##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spicyR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings spicyR_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/spicyR.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 'spicyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spicyR' version '1.7.2'
* 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 'spicyR' 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
calcWeights: no visible binding for global variable 'pairwiseAssoc'
calcWeights: no visible global function definition for 'quantile'
inhomL: no visible binding for global variable 'j'
inhomL: no visible binding for global variable 'value'
inhomL: no visible binding for global variable 'i'
inhomL: no visible binding for global variable 'd'
inhomL: no visible binding for global variable 'cellTypeI'
inhomL: no visible binding for global variable 'cellTypeJ'
inhomL: no visible global function definition for '.'
inhomL: no visible binding for global variable 'wt'
inhomLPair: no visible binding for global variable 'i'
Undefined global functions or variables:
  . cellTypeI cellTypeJ d i j pairwiseAssoc quantile value wt
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SegmentedCells-class':
SegmentedCells
  Code: function(cellData, cellProfiler = FALSE, spatialCoords = c("x",
                 "y"), cellTypeString = "cellType", intensityString =
                 "intensity_", morphologyString = "morphology_",
                 phenotypeString = "phenotype_", cellIDString =
                 "cellID", cellAnnotations = NULL, imageCellIDString =
                 "imageCellID", imageIDString = "imageID", verbose =
                 TRUE)
  Docs: function(cellData, cellProfiler = FALSE, spatialCoords = c("x",
                 "y"), cellTypeString = "cellType", intensityString =
                 "intensity_", morphologyString = "morphology_",
                 phenotypeString = "phenotype_", cellIDString =
                 "cellID", cellAnnotations = NULL, imageCellIDString =
                 "imageCellID", imageIDString = "imageID")
  Argument names in code not in docs:
    verbose

Codoc mismatches from documentation object 'getPairwise':
getPairwise
  Code: function(cells, from = unique(cellType(cells)), to =
                 unique(cellType(cells)), dist = NULL, window =
                 "convex", window.length = NULL, Rs = c(20, 50, 100),
                 sigma = NULL, minLambda = 0.05, fast = TRUE,
                 edgeCorrect = TRUE, includeZeroCells = TRUE, BPPARAM =
                 BiocParallel::SerialParam())
  Docs: function(cells, from = unique(cellType(cells)), to =
                 unique(cellType(cells)), dist = NULL, window =
                 "convex", window.length = NULL, Rs = c(20, 50, 100),
                 sigma = NULL, minLambda = 0.05, fast = TRUE,
                 edgeCorrect = TRUE, BPPARAM =
                 BiocParallel::SerialParam())
  Argument names in code not in docs:
    includeZeroCells
  Mismatches in argument names:
    Position: 12 Code: includeZeroCells Docs: BPPARAM

Codoc mismatches from documentation object 'SpicyResults-class':
spicy
  Code: function(cells, condition = NULL, subject = NULL, covariates =
                 NULL, from = NULL, to = NULL, dist = NULL, integrate =
                 TRUE, nsim = NULL, verbose = TRUE, weights = TRUE,
                 weightsByPair = FALSE, weightFactor = 1, window =
                 "convex", window.length = NULL, BPPARAM =
                 BiocParallel::SerialParam(), sigma = NULL, Rs = NULL,
                 minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE,
                 includeZeroCells = FALSE, ...)
  Docs: function(cells, condition = NULL, subject = NULL, covariates =
                 NULL, from = NULL, to = NULL, dist = NULL, integrate =
                 TRUE, nsim = NULL, verbose = TRUE, weights = TRUE,
                 weightsByPair = FALSE, weightFactor = 1, window =
                 "convex", window.length = NULL, BPPARAM =
                 BiocParallel::SerialParam(), sigma = NULL, Rs = NULL,
                 minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE,
                 ...)
  Argument names in code not in docs:
    includeZeroCells
  Mismatches in argument names:
    Position: 22 Code: includeZeroCells Docs: ...

* 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
getPairwise 345.56  39.88  382.23
spicy        13.39   0.17   13.58
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/spicyR.Rcheck/00check.log'
for details.

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'spicyR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spicyR'
    finding HTML links ... done
    Accessors                               html  
    SegmentedCells                          html  
    as.data.frame.SegmentedCells            html  
    diabetesData                            html  
    getPairwise                             html  
    plot-SegmentedCells                     html  
    show-SegmentedCells                     html  
    signifPlot                              html  
    spicy                                   html  
    spicyTest                               html  
    spicyTestBootstrap                      html  
    topPairs                                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 (spicyR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ppcseq' is missing or broken
 done