##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoStringNCTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings NanoStringNCTools_1.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/NanoStringNCTools.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 'NanoStringNCTools/DESCRIPTION' ... OK
* this is package 'NanoStringNCTools' version '1.3.1'
* 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 'NanoStringNCTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
autoplot.NanoStringRccSet : <anonymous>: warning in switch(x[2], A =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], B =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], C =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], D =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], E =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], G =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], H =
  qcCutoffs[["BindingDensity"]][["maximumBD"]], P =
  qcCutoffs[["BindingDensity"]][["maximumBDSprint"]], default =
  qcCutoffs[["BindingDensity"]][["maximumBD"]]): partial argument match
  of 'E' to 'EXPR'
setQCFlags,NanoStringRccSet : <anonymous>: warning in switch(x[2], A =
  maxBindDen, B = maxBindDen, C = maxBindDen, D = maxBindDen, E =
  maxBindDen, G = maxBindDen, H = maxBindDen, P = maxBindDenSprint,
  default = maxBindDen): partial argument match of 'E' to 'EXPR'
autoplot.NanoStringRccSet: no visible binding for global variable
  'xend'
autoplot.NanoStringRccSet: no visible binding for global variable
  'passingThreshold'
autoplot.NanoStringRccSet: no visible binding for global variable
  'GeomMean'
autoplot.NanoStringRccSet: no visible binding for global variable 'h'
autoplot.NanoStringRccSet: no visible binding for global variable
  'label'
Undefined global functions or variables:
  GeomMean h label passingThreshold xend
* 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/NanoStringNCTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL NanoStringNCTools
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'NanoStringNCTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NanoStringNCTools'
    finding HTML links ... done
    NanoStringRccSet-autoplot               html  
    NanoStringRccSet-class                  html  
    finding level-2 HTML links ... done

    SignatureSet                            html  
    geom_beeswarm_interactive               html  
    log2t                                   html  
    normalize                               html  
    readNanoStringRccSet                    html  
    readRccFile                             html  
    readRlfFile                             html  
    sScale                                  html  
    setQCFlags                              html  
    writeNanoStringRccSet                   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 (NanoStringNCTools)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'TCC' is missing or broken
 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.

> require("NanoStringNCTools") || stop("unable to load NanoStringNCTools package")
Loading required package: NanoStringNCTools
Loading required package: Biobase
Loading required package: BiocGenerics

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: ggplot2
[1] TRUE
> BiocGenerics:::testPackage("NanoStringNCTools")


RUNIT TEST PROTOCOL -- Thu Mar 17 19:44:41 2022 
*********************************************** 
Number of test functions: 52 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NanoStringNCTools RUnit Tests - 52 test functions, 0 errors, 0 failures
Number of test functions: 52 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   9.42    0.40    9.85