############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miloR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miloR_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/miloR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘miloR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miloR’ version ‘1.8.1’ * 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 ‘miloR’ 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 ... NOTE Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .fromMatrix: no visible binding for global variable ‘sce’ plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’ plotDAbeeswarm: no visible binding for global variable ‘logFC’ plotDAbeeswarm: no visible binding for global variable ‘is_signif’ plotDAbeeswarm: no visible binding for global variable ‘Nhood’ plotDAbeeswarm: no visible binding for global variable ‘logFC_color’ plotNhoodCounts: no visible binding for global variable ‘values’ plotNhoodCounts: no visible binding for global variable ‘..y..’ plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’ plotNhoodExpressionDA: no visible binding for global variable ‘logFC’ plotNhoodExpressionDA: no visible binding for global variable ‘SpatialFDR’ plotNhoodExpressionDA: no visible binding for global variable ‘logFC_rank’ plotNhoodExpressionDA: no visible binding for global variable ‘.’ plotNhoodExpressionDA: no visible binding for global variable ‘is_signif’ plotNhoodExpressionDA: no visible binding for global variable ‘feature’ plotNhoodExpressionDA: no visible binding for global variable ‘avg_expr’ plotNhoodExpressionDA: no visible binding for global variable ‘label’ plotNhoodExpressionGroups: no visible binding for global variable ‘Nhood’ plotNhoodExpressionGroups: no visible binding for global variable ‘NhoodGroup’ plotNhoodExpressionGroups: no visible binding for global variable ‘logFC’ plotNhoodExpressionGroups: no visible binding for global variable ‘feature’ plotNhoodExpressionGroups: no visible binding for global variable ‘logFC_rank’ plotNhoodExpressionGroups: no visible binding for global variable ‘avg_expr’ plotNhoodExpressionGroups: no visible binding for global variable ‘.’ plotNhoodExpressionGroups: no visible binding for global variable ‘label’ plotNhoodGraph: no visible binding for global variable ‘weight’ plotNhoodGraph: no visible binding for global variable ‘size’ plotNhoodGraphDA: no visible binding for global variable ‘layout’ plotNhoodGroups: no visible binding for global variable ‘layout’ plotNhoodMA: no visible binding for global variable ‘logCPM’ plotNhoodMA: no visible binding for global variable ‘logFC’ plotNhoodMA: no visible binding for global variable ‘Sig’ plotNhoodSizeHist: no visible binding for global variable ‘nh_size’ Undefined global functions or variables: . ..y.. Nhood NhoodGroup Sig SpatialFDR avg_expr feature is_signif label layout logCPM logFC logFC_color logFC_rank nh_size sce size values weight Consider adding importFrom("graphics", "layout") 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 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 testDiffExp 9.034 0.120 12.936 findNhoodMarkers 8.728 0.159 12.089 testNhoods 7.813 0.078 10.860 plotNhoodCounts 7.353 0.076 10.280 calcNhoodDistance 3.391 0.249 5.138 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/miloR.Rcheck/00check.log’ for details.