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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/spicyR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 4.1Mb
* 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
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 20.685 0.287 42.977
colTest 5.691 0.169 12.058
getPairwise 3.327 0.111 7.102
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/spicyR.Rcheck/00check.log’
for details.
