##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TarSeqQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TarSeqQC_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TarSeqQC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TarSeqQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TarSeqQC' 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 'TarSeqQC' 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
plotNtdPercentage,TargetExperiment: no visible global function
  definition for 'path'
plotRegion,TargetExperiment: no visible global function definition for
  'path'
readFrequencies,TargetExperiment: no visible global function definition
  for 'path'
Undefined global functions or variables:
  path
* 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
TargetExperiment-class             19.86   0.58  493.97
TargetExperiment-plotRegion         3.67   0.19  151.71
TargetExperiment-plotFeature        2.76   0.19  146.21
pileupCounts                        1.89   0.13   82.24
TargetExperiment-plotNtdPercentage  1.89   0.08  103.79
TargetExperiment-constructor        1.85   0.08   26.67
TargetExperiment-readFrequencies    1.11   0.01   17.48
plotInOutFeatures                   1.12   0.00   18.22
TargetExperiment-summarizePanel     0.79   0.03   17.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
TargetExperiment-class             20.67   0.50  526.38
TargetExperiment-plotRegion         3.31   0.14  111.27
TargetExperiment-plotFeature        3.23   0.09  117.16
TargetExperiment-constructor        2.38   0.08   45.48
TargetExperiment-plotNtdPercentage  1.97   0.09   78.36
pileupCounts                        1.86   0.08   68.27
TargetExperiment-readFrequencies    1.28   0.02   16.61
plotInOutFeatures                   1.25   0.04   16.66
TargetExperiment-summarizePanel     0.82   0.02   16.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TarSeqQC_1.18.0.tar.gz && rm -rf TarSeqQC.buildbin-libdir && mkdir TarSeqQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TarSeqQC.buildbin-libdir TarSeqQC_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TarSeqQC_1.18.0.zip && rm TarSeqQC_1.18.0.tar.gz TarSeqQC_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 1792k  100 1792k    0     0  21.9M      0 --:--:-- --:--:-- --:--:-- 23.9M

install for i386

* installing *source* package 'TarSeqQC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TarSeqQC'
    finding HTML links ... done
    TEList                                  html  
    TarSeqQC-package                        html  
    TargetExperiment-biasExploration        html  
    TargetExperiment-buildFeaturePanel      html  
    TargetExperiment-buildReport            html  
    TargetExperiment-class                  html  
    TargetExperiment-constructor            html  
    TargetExperiment-getters                html  
    TargetExperiment-initialize             html  
    TargetExperiment-plot                   html  
    TargetExperiment-plotAttrExpl           html  
    TargetExperiment-plotAttrPerform        html  
    TargetExperiment-plotFeatPerform        html  
    TargetExperiment-plotFeature            html  
    TargetExperiment-plotGeneAttrPerFeat    html  
    TargetExperiment-plotMetaDataExpl       html  
    TargetExperiment-plotNtdPercentage      html  
    TargetExperiment-plotRegion             html  
    TargetExperiment-print                  html  
    TargetExperiment-readFrequencies        html  
    TargetExperiment-setters                html  
    TargetExperiment-show                   html  
    TargetExperiment-statistics             html  
    TargetExperiment-summarizePanel         html  
    TargetExperimentList-class              html  
    TargetExperimentList-constructor        html  
    TargetExperimentList-initialize         html  
    TargetExperimentList-plotGlobalAttrExpl
                                            html  
    TargetExperimentList-plotPoolPerformance
                                            html  
    ampliPanel                              html  
    ampliPanel2                             html  
    checkBedFasta                           html  
    myCounts                                html  
    object                                  html  
    pileupCounts                            html  
    plotInOutFeatures                       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 'TarSeqQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TarSeqQC' as TarSeqQC_1.18.0.zip
* DONE (TarSeqQC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TarSeqQC' successfully unpacked and MD5 sums checked

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("TarSeqQC")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename