############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:crossmeta.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings crossmeta_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/crossmeta.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘crossmeta/DESCRIPTION’ ... OK * this is package ‘crossmeta’ version ‘1.25.0’ * 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 ‘crossmeta’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RCurl’ ‘XML’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed es_meta 23.816 0.640 24.456 diff_expr 19.424 0.624 20.137 symbol_annot 15.767 1.109 17.944 setup_prev 5.858 0.036 5.870 * 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: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-two-channel.R:60:3'): crossmeta produces similar results to limma ── Error in `limma::intraspotCorrelation(MA, mod)`: statmod package required but is not installed Backtrace: ▆ 1. └─crossmeta::diff_expr(...) at test-two-channel.R:60:2 2. └─crossmeta::run_limma(eset, annot, svobj, numsv) 3. └─crossmeta:::fit_lm(...) 4. └─crossmeta:::run_lmfit(eset, mod, rna_seq) 5. └─limma::intraspotCorrelation(MA, mod) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘crossmeta-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/crossmeta.Rcheck/00check.log’ for details.