Multiple platform build/check report for BioC 3.14 - CHECK results for CrispRVariants on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	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*

Package: CrispRVariants

Version: 1.22.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrispRVariants.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CrispRVariants_1.22.0.tar.gz

StartedAt: 2022-04-12 17:58:48 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 18:05:19 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 390.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: CrispRVariants.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CrispRVariants.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CrispRVariants_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CrispRVariants.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CrispRVariants/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrispRVariants' 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 'CrispRVariants' 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 ... WARNING
'::' or ':::' import not declared from: 'SummarizedExperiment'
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'indelLabels'
* 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 ... WARNING
Codoc mismatches from documentation object 'arrangePlots':
arrangePlots
  Code: function(top.plot, left.plot, right.plot, fig.height = NULL,
                 col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6),
                 left.plot.margin = grid::unit(c(0.1, 0.2, 3, 0.2),
                 "lines"))
  Docs: function(top.plot, left.plot, right.plot, fig.height = NULL,
                 col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6),
                 left.plot.margin = grid::unit(c(0.1, 0, 3, 0.2),
                 "lines"))
  Mismatches in argument default values:
    Name: 'left.plot.margin' Code: grid::unit(c(0.1, 0.2, 3, 0.2), "lines") Docs: grid::unit(c(0.1, 0, 3, 0.2), "lines")

Codoc mismatches from documentation object 'indelLabels':
indelLabels
  Code: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops =
                 c("I", "D", "N"), regions = NULL, as.string = TRUE,
                 ...)
  Docs: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops =
                 c("I", "D", "N"), regions = NULL, ...)
  Argument names in code not in docs:
    as.string
  Mismatches in argument names:
    Position: 6 Code: as.string Docs: ...

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... 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
plotVariants    7.44   0.16    7.60
CrisprSet-class 5.25   0.78    6.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotVariants    7.69   0.16    7.85
mergeCrisprSets 5.51   0.02    5.53
CrisprSet-class 5.14   0.04    5.18
* 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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CrispRVariants.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CrispRVariants_1.22.0.tar.gz && rm -rf CrispRVariants.buildbin-libdir && mkdir CrispRVariants.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrispRVariants.buildbin-libdir CrispRVariants_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CrispRVariants_1.22.0.zip && rm CrispRVariants_1.22.0.tar.gz CrispRVariants_1.22.0.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
  6 1394k    6 86281    0     0   317k      0  0:00:04 --:--:--  0:00:04  317k
 77 1394k   77 1079k    0     0   854k      0  0:00:01  0:00:01 --:--:--  854k
100 1394k  100 1394k    0     0   960k      0  0:00:01  0:00:01 --:--:--  961k

install for i386

* installing *source* package 'CrispRVariants' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CrispRVariants'
    finding HTML links ... done
    CrisprRun-class                         html  
    CrisprSet-class                         html  
    abifToFastq                             html  
    addClipped                              html  
    addCodonFrame                           html  
    alleleLabelsHelpers                     html  
    alleles                                 html  
    alns                                    html  
    annotateGenePlot                        html  
    arrangePlots                            html  
    barplotAlleleFreqs                      html  
    collapsePairs                           html  
    consensusSeqs                           html  
    dispatchDots                            html  
    excludeFromBam                          html  
    explodeCigarOpCombs                     html  
    findChimeras                            html  
    findSNVs                                html  
    getAxisCoords                           html  
    getChimeras                             html  
    getInsertionsTable                      html  
    gol_clutch1                             html  
    indelCounts                             html  
    indelLabels                             html  
    intersperse                             html  
    makeAlignmentTilePlot                   html  
    mergeChimeras                           html  
    mergeCrisprSets                         html  
    mismatchLabels                          html  
    mutationEfficiency                      html  
    narrowAlignments                        html  
    plotAlignments                          html  
    plotChimeras                            html  
    plotFreqHeatmap                         html  
    plotVariants                            html  
    rcAlns                                  html  
    readTargetBam                           html  
    readsByPCRPrimer                        html  
    readsToTarget                           html  
    refFromAlns                             html  
    reverseCigar                            html  
    rmMultiPCRChimera                       html  
    selectAlnRegionsHelpers                 html  
    selectOps                               html  
    seqsToAln                               html  
    setDNATileColours                       html  
    setMismatchTileColours                  html  
    transformAlnsToLong                     html  
    variantCounts                           html  
    writeFastq                              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 'CrispRVariants' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrispRVariants' as CrispRVariants_1.22.0.zip
* DONE (CrispRVariants)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CrispRVariants' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  23.34    1.59   24.92


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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)
> test_check("CrispRVariants")
Loading required package: CrispRVariants
Loading required package: ggplot2
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ]
> 
> proc.time()
   user  system elapsed 
  25.78    0.65   26.42

name	user	system	elapsed
CrisprRun-class	0.75	0.11	0.87
CrisprSet-class	5.25	0.78	6.22
abifToFastq	0.41	0.06	0.51
alleles	0.16	0.02	0.17
alns	0.14	0.01	0.16
barplotAlleleFreqs	0.73	0.05	0.78
consensusSeqs	0.39	0.00	0.39
dispatchDots	0.02	0.00	0.02
findChimeras	0.04	0.00	0.06
getChimeras	0.05	0.02	0.06
indelCounts	0.16	0.00	0.16
intersperse	0	0	0
mergeCrisprSets	4.83	0.01	4.84
mutationEfficiency	0.03	0.00	0.03
narrowAlignments	0.29	0.00	0.30
plotAlignments	0.74	0.00	0.74
plotChimeras	1.28	0.00	1.28
plotFreqHeatmap	0.26	0.00	0.26
plotVariants	7.44	0.16	7.60
readsToTarget	3.62	0.12	3.75
selectAlnRegionsHelpers	0	0	0
variantCounts	0.03	0.00	0.03

name	user	system	elapsed
CrisprRun-class	0.78	0.07	0.85
CrisprSet-class	5.14	0.04	5.18
abifToFastq	0.23	0.03	0.27
alleles	0.13	0.00	0.12
alns	0.09	0.00	0.09
barplotAlleleFreqs	0.8	0.0	0.8
consensusSeqs	0.5	0.0	0.5
dispatchDots	0.01	0.00	0.02
findChimeras	0.04	0.00	0.03
getChimeras	0.03	0.00	0.03
indelCounts	0.11	0.00	0.11
intersperse	0	0	0
mergeCrisprSets	5.51	0.02	5.53
mutationEfficiency	0.03	0.00	0.03
narrowAlignments	0.3	0.0	0.3
plotAlignments	0.92	0.00	0.93
plotChimeras	1.4	0.0	1.4
plotFreqHeatmap	0.36	0.03	0.39
plotVariants	7.69	0.16	7.85
readsToTarget	4.77	0.02	4.78
selectAlnRegionsHelpers	0	0	0
variantCounts	0.03	0.00	0.03

CHECK results for CrispRVariants on tokay2

Summary

Command output

Installation output

Tests output

Example timings