############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:restfulSE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings restfulSE_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/restfulSE.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘restfulSE/DESCRIPTION’ ... OK * this is package ‘restfulSE’ version ‘1.23.0’ * 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 ‘restfulSE’ 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 ... NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE BQ3_ArraySeed: no visible global function definition for ‘is’ BQ3_ArraySeed: no visible global function definition for ‘new’ BQ3_Source: no visible global function definition for ‘slot’ BQ3_Source: no visible binding for global variable ‘SampleTypeLetterCode’ BQ3_Source: no visible global function definition for ‘new’ BQ3m2: no visible binding for global variable ‘SampleTypeLetterCode’ BQM_ArraySeed: no visible global function definition for ‘is’ BQM_ArraySeed: no visible global function definition for ‘new’ BQM_Source: no visible global function definition for ‘new’ TCGA_tablerefs: no visible global function definition for ‘new’ newDA: no visible global function definition for ‘new’ replaceSlots: no visible global function definition for ‘validObject’ seByTumor: no visible global function definition for ‘new’ unsafe_replaceSlots: no visible global function definition for ‘slot’ unsafe_replaceSlots: no visible global function definition for ‘slot<-’ coerce,BQ3_Array-BQ3_Matrix: no visible global function definition for ‘new’ coerce,BQM_Array-BQM_Matrix: no visible global function definition for ‘new’ Undefined global functions or variables: SampleTypeLetterCode is new slot slot<- validObject Consider adding importFrom("methods", "is", "new", "slot", "slot<-", "validObject") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed gtexTiss 3.646 0.144 9.808 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘restfulSE.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/restfulSE.Rcheck/00check.log’ for details.