############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings flowCore_2.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/flowCore.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘flowCore/DESCRIPTION’ ... OK * this is package ‘flowCore’ version ‘2.14.2’ * 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 ‘flowCore’ can be installed ... WARNING Found the following significant warnings: Hyperlog.cpp:47:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=] Hyperlog.cpp:53:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=] See ‘/home/biocbuild/bbs-3.18-bioc/meat/flowCore.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 16.3Mb sub-directories of 1Mb or more: R 1.1Mb data 5.4Mb extdata 1.1Mb libs 7.8Mb * 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: ‘Rcpp’ 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 eval,compensatedParameter-missing : : no visible binding for global variable ‘mat’ eval,compensatedParameter-missing : : no visible binding for global variable ‘msv’ show,flowFrame: no visible global function definition for ‘capture.output’ Undefined global functions or variables: capture.output mat msv Consider adding importFrom("utils", "capture.output") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^ checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^ checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘multiRangeGate’ Undocumented S4 classes: ‘multiRangeGate’ Undocumented S4 methods: generic '%in%' and siglist 'flowFrame,multiRangeGate' generic 'show' and siglist 'multiRangeGate' 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 ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/flowCore/libs/flowCore.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘rand’, possibly from ‘rand’ (C) Found ‘srand’, possibly from ‘srand’ (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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... ‘HowTo-flowCore.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/flowCore.Rcheck/00check.log’ for details.