############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RNAsense.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RNAsense_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RNAsense.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘RNAsense/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RNAsense’ version ‘1.14.0’ * 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 ‘RNAsense’ can be installed ... OK * 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE combineResults: no visible binding for global variable ‘resultSwitch’ combineResults: no visible binding for global variable ‘resultFC’ combineResults : getFCupdown: no visible binding for global variable ‘resultFC’ combineResults : getFCupdown: no visible binding for global variable ‘name’ combineResults : getFCupdown: no visible binding for global variable ‘FCdetect’ getFC: no visible binding for global variable ‘mydata’ getFC: no visible binding for global variable ‘analyzeConditions’ getFC: no visible binding for global variable ‘times’ getSwitch: no visible binding for global variable ‘mydata’ getSwitch: no visible binding for global variable ‘times’ outputGeneTables: no visible binding for global variable ‘resultCombined’ outputGeneTables: no visible binding for global variable ‘times’ outputGeneTables: no visible binding for global variable ‘analyzeConditions’ outputGeneTables: no visible binding for global variable ‘timepoint’ outputGeneTables: no visible binding for global variable ‘FCdown’ outputGeneTables: no visible binding for global variable ‘FCup’ outputGeneTables: no visible binding for global variable ‘experiment’ plotSSGS: no visible binding for global variable ‘resultCombined’ plotSSGS: no visible binding for global variable ‘times’ plotSSGS: no visible binding for global variable ‘analyzeConditions’ plotSSGS : getFT: no visible binding for global variable ‘result’ plotSSGS : getFT: no visible binding for global variable ‘timepoint’ plotSSGS : getFT: no visible binding for global variable ‘FCdown’ plotSSGS : getFT: no visible binding for global variable ‘FCup’ plotSSGS : : : : : no visible binding for global variable ‘experiment’ plotSSGS: no visible binding for global variable ‘xaxis’ plotSSGS: no visible binding for global variable ‘cluster’ Undefined global functions or variables: FCdetect FCdown FCup analyzeConditions cluster experiment mydata name result resultCombined resultFC resultSwitch timepoint times xaxis * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'getFC.Rd': ‘DataFrame’ Missing link or links in documentation object 'getSwitch.Rd': ‘DataFrame’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed combineResults 117.233 1.471 118.705 outputGeneTables 116.620 0.360 116.979 plotSSGS 112.985 0.320 113.305 getSwitch 73.221 0.304 73.524 getFC 24.031 0.093 24.122 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘example.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/RNAsense.Rcheck/00check.log’ for details.