############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:vtpnet.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings vtpnet_0.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/vtpnet.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 ‘vtpnet/DESCRIPTION’ ... OK * this is package ‘vtpnet’ version ‘0.46.0’ * 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 ‘vtpnet’ can be installed ... OK * checking installed package size ... NOTE installed size is 20.1Mb sub-directories of 1Mb or more: data 20.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 'library' or 'require' calls to packages already attached by Depends: ‘doParallel’ ‘foreach’ Please remove these calls from your code. 'library' or 'require' call to ‘MotifDb’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘doParallel’ ‘foreach’ 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 rng2facHits: warning in dir(patt = "rda$"): partial argument match of 'patt' to 'pattern' runfimo: warning in dir(patt = "_out"): partial argument match of 'patt' to 'pattern' filterGWASbyMap: no visible global function definition for ‘as’ getMtags: no visible global function definition for ‘is’ getOneHits: no visible global function definition for ‘queryHits’ getOneHits: no visible global function definition for ‘subjectHits’ getOneHits: no visible global function definition for ‘metadata’ getOneHits: no visible global function definition for ‘metadata<-’ gwMatchPWM: no visible binding for global variable ‘Hsapiens’ gwMatchPWM: no visible global function definition for ‘is’ gwMatchPWM: no visible global function definition for ‘%dopar%’ gwMatchPWM: no visible global function definition for ‘foreach’ gwMatchPWM: no visible binding for global variable ‘i’ gwMatchPWM: no visible global function definition for ‘matchPWM’ gwMatchPWM: no visible global function definition for ‘PWMscoreStartingAt’ gwMatchPWM: no visible global function definition for ‘subject’ gwMatchPWM: no visible global function definition for ‘as’ rng2facHits: no visible global function definition for ‘as’ rng2facHits: no visible global function definition for ‘registerDoParallel’ rng2facHits: no visible global function definition for ‘%dopar%’ rng2facHits: no visible global function definition for ‘foreach’ rng2facHits: no visible binding for global variable ‘i’ runfimo: no visible global function definition for ‘%dopar%’ runfimo: no visible global function definition for ‘foreach’ runfimo: no visible binding for global variable ‘i’ setupGWPM: no visible global function definition for ‘registerDoParallel’ Undefined global functions or variables: %dopar% Hsapiens PWMscoreStartingAt as foreach i is matchPWM metadata metadata<- queryHits registerDoParallel subject subjectHits Consider adding importFrom("methods", "as", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: vtpnet-package.Rd:48-50: Dropping empty section \references prepare_Rd: vtpnet-package.Rd:53-54: Dropping empty section \seealso prepare_Rd: vtpnet-package.Rd:55-56: Dropping empty section \examples * 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 files in ‘vignettes’ ... OK * checking examples ... NONE * 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: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/vtpnet.Rcheck/00check.log’ for details.