##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeomxTools.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GeomxTools_3.4.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeomxTools/DESCRIPTION' ... OK
* this is package 'GeomxTools' version '3.4.0'
* 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 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.4Mb
* 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
qgrubbs: no visible global function definition for 'qtable'
readPKCFile: no visible binding for global variable 'RTS_ID'
readPKCFile: no visible binding for global variable 'Module'
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'
setTargetFlags: no visible global function definition for 'analtye'
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 RTS_ID TargetName analtye assayDataElement2 qtable
  setSigFuncs<-
* checking Rd files ... WARNING
checkRd: (5) NanoStringGeoMxSet-class.Rd:109-112: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:113-116: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:117-120: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:121-124: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:125-128: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:129-132: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:133-136: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:137-140: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:141-144: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:145-149: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:150-154: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) NanoStringGeoMxSet-class.Rd:163-166: \item in \describe must have non-empty label
* 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               49.46   2.60   52.10
writeNanoStringGeoMxSet              22.05   2.00   24.11
NanoStringGeoMxSet-class             19.86   1.14   25.66
setQCFlags-NanoStringGeoMxSet-method 16.53   0.16   16.69
setBioProbeQCFlags                   16.02   0.12   16.14
mixedModelDE                         14.69   0.53   75.15
readPKCFile                          11.64   0.50   12.17
aggregateCounts                      11.83   0.19   13.72
as.SpatialExperiment                  5.97   1.08    6.62
* 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: 1 WARNING, 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/GeomxTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GeomxTools
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'GeomxTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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, aperm, 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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: ggplot2
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
> 
> test_check("GeomxTools")

Attaching package: 'EnvStats'

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

    predict, predict.lm

Attaching SeuratObject
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    iqr

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

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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

    rowMedians

Loading required package: GenomicRanges
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb

Attaching package: 'SummarizedExperiment'

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

    Assays

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

    Assays


Attaching package: 'SingleCellExperiment'

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

    weights<-

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 285 ]
> 
> proc.time()
   user  system elapsed 
 673.09   18.89  694.65