############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:pepStat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings pepStat_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pepStat.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pepStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pepStat’ version ‘1.41.0’ * 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 ‘pepStat’ can be installed ... OK * checking installed package size ... OK * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’, ‘values’ 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 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 .findFDR : : no visible global function definition for ‘median’ .sanitize_mapping_file2: no visible global function definition for ‘read.csv’ create_db: no visible global function definition for ‘mcols<-’ create_db: no visible global function definition for ‘mcols’ getPlotCoords: no visible global function definition for ‘values’ getWeightedEstimator : : no visible global function definition for ‘lm.fit’ getWeightedEstimator : : no visible global function definition for ‘lm.wfit’ getWeightedEstimator : : : no visible global function definition for ‘sd’ getZpep: no visible global function definition for ‘values’ getZpep : : no visible global function definition for ‘values’ plotArrayImage: no visible global function definition for ‘dev.interactive’ plotArrayImage: no visible global function definition for ‘devAskNewPage’ plotArrayImage: no visible global function definition for ‘dev.hold’ plotArrayImage: no visible global function definition for ‘dev.flush’ plotArrayResiduals: no visible global function definition for ‘dev.interactive’ plotArrayResiduals: no visible global function definition for ‘devAskNewPage’ plotArrayResiduals: no visible global function definition for ‘dev.hold’ plotArrayResiduals: no visible global function definition for ‘dev.flush’ summarizePeptides: no visible global function definition for ‘values<-’ summarizePeptides: no visible global function definition for ‘values’ coerce,peptideSet-ExpressionSet: no visible global function definition for ‘annotation’ end,peptideSet: no visible global function definition for ‘end’ featureID,peptideSet: no visible global function definition for ‘values’ pepZscore,GRanges: no visible global function definition for ‘values’ peptide,peptideSet: no visible global function definition for ‘values’ peptide<-,peptideSet-character: no visible global function definition for ‘values’ peptide<-,peptideSet-character: no visible global function definition for ‘values<-’ position,peptideSet: no visible global function definition for ‘start’ position,peptideSet: no visible global function definition for ‘end’ start,peptideSet: no visible global function definition for ‘start’ values,peptideSet: no visible global function definition for ‘values’ values<-,peptideSet: no visible global function definition for ‘values<-’ write.pSet,peptideSet: no visible global function definition for ‘start’ write.pSet,peptideSet: no visible global function definition for ‘end’ write.pSet,peptideSet: no visible global function definition for ‘write.csv’ Undefined global functions or variables: annotation dev.flush dev.hold dev.interactive devAskNewPage end lm.fit lm.wfit mcols mcols<- median read.csv sd start values values<- write.csv Consider adding importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive", "devAskNewPage") importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd", "start") importFrom("utils", "read.csv", "write.csv") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: create_db.Rd: GRanges makePeptideSet.Rd: read.maimages, backgroundCorrect peptideSet.Rd: ExpressionSet Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed makeCalls 6.197 0.172 7.328 summarizePeptides 5.305 0.064 5.921 restab 5.293 0.031 6.884 slidingMean 5.227 0.084 5.819 normalizeArray 5.145 0.108 6.082 plotArray 5.168 0.068 5.981 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/pepStat.Rcheck/00check.log’ for details.