############################################################################## ############################################################################## ### ### Running command: ### ### /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_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.18.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 code 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 .format_data: no visible binding for global variable ‘imageID’ .format_data: no visible binding for global variable ‘cellType’ bubblePlot: no visible binding for global variable ‘parent’ bubblePlot: no visible binding for global variable ‘cellTypeB_id’ bubblePlot: no visible binding for global variable ‘cellTypeB_numeric’ bubblePlot: no visible binding for global variable ‘condition’ convPairs: no visible binding for global variable ‘rowname’ convPairs: no visible binding for global variable ‘cellType_from’ convPairs: no visible binding for global variable ‘cellType_to’ convPairs: no visible binding for global variable ‘one’ convPairs: no visible binding for global variable ‘n_close’ convPairs: no visible binding for global variable ‘n’ convPairs: no visible binding for global variable ‘test’ convPairs: no visible binding for global variable ‘association’ getCellSummary: no visible binding for global variable ‘cellID’ getCellSummary: no visible binding for global variable ‘imageCellID’ getCellSummary: no visible binding for global variable ‘x’ getCellSummary: no visible binding for global variable ‘y’ getCellSummary: no visible binding for global variable ‘cellType’ getCellSummary: no visible binding for global variable ‘.’ getCellType: no visible binding for global variable ‘cellType’ 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 ‘cellTypeI’ inhomLPair: no visible binding for global variable ‘cellTypeJ’ spatialSurv : : no visible global function definition for ‘pchisq’ spatialSurv: no visible binding for global variable ‘test’ spatialSurv: no visible binding for global variable ‘coef’ spatialSurv: no visible binding for global variable ‘se.coef’ spatialSurv: no visible binding for global variable ‘p.value’ spicyBoxPlot: no visible binding for global variable ‘condition’ survBubble: no visible binding for global variable ‘test’ survBubble: no visible binding for global variable ‘parent’ survBubble: no visible binding for global variable ‘to’ survBubble: no visible binding for global variable ‘from’ survBubble: no visible global function definition for ‘filter’ survBubble: no visible binding for global variable ‘p.value’ survBubble: no visible binding for global variable ‘logP’ survBubble: no visible binding for global variable ‘coef’ survBubble: no visible binding for global variable ‘sig’ Undefined global functions or variables: . association cellID cellType cellTypeB_id cellTypeB_numeric cellTypeI cellTypeJ cellType_from cellType_to coef condition d filter from i imageCellID imageID j logP n n_close one p.value parent pchisq rowname se.coef sig test to value wt x y Consider adding importFrom("stats", "coef", "filter", "pchisq") 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 ... OK * 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 14.766 0.241 15.068 convPairs 9.540 0.620 10.238 getPairwise 4.988 0.240 5.245 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck/00check.log’ for details.