############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:distinct.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings distinct_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/distinct.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 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 ‘distinct/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘distinct’ version ‘1.14.0’ * 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 ‘distinct’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 10.1Mb sub-directories of 1Mb or more: data 1.0Mb libs 8.8Mb * 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 Namespace in Imports field not imported from: ‘Rfast’ 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 ... NOTE perm_test_parallel_R: no visible binding for global variable ‘cl_id’ perm_test_parallel_covariates_R: no visible binding for global variable ‘cl_id’ plot_cdfs: no visible binding for global variable ‘group’ plot_densities: no visible binding for global variable ‘group’ Undefined global functions or variables: cl_id group * 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 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 $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed distinct_test 2.678 1.295 82.3 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 2. └─distinct:::perm_test_parallel_R(...) 3. ├─... %dorng% ... 4. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame()) 5. └─foreach (local) `<fn>`(...) 6. └─e$fun(obj, substitute(ex), parent.frame(), e$data) 7. └─parallel::clusterApplyLB(cl, argsList, evalWrapper) 8. └─parallel:::dynamicClusterApply(cl, fun, length(x), argfun) 9. └─parallel:::recvOneResult(cl) 10. ├─parallel:::recvOneData(cl) 11. └─parallel:::recvOneData.SOCKcluster(cl) 12. └─base::unserialize(socklist[[n]]) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 7 ] 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/distinct.Rcheck/00check.log’ for details.