable 'aa'
.boxPlot: no visible binding for global variable 'x'
.boxPlot: no visible binding for global variable 'y'
.cloneDistHist: no visible binding for global variable 'prop'
.cloneDistHist: no visible binding for global variable '..count..'
.cloneDistMarginal: no visible binding for global variable 'prop'
.cloneDistMarginal: no visible binding for global variable '..scaled..'
.hmFromMatrix: no visible binding for global variable 'Var2'
.hmFromMatrix: no visible binding for global variable 'Var1'
.hmFromMatrix: no visible binding for global variable 'value'
.plotDist: no visible binding for global variable 'x'
.plotDist: no visible binding for global variable 'y'
.plotDuplication: no visible binding for global variable 'x'
.plotDuplication: no visible binding for global variable 'y'
.plotDuplication: no visible binding for global variable 'region'
.plotRarefaction: no visible binding for global variable 'x'
.plotRarefaction: no visible binding for global variable 'y'
.plotRarefaction: no visible binding for global variable 'region'
.plotRarefaction: no visible binding for global variable 'ci'
.plotRarefaction: no visible binding for global variable 'compound'
.plotRecapture: no visible binding for global variable 'x'
.plotRecapture: no visible binding for global variable 'y'
.plotRecapture: no visible binding for global variable 'region'
.plotRecapture: no visible binding for global variable 'ci'
.plotRecapture: no visible binding for global variable 'compound'
.plotSpectratype: no visible binding for global variable 'percent'
.productivityPlot: no visible binding for global variable 'Percentage'
.productivityPlot: no visible binding for global variable 'Reason'
.regionAnalysis: no visible binding for global variable 'cdr3'
.regionAnalysis: no visible binding for global variable 'value'
.regionAnalysis: no visible binding for global variable 'variable'
.scatterPlot: no visible binding for global variable 'Count.x'
.scatterPlot: no visible binding for global variable 'Count.y'
.scatterPlotComplex: no visible binding for global variable 'prop.x'
.scatterPlotComplex: no visible binding for global variable 'prop.y'
.topNDist: no visible binding for global variable 'normPerc'
.topNDist: no visible binding for global variable 'Clonotype'
Undefined global functions or variables:
  ..count.. ..scaled.. Clonotype Count.x Count.y Percentage Reason Var1
  Var2 aa cdr3 ci compound normPerc percent position prop prop.x prop.y
  proportion region value variable x y
* 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
AbSeqCRep-class 0.37   0.03    9.23
** running examples for arch 'x64' ... OK
* 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/abseqR.Rcheck/00check.log'
for details.



Installation output

abseqR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/abseqR_1.12.0.tar.gz && rm -rf abseqR.buildbin-libdir && mkdir abseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=abseqR.buildbin-libdir abseqR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL abseqR_1.12.0.zip && rm abseqR_1.12.0.tar.gz abseqR_1.12.0.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 1519k  100 1519k    0     0  5208k      0 --:--:-- --:--:-- --:--:-- 5220k

