Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:06 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 ENmix package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ENmix.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 608/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ENmix 1.34.02 (landing page) Zongli Xu
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: ENmix |
Version: 1.34.02 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ENmix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ENmix_1.34.02.tar.gz |
StartedAt: 2023-04-10 20:03:19 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 20:08:04 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 284.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ENmix.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ENmix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ENmix_1.34.02.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ENmix.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ENmix/DESCRIPTION’ ... OK * this is package ‘ENmix’ version ‘1.34.02’ * package encoding: UTF-8 * 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 ‘ENmix’ 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 ... 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: OK
ENmix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ENmix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘ENmix’ ... ** using staged installation ** R ** 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 (ENmix)
ENmix.Rcheck/tests/runTests.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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("ENmix") 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 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname 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 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading required package: minfiData Loading required package: minfi Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: bumphunter Loading required package: locfit locfit 1.5-9.7 2023-01-02 Loading required package: IlluminaHumanMethylation450kmanifest Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 Loading required package: digest [read.metharray.sheet] Found the following CSV files: [1] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/minfiData/extdata/SampleSheet.csv" RUNIT TEST PROTOCOL -- Mon Apr 10 20:07:53 2023 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : ENmix RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 13.480 0.738 14.252
ENmix.Rcheck/ENmix-Ex.timings
name | user | system | elapsed | |
B2M | 0.000 | 0.000 | 0.001 | |
M2B | 0 | 0 | 0 | |
QCinfo | 0 | 0 | 0 | |
calcdetP | 0 | 0 | 0 | |
combp | 0 | 0 | 0 | |
ctrlsva | 0 | 0 | 0 | |
dupicc | 0 | 0 | 0 | |
estimateCellProp | 0 | 0 | 0 | |
freqpoly | 0.000 | 0.000 | 0.001 | |
getB | 0 | 0 | 0 | |
getCGinfo | 0 | 0 | 0 | |
getmeth | 0 | 0 | 0 | |
ipdmr | 0 | 0 | 0 | |
methDataSet-class | 0.001 | 0.000 | 0.002 | |
methyAge | 0 | 0 | 0 | |
mhtplot | 0.000 | 0.000 | 0.001 | |
mpreprocess | 0 | 0 | 0 | |
multifreqpoly | 0 | 0 | 0 | |
nmode | 0 | 0 | 0 | |
norm.quantile | 0 | 0 | 0 | |
oxBS.MLE | 0 | 0 | 0 | |
p.qqplot | 0.000 | 0.001 | 0.000 | |
pcrplot | 0 | 0 | 0 | |
plotCtrl | 0 | 0 | 0 | |
predSex | 0 | 0 | 0 | |
preprocessENmix | 0 | 0 | 0 | |
qcfilter | 0 | 0 | 0 | |
rcp | 0 | 0 | 0 | |
readidat | 0 | 0 | 0 | |
readmanifest | 0 | 0 | 0 | |
relic | 0 | 0 | 0 | |
repicc | 0 | 0 | 0 | |
rgDataSet-class | 0.000 | 0.000 | 0.001 | |
simubed | 0 | 0 | 0 | |