##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TarSeqQC.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TarSeqQC_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TarSeqQC.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.25.1'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
TargetExperiment-class             13.33   0.42  220.53
TargetExperiment-plotRegion         2.12   0.11   64.22
TargetExperiment-plotFeature        2.11   0.06   47.29
TargetExperiment-plotNtdPercentage  1.47   0.06   27.63
TargetExperiment-constructor        1.33   0.10   28.48
pileupCounts                        1.25   0.06   26.08
TargetExperiment-readFrequencies    0.83   0.03   15.24
plotInOutFeatures                   0.82   0.04   15.31
TargetExperiment-summarizePanel     0.76   0.02   13.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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
  'D:/biocbuild/bbs-3.15-bioc/meat/TarSeqQC.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TarSeqQC
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-TarSeqQC/00new/TarSeqQC/help/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
* DONE (TarSeqQC)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("TarSeqQC")

Attaching package: 'BiocGenerics'

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.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


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



RUNIT TEST PROTOCOL -- Thu Mar 17 20:39:44 2022 
*********************************************** 
Number of test functions: 33 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TarSeqQC RUnit Tests - 33 test functions, 0 errors, 0 failures
Number of test functions: 33 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
2: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
> 
> proc.time()
   user  system elapsed 
  14.40    0.76  107.68