############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings multtest_2.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/multtest.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘multtest/DESCRIPTION’ ... OK * this is package ‘multtest’ version ‘2.50.0’ * 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 ‘multtest’ can be installed ... WARNING Found the following significant warnings: stat_func.c:703:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] stat_func.c:705:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] stat_func.c:710:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] stat_func.c:714:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] See ‘/home/biocbuild/bbs-3.14-bioc/meat/multtest.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘multtest/R/zzz.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. EBMTP: no visible global function definition for ‘makeCluster’ EBMTP: no visible global function definition for ‘clusterEvalQ’ EBMTP: no visible global function definition for ‘stopCluster’ MTP: no visible global function definition for ‘makeCluster’ MTP: no visible global function definition for ‘clusterEvalQ’ MTP: no visible global function definition for ‘stopCluster’ boot.null: no visible global function definition for ‘clusterApply’ boot.null: no visible global function definition for ‘clusterApplyLB’ EBupdate,EBMTP: no visible binding for global variable ‘y’ update,MTP: no visible binding for global variable ‘y’ Undefined global functions or variables: clusterApply clusterApplyLB clusterEvalQ makeCluster stopCluster y * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'EBMTP,ANY,ANY,ANY' generic '[' and siglist 'MTP,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 File ‘/home/biocbuild/bbs-3.14-bioc/R/library/multtest/libs/multtest.so’: Found ‘stderr’, possibly from ‘stderr’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘MTP.pdf’, ‘MTP.tex’, ‘MTPALL.pdf’, ‘golub.R’, ‘multtest.bib’, ‘multtest.pdf’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/multtest.Rcheck/00check.log’ for details.