Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:54 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the stageR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/stageR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1851/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
stageR 1.14.0 (landing page) Koen Van den Berge
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: stageR |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:stageR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings stageR_1.14.0.tar.gz |
StartedAt: 2021-10-14 11:45:55 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:47:52 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 116.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: stageR.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:stageR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings stageR_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/stageR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘stageR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘stageR’ version ‘1.14.0’ * 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 ‘stageR’ 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. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘methods’ ‘stats’ 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 .stageWiseTest : <anonymous>: warning in gsub(x = paste(namesList[ii], namesListElements[[ii]]), pattern = " ", replace = ":"): partial argument match of 'replace' to 'replacement' .stageWiseTest: no visible global function definition for ‘p.adjust’ stageR: no visible global function definition for ‘new’ stageRTx: no visible global function definition for ‘new’ Undefined global functions or variables: new p.adjust Consider adding importFrom("methods", "new") importFrom("stats", "p.adjust") 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 ... WARNING Missing link or links in documentation object 'getAdjustedPValues.Rd': ‘stageWiseAdjustment,stageR,character,numeric-method’ Missing link or links in documentation object 'stageRClass.Rd': ‘getAdjustedPValues,stageR,logical,logical-method’ ‘getResults,stageR-method’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented S4 classes: ‘stageR’ ‘stageRTx’ Undocumented S4 methods: generic 'adjustedAlphaLevel' and siglist 'stageR' generic 'getAdjustedPValues' and siglist 'stageR,logical,logical' generic 'getAlpha' and siglist 'stageR' generic 'getMethod' and siglist 'stageR' generic 'getPConfirmation' and siglist 'stageR' generic 'getPScreen' and siglist 'stageR' generic 'getResults' and siglist 'stageR' generic 'getSignificantGenes' and siglist 'stageRTx' generic 'getSignificantTx' and siglist 'stageRTx' generic 'getTx2gene' and siglist 'stageRTx' generic 'isAdjusted' and siglist 'stageR' generic 'isPScreenAdjusted' and siglist 'stageR' generic 'stageWiseAdjustment' and siglist 'stageR,character,numeric' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'adjustedAlphaLevel' ‘...’ Objects in \usage without \alias in documentation object 'adjustedAlphaLevel': ‘\S4method{adjustedAlphaLevel}{stageR}’ Objects in \usage without \alias in documentation object 'getAdjustedPValues': ‘\S4method{getAdjustedPValues}{stageR,logical,logical}’ Objects in \usage without \alias in documentation object 'getAlpha': ‘\S4method{getAlpha}{stageR}’ Objects in \usage without \alias in documentation object 'getMethod': ‘\S4method{getMethod}{stageR}’ Undocumented arguments in documentation object 'getPConfirmation' ‘...’ Objects in \usage without \alias in documentation object 'getPConfirmation': ‘\S4method{getPConfirmation}{stageR}’ Objects in \usage without \alias in documentation object 'getPScreen': ‘\S4method{getPScreen}{stageR}’ Undocumented arguments in documentation object 'getResults' ‘...’ Objects in \usage without \alias in documentation object 'getResults': ‘\S4method{getResults}{stageR}’ Undocumented arguments in documentation object 'getSignificantGenes' ‘...’ Objects in \usage without \alias in documentation object 'getSignificantGenes': ‘\S4method{getSignificantGenes}{stageRTx}’ Undocumented arguments in documentation object 'getSignificantTx' ‘...’ Objects in \usage without \alias in documentation object 'getSignificantTx': ‘\S4method{getSignificantTx}{stageRTx}’ Objects in \usage without \alias in documentation object 'getTx2gene': ‘\S4method{getTx2gene}{stageRTx}’ Objects in \usage without \alias in documentation object 'isAdjusted': ‘\S4method{isAdjusted}{stageR}’ Objects in \usage without \alias in documentation object 'isPScreenAdjusted': ‘\S4method{isPScreenAdjusted}{stageR}’ Documented arguments not in \usage in documentation object 'stageR': ‘...’ Documented arguments not in \usage in documentation object 'stageRTx': ‘...’ Objects in \usage without \alias in documentation object 'stageWiseAdjustment': ‘\S4method{stageWiseAdjustment}{stageR,character,numeric}’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/stageR.Rcheck/00check.log’ for details.
stageR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL stageR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘stageR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (stageR)
stageR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(stageR) Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'stageR' The following object is masked from 'package:methods': getMethod > > test_check("stageR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ] > > proc.time() user system elapsed 5.871 0.292 6.148
stageR.Rcheck/stageR-Ex.timings
name | user | system | elapsed | |
adjustedAlphaLevel | 0.019 | 0.003 | 0.023 | |
getAdjustedPValues | 0.029 | 0.003 | 0.033 | |
getAlpha | 0.023 | 0.000 | 0.023 | |
getMethod | 0.011 | 0.011 | 0.023 | |
getPConfirmation | 0.002 | 0.007 | 0.011 | |
getPScreen | 0.006 | 0.001 | 0.006 | |
getResults | 0.024 | 0.001 | 0.024 | |
getSignificantGenes | 0.046 | 0.010 | 0.057 | |
getSignificantTx | 0.04 | 0.00 | 0.04 | |
getTx2gene | 0.008 | 0.020 | 0.028 | |
isAdjusted | 0.019 | 0.000 | 0.020 | |
isPScreenAdjusted | 0.001 | 0.000 | 0.000 | |
stageR | 0.002 | 0.000 | 0.002 | |
stageRTx | 0.001 | 0.000 | 0.002 | |
stageWiseAdjustment | 0.021 | 0.004 | 0.024 | |