############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:garfield.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings garfield_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/garfield.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * 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 ‘garfield/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘garfield’ version ‘1.32.0’ * 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 ‘garfield’ can be installed ... WARNING Found the following significant warnings: garfield_perm.cpp:306:15: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘long int’ [-Wformat=] garfield_perm.cpp:306:18: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘int’ [-Wformat=] garfield_perm.cpp:306:24: warning: format ‘%s’ expects argument of type ‘char*’, but argument 4 has type ‘double’ [-Wformat=] garfield_perm.cpp:306:27: warning: unknown conversion type character ‘\x09’ in format [-Wformat=] garfield_perm.cpp:306:32: warning: format ‘%s’ expects argument of type ‘char*’, but argument 5 has type ‘int’ [-Wformat=] garfield_perm.cpp:306:69: warning: format ‘%s’ expects argument of type ‘char*’, but argument 6 has type ‘double’ [-Wformat=] garfield_perm.cpp:356:13: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘int’ [-Wformat=] See ‘/home/biocbuild/bbs-3.19-bioc/meat/garfield.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: extdata 3.0Mb libs 2.3Mb * 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 code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE garfield.plot: no visible global function definition for ‘read.table’ garfield.plot: no visible global function definition for ‘colorRampPalette’ garfield.plot: no visible global function definition for ‘pdf’ garfield.plot: no visible global function definition for ‘layout’ garfield.plot: no visible global function definition for ‘par’ garfield.plot: no visible global function definition for ‘title’ garfield.plot: no visible global function definition for ‘legend’ garfield.plot: no visible global function definition for ‘dev.off’ garfield.plot.fnx: no visible global function definition for ‘par’ garfield.plot.fnx: no visible global function definition for ‘polygon’ garfield.plot.fnx: no visible global function definition for ‘segments’ garfield.plot.fnx: no visible global function definition for ‘points’ garfield.plot.fnx: no visible global function definition for ‘lines’ garfield.plot.fnx: no visible global function definition for ‘median’ garfield.plot.fnx: no visible global function definition for ‘text’ Undefined global functions or variables: colorRampPalette dev.off layout legend lines median par pdf points polygon read.table segments text title Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "layout", "legend", "lines", "par", "points", "polygon", "segments", "text", "title") importFrom("stats", "median") importFrom("utils", "read.table") to your NAMESPACE file. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/garfield/libs/garfield.so’: 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/garfield.Rcheck/00check.log’ for details.