############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CoCiteStats.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CoCiteStats_1.78.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CoCiteStats.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘CoCiteStats/DESCRIPTION’ ... OK * this is package ‘CoCiteStats’ version ‘1.78.0’ * 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 ‘CoCiteStats’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE Package in Depends field not imported from: ‘org.Hs.eg.db’ 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 gene.geneslist.sig: no visible global function definition for ‘Lkeys’ gene.geneslist.sig: no visible binding for global variable ‘org.Hs.egPMID’ paperLen: no visible global function definition for ‘toTable’ paperLen: no visible binding for global variable ‘org.Hs.egPMID’ paperLen: no visible global function definition for ‘nhit’ paperLen: no visible global function definition for ‘revmap’ Undefined global functions or variables: Lkeys nhit org.Hs.egPMID revmap toTable * checking Rd files ... NOTE prepare_Rd: gene.geneslist.statistic.Rd:19-21: Dropping empty section \details * 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 examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed gene.geneslist.sig 26.518 0.264 26.783 actorAdjTable 19.756 2.156 21.915 gene.geneslist.statistic 17.160 0.117 17.277 gene.gene.statistic 15.884 0.281 16.167 twowayTable 14.996 0.171 15.167 twTStats 14.207 0.087 14.294 paperLen 13.611 0.135 13.747 * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/CoCiteStats.Rcheck/00check.log’ for details.