############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPOTlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPOTlight_1.12.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SPOTlight.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SPOTlight/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SPOTlight’ 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 ‘SPOTlight’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 .extract_coord: no visible global function definition for ‘is’ .extract_counts: no visible global function definition for ‘is’ .extract_image: no visible global function definition for ‘is’ .pred_hp: no visible global function definition for ‘as’ .set_groups_if_null: no visible global function definition for ‘is’ plotImage: no visible global function definition for ‘is’ plotSpatialScatterpie: no visible global function definition for ‘is’ plotSpatialScatterpie: no visible global function definition for ‘as’ plotTopicProfiles: no visible global function definition for ‘is’ runDeconvolution: no visible global function definition for ‘is’ runDeconvolution: no visible global function definition for ‘as’ trainNMF: no visible global function definition for ‘is’ trainNMF: no visible global function definition for ‘as’ Undefined global functions or variables: as is Consider adding importFrom("methods", "as", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) dot-filter.Rd:11-56: Lost braces 11 | weight_id = "weight") { | ^ checkRd: (-1) dot-filter.Rd:13-15: Lost braces 13 | if (is.null(n_top)) { | ^ checkRd: (-1) dot-filter.Rd:29-33: Lost braces 29 | mgs <- lapply(mgs, function(df) { | ^ checkRd: (-1) dot-filter.Rd:36-40: Lost braces 36 | mgs <- lapply(ks, function(k) { | ^ checkRd: (-1) dot-filter.Rd:44-50: Lost braces 44 | W <- vapply(ks, function(k) { | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SPOTlight 5.568 0.189 5.769 * 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: [ FAIL 1 | WARN 1 | SKIP 0 | PASS 291 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plotInteractions.R:93:5'): plotInteractions(), which = 'network', tunning ── Error in `p[[1]][[10]][[2]][[9]]`: subscript out of bounds Backtrace: ▆ 1. └─testthat::expect_equal(p[[1]][[10]][[2]][[9]], "maroon") at test-plotInteractions.R:93:5 2. └─testthat::quasi_label(enquo(object), label, arg = "object") 3. └─rlang::eval_bare(expr, quo_get_env(quo)) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 291 ] 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/SPOTlight.Rcheck/00check.log’ for details.