############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRNApath_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/miRNApath.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘miRNApath/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miRNApath’ version ‘1.60.0’ * 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 ‘miRNApath’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release. Cannot process chunk/lines: Changed objects to S4 format Cannot process chunk/lines: Updated runEnrichment and mirnaTable to remove the "Enriched by miRNA" Cannot process chunk/lines: concatenated strings, which were way too long to be useful. Cannot process chunk/lines: Updated the miRNA-gene counts methodology; fixed Cannot process chunk/lines: the strategy for ignoring pathways with no hits. Cannot process chunk/lines: Updated permutation logic to handle empty when permutations Cannot process chunk/lines: show enrichment in only a subset of overall pathways. * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘miRNApath’ for: ‘show’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘methods’ 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 loadmirnapath: no visible global function definition for ‘read.table’ loadmirnapath: no visible global function definition for ‘new’ loadmirnapathways: no visible global function definition for ‘read.table’ loadmirnatogene: no visible global function definition for ‘read.table’ mirnaTable: no visible global function definition for ‘reshape’ runEnrichment : : : no visible global function definition for ‘phyper’ runEnrichment: no visible global function definition for ‘slotNames’ Undefined global functions or variables: new phyper read.table reshape slotNames Consider adding importFrom("methods", "new", "slotNames") importFrom("stats", "phyper", "reshape") importFrom("utils", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) runEnrichment.Rd:119: Escaped LaTeX specials: \$ * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mirnaTable 27.04 0.603 42.057 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/miRNApath.Rcheck/00check.log’ for details.