############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ACME_2.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ACME.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ACME/DESCRIPTION’ ... OK * this is package ‘ACME’ version ‘2.62.0’ * 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 ‘ACME’ can be installed ... WARNING Found the following significant warnings: windowChisq.c:58:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] windowChisq.c:63:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] windowChisq.c:86:20: warning: initialization of ‘void * (*)(void)’ from incompatible pointer type ‘struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)’ [-Wincompatible-pointer-types] See ‘/home/biocbuild/bbs-3.20-bioc/meat/ACME.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 30.8Mb sub-directories of 1Mb or more: data 3.1Mb extdata 27.3Mb * 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 .plotACMECalcSet: no visible global function definition for ‘par’ .plotACMECalcSet: no visible global function definition for ‘axis’ .plotACMECalcSet: no visible global function definition for ‘abline’ .plotACMESet: no visible global function definition for ‘par’ do.aGFF.calc: no visible global function definition for ‘quantile’ findClosestGene: no visible binding for global variable ‘refflat’ findClosestGene: no visible binding for '<<-' assignment to ‘refflat’ findRegions : : no visible global function definition for ‘median’ getRefflat: no visible global function definition for ‘download.file’ getRefflat: no visible global function definition for ‘read.delim’ plotgff: no visible global function definition for ‘par’ plotgffcalc: no visible global function definition for ‘par’ plotgffcalc: no visible global function definition for ‘axis’ plotgffcalc: no visible global function definition for ‘abline’ read.resultsGFF: no visible global function definition for ‘read.delim’ windowChisq: no visible global function definition for ‘pchisq’ write.bedGraph: no visible global function definition for ‘write.table’ write.sgr: no visible global function definition for ‘write.table’ plot,ACMECalcSet: no visible global function definition for ‘par’ plot,ACMECalcSet: no visible global function definition for ‘axis’ plot,ACMECalcSet: no visible global function definition for ‘abline’ plot,ACMESet: no visible global function definition for ‘par’ plot,aGFF: no visible global function definition for ‘par’ plot,aGFFCalc: no visible global function definition for ‘par’ plot,aGFFCalc: no visible global function definition for ‘axis’ plot,aGFFCalc: no visible global function definition for ‘abline’ Undefined global functions or variables: abline axis download.file median par pchisq quantile read.delim refflat write.table Consider adding importFrom("graphics", "abline", "axis", "par") importFrom("stats", "median", "pchisq", "quantile") importFrom("utils", "download.file", "read.delim", "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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findClosestGene 1.535 0.224 7.717 getRefflat 1.285 0.040 7.040 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ACME.Rcheck/00check.log’ for details.