Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:06 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the bigmelon package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 148/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bigmelon 1.20.0 (landing page) Tyler J. Gorrie-Stone
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: bigmelon |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings bigmelon_1.20.0.tar.gz |
StartedAt: 2022-04-12 06:30:59 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 06:36:54 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 354.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: bigmelon.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:bigmelon.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings bigmelon_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/bigmelon.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bigmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bigmelon’ version ‘1.20.0’ * 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 ‘bigmelon’ can be installed ... OK * 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 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 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 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’ Undefined global functions or variables: %dorng% 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 ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'iadd': iadd Code: function(bar, gds, n = TRUE, force = TRUE, target_cpgs = NULL, ...) Docs: function(bar, gds, n = TRUE, force = FALSE, target_cpgs = NULL, ...) Mismatches in argument default values: Name: 'force' Code: TRUE Docs: FALSE iadd2 Code: function(path, gds, chunksize = NULL, force = TRUE, ...) Docs: function(path, gds, chunksize = NULL, force = FALSE, ...) Mismatches in argument default values: Name: 'force' Code: TRUE Docs: FALSE * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'iadd' ‘force’ ‘barcodes’ Documented arguments not in \usage in documentation object 'iadd': ‘Force’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed iadd 41.484 1.96 43.568 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/bigmelon.Rcheck/00check.log’ for details.
bigmelon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL bigmelon ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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’ ** 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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > 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, 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 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 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 1.5-9.5 2022-03-01 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 /home/biocbuild/bbs-3.14-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 -- Tue Apr 12 06:36:51 2022 *********************************************** 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 14.830 0.727 15.538
bigmelon.Rcheck/bigmelon-Ex.timings
name | user | system | elapsed | |
GEOtoGDS | 0 | 0 | 0 | |
app2gds | 0.276 | 0.011 | 0.288 | |
backupGdsn | 0.152 | 0.004 | 0.161 | |
bigmelon-accessors | 0.258 | 0.008 | 0.270 | |
bigmelon-internal | 0.148 | 0.006 | 0.158 | |
bigmelon-normalization | 2.817 | 0.173 | 2.998 | |
combogds | 0.374 | 0.012 | 0.397 | |
es2gds | 0.175 | 0.011 | 0.190 | |
finalreport2gds | 0 | 0 | 0 | |
gds2mlumi | 0.380 | 0.007 | 0.391 | |
getquantilesandranks | 0.258 | 0.021 | 0.282 | |
iadd | 41.484 | 1.960 | 43.568 | |
pfiltergds | 0.240 | 0.014 | 0.260 | |
prcompgdsn | 0.324 | 0.013 | 0.341 | |
pwodgdsn | 0.294 | 0.000 | 0.299 | |
rankednorm | 0.155 | 0.002 | 0.162 | |
redirect | 0.160 | 0.001 | 0.166 | |