Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 167/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bigmelon 1.31.3 (landing page) Leonard C. Schalkwyk
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the bigmelon package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bigmelon.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: bigmelon |
Version: 1.31.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bigmelon_1.31.3.tar.gz |
StartedAt: 2024-08-26 19:41:28 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 19:43:57 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 148.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: bigmelon.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bigmelon_1.31.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bigmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bigmelon’ version ‘1.31.3’ * 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 ‘bigmelon’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'readPepo(barcodes = sets[!is.na(sets)], ': unused argument (barcodes = sets[!is.na(sets)]) See ‘/Users/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ 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 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 whether startup messages can be suppressed ... NOTE No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... WARNING Missing or unexported object: ‘GEOquery::gunzip’ Unexported objects imported by ':::' calls: ‘bumphunter:::greaterOrEqual’ ‘minfi:::pickCompProbes’ ‘minfi:::projectCellType’ ‘wateRmelon:::.impose’ ‘wateRmelon:::.normalizeQuantiles2’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bigpepo: possible error in readPepo(barcodes = sets[!is.na(sets)], manifest = manifest, n = TRUE, oob = FALSE, idatdir = path, ): unused argument (barcodes = sets[!is.na(sets)]) bumphunterEngine.gdsn: no visible binding for global variable ‘locfitByCluster’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParRegistered’ bumphunterEngine.gdsn: no visible global function definition for ‘registerDoSEQ’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParWorkers’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParName’ bumphunterEngine.gdsn: no visible global function definition for ‘getDoParVersion’ bumphunterEngine.gdsn: no visible global function definition for ‘smoother’ bumphunterEngine.gdsn: no visible global function definition for ‘regionFinder’ bumphunterEngine.gdsn: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn: no visible global function definition for ‘iter’ bumphunterEngine.gdsn: no visible binding for global variable ‘regionFinder’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn : computation.tots: no visible global function definition for ‘iter’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘%dorng%’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘foreach’ bumphunterEngine.gdsn : computation.tots2: no visible global function definition for ‘iter’ es2gds: no visible global function definition for ‘colData’ estimateCellCounts.gds: no visible global function definition for ‘colData’ idats2gds: no visible binding for global variable ‘ChipType’ Undefined global functions or variables: %dorng% ChipType colData foreach getDoParName getDoParRegistered getDoParVersion getDoParWorkers iter locfitByCluster regionFinder registerDoSEQ smoother * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘dim.gdsn.class’ ‘dimnames.gds.class’ ‘dimnames.gdsn.class’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'iadd.Rd': iadd Code: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL, idatpath = NULL, ...) Docs: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL, ...) Argument names in code not in docs: idatpath Mismatches in argument names: Position: 6 Code: idatpath Docs: ... * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'bigPepo.Rd' ‘path’ ‘gds’ ‘manifest’ ‘chunksize’ ‘force’ ‘...’ Undocumented arguments in Rd file 'dim.gds.class.Rd' ‘gfile’ ‘v’ 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 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 iadd 7.911 0.214 8.153 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: 5 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck/00check.log’ for details.
bigmelon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bigmelon ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘bigmelon’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ Creating a new generic function for ‘fot’ in package ‘bigmelon’ Note: possible error in 'readPepo(barcodes = sets[!is.na(sets)], ': unused argument (barcodes = sets[!is.na(sets)]) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (bigmelon)
bigmelon.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > BiocGenerics:::testPackage("bigmelon") Attaching package: 'BiocGenerics' 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, aperm, 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, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname 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 The following object is masked from 'package:Biobase': rowMedians Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit locfit 1.5-9.10 2024-06-24 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Attaching package: 'lumi' The following objects are masked from 'package:methylumi': estimateM, getHistory Attaching package: 'bigmelon' The following object is masked from 'package:wateRmelon': fot t8.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t9.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t2.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. appending to /Users/biocbuild/bbs-3.20-bioc/meat/bigmelon.Rcheck/tests/t2.gds betas... pvals... methylated... unmethylated... fData... pData... qcdata... t3.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t4.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t0.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t5.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t7.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. t6.gds doesn't exist, creating new file creating gdsfile... betas... pvals... methylated... unmethylated... fData... pData... qcdata... finished creating gdsfile Directing 'rownames' to fData/TargetID by default, change with redirect.gds if incorrect. Directing 'colnames' to pData/sampleID by default, change with redirect.gds if incorrect. RUNIT TEST PROTOCOL -- Mon Aug 26 19:43:53 2024 *********************************************** Number of test functions: 8 Number of errors: 0 Number of failures: 0 1 Test Suite : bigmelon RUnit Tests - 8 test functions, 0 errors, 0 failures Number of test functions: 8 Number of errors: 0 Number of failures: 0 > > > proc.time() user system elapsed 5.934 0.244 6.193
bigmelon.Rcheck/bigmelon-Ex.timings
name | user | system | elapsed | |
GEOtoGDS | 0 | 0 | 0 | |
app2gds | 0.112 | 0.013 | 0.128 | |
backupGdsn | 0.093 | 0.010 | 0.105 | |
bigmelon-accessors | 0.081 | 0.010 | 0.094 | |
bigmelon-internal | 0.070 | 0.007 | 0.079 | |
bigmelon-normalization | 1.545 | 0.059 | 1.606 | |
combogds | 0.125 | 0.019 | 0.150 | |
es2gds | 0.068 | 0.008 | 0.079 | |
finalreport2gds | 0 | 0 | 0 | |
gds2mlumi | 0.120 | 0.008 | 0.132 | |
getquantilesandranks | 0.089 | 0.011 | 0.101 | |
iadd | 7.911 | 0.214 | 8.153 | |
pfiltergds | 0.654 | 0.031 | 0.688 | |
prcompgdsn | 0.071 | 0.009 | 0.083 | |
pwodgdsn | 0.124 | 0.012 | 0.138 | |
rankednorm | 0.073 | 0.009 | 0.093 | |
redirect | 0.072 | 0.008 | 0.085 | |