############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ncdfFlow.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ncdfFlow_2.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ncdfFlow.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 ‘ncdfFlow/DESCRIPTION’ ... OK * this is package ‘ncdfFlow’ version ‘2.48.0’ * 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 ‘ncdfFlow’ 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 18.3Mb sub-directories of 1Mb or more: lib 1.1Mb libs 16.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Non-standard license specification: AGPL-3.0-only Standardizable: FALSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘flowCore’ A package should be listed in only one of these fields. * 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 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 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘BH’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ncdfFlowSet,flowSet: warning in assign(guid, new("flowFrame", exprs = matrix(numeric(0), nrow = 0, ncol = 0), parameters(x[[guid]]), keyword(x[[guid]])), env = e1): partial argument match of 'env' to 'envir' rbind2,ncdfFlowList-ANY : : : warning in assign(curSample, NA, env = indiceEnv): partial argument match of 'env' to 'envir' read.ncdfFlowSet: no visible global function definition for ‘mclapply’ Undefined global functions or variables: mclapply * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object '[[,ncdfFlowSet,ANY-method': \S4method{[[}{ncdfFlowSet,ANY} Code: function(x, i, j, ...) Docs: function(x, i, j, use.exprs = TRUE, ...) Argument names in docs not in code: use.exprs Mismatches in argument names: Position: 4 Code: ... Docs: use.exprs * 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 ... WARNING Found the following file(s) containing GNU extensions: src/Makevars Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.3.1/site-library/ncdfFlow/libs/ncdfFlow.so’: Found ‘abort’, possibly from ‘abort’ (C) Found ‘rand_r’, possibly from ‘rand_r’ (C) Found ‘sprintf’, possibly from ‘sprintf’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 nor [v]sprintf. 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Indices 6.881 0.224 7.28 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 3 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/ncdfFlow.Rcheck/00check.log’ for details.