##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings spicyR_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/spicyR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘spicyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spicyR’ version ‘1.12.2’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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
bubblePlot: no visible binding for global variable ‘condition’
calcWeights: no visible binding for global variable ‘pairwiseAssoc’
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’
spatialLMBootstrap : functionToReplicate: no visible global function
  definition for ‘nrows’
spicy: no visible global function definition for ‘column_to_rownames’
spicy: no visible global function definition for ‘%>%’
spicy: no visible global function definition for ‘select’
spicy: no visible binding for global variable ‘test’
spicy: no visible binding for global variable ‘konditional’
spicy: no visible global function definition for ‘pivot_wider’
spicy: no visible global function definition for ‘mutate’
spicy: no visible global function definition for ‘separate’
spicy: no visible binding for global variable ‘fromName’
spicy: no visible binding for global variable ‘parent’
Undefined global functions or variables:
  %>% . cellTypeI cellTypeJ column_to_rownames condition d fromName i j
  konditional mutate nrows pairwiseAssoc parent pivot_wider select
  separate test value wt
* 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 'getPairwise':
getPairwise
  Code: function(cells, from = NULL, to = NULL, dist = NULL, window =
                 "convex", window.length = NULL, Rs = c(20, 50, 100),
                 sigma = NULL, minLambda = 0.05, edgeCorrect = TRUE,
                 includeZeroCells = TRUE, BPPARAM =
                 BiocParallel::SerialParam(), imageID = "imageID",
                 cellType = "cellType", spatialCoords = c("x", "y"),
                 fast = TRUE)
  Docs: function(cells, from = NULL, to = NULL, 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(), imageID = "imageID",
                 cellType = "cellType", spatialCoords = c("x", "y"))
  Mismatches in argument names (first 3):
    Position: 10 Code: edgeCorrect Docs: fast
    Position: 11 Code: includeZeroCells Docs: edgeCorrect
    Position: 12 Code: BPPARAM Docs: includeZeroCells

Codoc mismatches from documentation object 'SpicyResults-class':
spicy
  Code: function(cells, condition = NULL, subject = NULL, covariates =
                 NULL, from = NULL, to = NULL, dist = NULL,
                 alternateResult = NULL, integrate = TRUE, verbose =
                 TRUE, weights = TRUE, weightsByPair = FALSE,
                 weightFactor = 1, window = "convex", window.length =
                 NULL, BPPARAM = BiocParallel::SerialParam(), sigma =
                 NULL, Rs = NULL, minLambda = 0.05, edgeCorrect = TRUE,
                 includeZeroCells = FALSE, imageID = "imageID",
                 cellType = "cellType", spatialCoords = c("x", "y"),
                 fast = TRUE, nsim = NULL, ...)
  Docs: function(cells, condition = NULL, subject = NULL, covariates =
                 NULL, from = NULL, to = NULL, dist = NULL,
                 alternateResult = 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, imageID
                 = "imageID", cellType = "cellType", spatialCoords =
                 c("x", "y"), ...)
  Mismatches in argument names (first 3):
    Position: 10 Code: verbose Docs: nsim
    Position: 11 Code: weights Docs: verbose
    Position: 12 Code: weightsByPair Docs: weights

* 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 LazyData ... 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
spicy   16.837  0.288  16.256
colTest  5.099  0.276   5.375
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘spicyR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/spicyR.Rcheck/00check.log’
for details.