############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spicyR_1.17.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.17.4’ * 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 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 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 .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 ‘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’ spicyBoxPlot: no visible binding for global variable ‘condition’ spicyBoxPlot: no visible binding for global variable ‘imageID’ Undefined global functions or variables: . association cellID cellType cellTypeI cellTypeJ cellType_from cellType_to condition d i imageCellID imageID j n n_close one rowname test value wt x y * 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 24.251 1.484 25.775 convPairs 15.848 0.615 16.510 signifPlot 11.230 1.091 12.360 getPairwise 9.010 0.208 9.182 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [1] 0.90071658 - 0.90071640 [1] [2] 0.87283152 - 0.87283122 [2] [3] 0.98508347 - 0.98508301 [3] [4] 1.05656640 - 1.05656589 [4] [5] 0.88561127 - 0.88561091 [5] [6] 0.91718536 - 0.91718520 [6] [7] 1.29107050 - 1.29107120 [7] [8] 0.96643415 - 0.96643366 [8] [9] 0.91078706 - 0.91078691 [9] [10] 1.13060414 - 1.13060386 [10] ... ... ... and 110 more ... [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck/00check.log’ for details.