############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:jazzPanda.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings jazzPanda_1.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/jazzPanda.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘jazzPanda/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘jazzPanda’ version ‘1.1.1’ * 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 ‘jazzPanda’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 .get_gene_vectors_cm : calculate_one_gene: no visible binding for global variable ‘index_vec’ Undefined global functions or variables: index_vec * 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 compute_permp 5.239 1.674 20.422 get_perm_p 2.039 0.113 15.154 get_perm_adjp 1.990 0.068 15.154 get_cor 1.974 0.044 15.238 * 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: reflect, shift [ FAIL 1 | WARN 5 | SKIP 0 | PASS 138 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-lasso_markers.R:398:5'): set gene as NA if no clusters are significant ── sort(unique(full_res_bg$cluster)) (`actual`) not equal to c("A", "B", "dummy_A1", "dummy_A2", "dummy_B1", "dummy_B2") (`expected`). `actual[4:8]`: "dummy_A2" "dummy_B1" "dummy_B2" "sample1" "sample2" `expected[4:6]`: "dummy_A2" "dummy_B1" "dummy_B2" [ FAIL 1 | WARN 5 | SKIP 0 | PASS 138 ] 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/jazzPanda.Rcheck/00check.log’ for details.