install for i386

* installing *source* package 'abseqR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'abseqR'
    finding HTML links ... done
    AbSeqCRep-class                         html  
    AbSeqRep-class                          html  
    abseqReport                             html  
    dot-UTR5Analysis                        html  
    dot-abundanceAnalysis                   html  
    dot-abundancePlot                       html  
    dot-alignQualityHeatMaps                html  
    dot-allPrimerNames                      html  
    dot-aminoAcidBar                        html  
    dot-aminoAcidPlot                       html  
    dot-analyzeUpstreamValidity             html  
    dot-annotAnalysis                       html  
    dot-asRepertoireAlignLen                html  
    dot-asRepertoireBitscore                html  
    dot-asRepertoireChain                   html  
    dot-asRepertoireDir                     html  
    dot-asRepertoireList                    html  
    dot-asRepertoireName                    html  
    dot-asRepertoirePrimer3                 html  
    dot-asRepertoirePrimer5                 html  
    dot-asRepertoireQueryStart              html  
    dot-asRepertoireSubjectStart            html  
    dot-asRepertoireUpstream                html  
    dot-boxPlot                             html  
    dot-calculateDInd                       html  
    dot-calculateDiversityEstimates         html  
    dot-canonicalizeTitle                   html  
    dot-capitalize                          html  
    dot-checkVert                           html  
    dot-cloneDistHist                       html  
    dot-cloneDistMarginal                   html  
    dot-clonotypeAnalysis                   html  
    dot-collateReports                      html  
    dot-commonPrimerNames                   html  
    dot-correlationTest                     html  
    dot-distanceMeasure                     html  
    dot-diversityAnalysis                   html  
    dot-emptyPlot                           html  
    dot-findRepertoires                     html  
    dot-generateAllSpectratypes             html  
    dot-generateDelayedReport               html  
    dot-generateReport                      html  
    dot-getLineTypes                        html  
    dot-getTotal                            html  
    dot-hmFromMatrix                        html  
    dot-inferAnalyzed                       html  
    dot-loadMatrixFromDF                    html  
    dot-loadSamplesFromString               html  
    dot-pairwiseComparison                  html  
    dot-plotCirclize                        html  
    dot-plotDist                            html  
    dot-plotDiversityCurves                 html  
    dot-plotDuplication                     html  
    dot-plotErrorDist                       html  
    dot-plotIGVErrors                       html  
    dot-plotIGVUpstreamLenDist              html  
    dot-plotIGVUpstreamLenDistDetailed      html  
    dot-plotPrimerIGVStatus                 html  
    dot-plotPrimerIntegrity                 html  
    dot-plotRarefaction                     html  
    dot-plotRecapture                       html  
    dot-plotSamples                         html  
    dot-plotSpectratype                     html  
    dot-plotUpstreamLength                  html  
    dot-plotUpstreamLengthDist              html  
    dot-primerAnalysis                      html  
    dot-prodDistPlot                        html  
    dot-productivityAnalysis                html  
    dot-productivityPlot                    html  
    dot-readSummary                         html  
    dot-regionAnalysis                      html  
    dot-reportLBE                           html  
    dot-saveAs                              html  
    dot-scatterPlot                         html  
    dot-scatterPlotComplex                  html  
    dot-secretionSignalAnalysis             html  
    dot-substituteStringInFile              html  
    dot-summarySE                           html  
    dot-topNDist                            html  
    dot-vennIntersection                    html  
    plus-AbSeqCRep-AbSeqCRep-method         html  
    plus-AbSeqCRep-AbSeqRep-method          html  
    plus-AbSeqRep-AbSeqCRep-method          html  
    plus-AbSeqRep-AbSeqRep-method           html  
    report                                  html  
*** copying figures
** 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 'abseqR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'abseqR' as abseqR_1.12.0.zip
* DONE (abseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'abseqR' successfully unpacked and MD5 sums checked

Tests output

abseqR.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(abseqR)
> 
> test_check("abseqR")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
  40.65    2.29   59.54 

abseqR.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(abseqR)
> 
> test_check("abseqR")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 30 ]
> 
> proc.time()
   user  system elapsed 
  43.79    1.89   47.67 

Example timings

abseqR.Rcheck/examples_i386/abseqR-Ex.timings

nameusersystemelapsed
AbSeqCRep-class0.370.039.23
AbSeqRep-class0.070.100.16
abseqReport0.130.060.18
plus-AbSeqCRep-AbSeqCRep-method0.070.140.22
plus-AbSeqCRep-AbSeqRep-method0.110.110.22
plus-AbSeqRep-AbSeqCRep-method0.080.110.18
plus-AbSeqRep-AbSeqRep-method0.090.120.22
report0.090.080.17

abseqR.Rcheck/examples_x64/abseqR-Ex.timings

nameusersystemelapsed
AbSeqCRep-class0.390.142.88
AbSeqRep-class0.090.060.15
abseqReport0.140.080.22
plus-AbSeqCRep-AbSeqCRep-method0.140.080.22
plus-AbSeqCRep-AbSeqRep-method0.080.140.22
plus-AbSeqRep-AbSeqCRep-method0.090.090.18
plus-AbSeqRep-AbSeqRep-method0.080.100.19
report0.060.070.14