############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiRewire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiRewire_3.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiRewire.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiRewire/DESCRIPTION’ ... OK * this is package ‘BiRewire’ version ‘3.38.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘BiRewire’ can be installed ... WARNING Found the following significant warnings: BiRewire.c:149:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:221:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:229:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:280:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:332:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:339:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:402:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:454:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:461:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:588:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:652:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:737:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:844:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:893:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:962:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:1096:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:1144:37: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] BiRewire.c:1183:35: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] interface.c:105:68: warning: data argument not used by format string [-Wformat-extra-args] interface.c:147:68: warning: data argument not used by format string [-Wformat-extra-args] interface.c:252:68: warning: data argument not used by format string [-Wformat-extra-args] interface.c:296:68: warning: data argument not used by format string [-Wformat-extra-args] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiRewire.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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 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 birewire.analysis.bipartite: no visible binding for global variable ‘sd’ birewire.analysis.bipartite: no visible global function definition for ‘qt’ birewire.analysis.bipartite: no visible global function definition for ‘par’ birewire.analysis.bipartite: no visible global function definition for ‘polygon’ birewire.analysis.bipartite: no visible global function definition for ‘lines’ birewire.analysis.bipartite: no visible global function definition for ‘abline’ birewire.analysis.bipartite: no visible global function definition for ‘legend’ birewire.analysis.dsg: no visible global function definition for ‘dev.off’ birewire.analysis.dsg: no visible binding for global variable ‘sd’ birewire.analysis.dsg: no visible global function definition for ‘qt’ birewire.analysis.dsg: no visible global function definition for ‘polygon’ birewire.analysis.dsg: no visible global function definition for ‘lines’ birewire.analysis.dsg: no visible global function definition for ‘abline’ birewire.analysis.dsg: no visible global function definition for ‘legend’ birewire.analysis.undirected: no visible binding for global variable ‘sd’ birewire.analysis.undirected: no visible global function definition for ‘qt’ birewire.analysis.undirected: no visible global function definition for ‘par’ birewire.analysis.undirected: no visible global function definition for ‘polygon’ birewire.analysis.undirected: no visible global function definition for ‘lines’ birewire.analysis.undirected: no visible global function definition for ‘abline’ birewire.analysis.undirected: no visible global function definition for ‘legend’ birewire.load.dsg: no visible global function definition for ‘read.table’ birewire.sampler.bipartite: no visible global function definition for ‘write.table’ birewire.sampler.undirected: no visible global function definition for ‘write.table’ birewire.save.dsg: no visible global function definition for ‘write.table’ birewire.visual.monitoring.bipartite: no visible global function definition for ‘par’ birewire.visual.monitoring.bipartite: no visible global function definition for ‘colorRampPalette’ birewire.visual.monitoring.bipartite: no visible global function definition for ‘text’ birewire.visual.monitoring.dsg: no visible global function definition for ‘par’ birewire.visual.monitoring.dsg: no visible global function definition for ‘colorRampPalette’ birewire.visual.monitoring.dsg: no visible global function definition for ‘text’ birewire.visual.monitoring.undirected: no visible global function definition for ‘par’ birewire.visual.monitoring.undirected: no visible global function definition for ‘colorRampPalette’ birewire.visual.monitoring.undirected: no visible global function definition for ‘text’ Undefined global functions or variables: abline colorRampPalette dev.off legend lines par polygon qt read.table sd text write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off") importFrom("graphics", "abline", "legend", "lines", "par", "polygon", "text") importFrom("stats", "qt", "sd") importFrom("utils", "read.table", "write.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 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed birewire.analysis.undirected 51.822 0.101 51.939 birewire.visual.monitoring.dsg 13.469 0.054 13.539 birewire.visual.monitoring.undirected 5.219 0.526 5.755 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiRewire.Rcheck/00check.log’ for details.