##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeomxTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeomxTools_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GeomxTools.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 'GeomxTools/DESCRIPTION' ... OK
* this is package 'GeomxTools' version '2.1.0'
* 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 'GeomxTools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    extdata  11.7Mb
* 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
aggregateCounts: no visible binding for global variable 'TargetName'
hkNorm: no visible binding for global variable 'TargetName'
mixedModelDE: multiple local function definitions for 'deFunc' with
  different formal arguments
setGrubbsFlags: no visible binding for global variable 'TargetName'
setGrubbsFlags : <anonymous>: no visible binding for global variable
  'Module'
setProbeRatioFlags: no visible binding for global variable 'TargetName'
subtractBackground : <anonymous>: no visible binding for global
  variable 'Module'
setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global
  function definition for 'setSigFuncs<-'
signatureScores,NanoStringGeoMxSet: no visible global function
  definition for 'assayDataElement2'
signatureScores,NanoStringGeoMxSet: no visible global function
  definition for '.sigCalc'
Undefined global functions or variables:
  .sigCalc Module TargetName assayDataElement2 setSigFuncs<-
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
readNanoStringGeoMxSet               40.85   6.00   46.84
setBioProbeQCFlags                   36.52   0.05   36.57
setQCFlags-NanoStringGeoMxSet-method 34.27   0.06   34.49
NanoStringGeoMxSet-class             15.11   2.27   17.37
writeNanoStringGeoMxSet              15.01   1.83   17.14
mixedModelDE                         11.50   0.02   29.04
aggregateCounts                      11.21   0.14   11.35
readPKCFile                           6.12   1.00    7.12
readDccFile                           4.97   0.11    5.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/GeomxTools.Rcheck/00check.log'
for details.

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

    aggregateCounts                         html  
    checkQCFlags-NanoStringGeoMxSet-method
                                            html  
    checkQCFlags                            html  
    countsShiftedByOne                      html  
    logtBase                                html  
    mixedModelDE                            html  
    ngeoMean                                html  
    ngeoSD                                  html  
    normalize-NanoStringGeoMxSet-method     html  
    readDccFile                             html  
    readNanoStringGeoMxSet                  html  
    readPKCFile                             html  
    setBackgroundQCFlags                    html  
    setBioProbeQCFlags                      html  
    setGeoMxQCFlags                         html  
    setQCFlags-NanoStringGeoMxSet-method    html  
    setSegmentQCFlags                       html  
    setSeqQCFlags                           html  
    shiftCountsOne                          html  
    summarizeNegatives                      html  
    writeNanoStringGeoMxSet                 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 (GeomxTools)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'DEsubs' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'zinbwave' 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.

> library(testthat)
> library(GeomxTools)
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: NanoStringNCTools
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
> 
> test_check("GeomxTools")

Attaching package: 'EnvStats'

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

    predict, predict.lm

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

    print.default

Loading required package: lme4
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand


Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

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

    step

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
> 
> proc.time()
   user  system elapsed 
 302.82    8.48  331.06