Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:30 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1230/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mia 1.11.1 (landing page) Tuomas Borman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the mia package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mia.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: mia |
Version: 1.11.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.11.1.tar.gz |
StartedAt: 2024-03-02 06:41:40 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 07:21:41 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 2400.5 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: mia.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ version ‘1.11.1’ * 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 ‘mia’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Changes in version 1.11.x * 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 ... NOTE Unknown package ‘https’ in Rd xrefs * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 101 marked UTF-8 strings * 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 splitOn 99.936 2.821 122.832 calculateDMN 101.211 0.651 123.328 runCCA 87.875 1.020 99.389 taxonomy-methods 34.218 0.791 41.060 agglomerate-methods 30.280 0.715 37.970 splitByRanks 20.563 0.364 24.196 estimateDiversity 19.470 1.149 25.456 mergeSEs 17.056 0.170 20.025 getPrevalence 16.045 0.176 20.387 makeTreeSEFromDADA2 11.454 0.458 14.073 getExperimentCrossAssociation 9.950 0.090 12.956 summaries 8.455 0.102 10.147 loadFromMetaphlan 8.327 0.082 10.724 calculateJSD 7.121 0.650 9.148 perSampleDominantTaxa 5.572 0.105 6.580 makePhyloseqFromTreeSE 4.377 0.104 5.332 estimateDivergence 4.309 0.131 5.207 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
mia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mia ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘mia’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mia)
mia.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(mia) 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 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches 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 Loading required package: SingleCellExperiment Loading required package: TreeSummarizedExperiment Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: MultiAssayExperiment > > test_check("mia") ================================================================================ Time difference of 13.44 secs Initializing error rates to maximum possible estimate. selfConsist step 1 . selfConsist step 2 selfConsist step 3 selfConsist step 4 Convergence after 4 rounds. Initializing error rates to maximum possible estimate. selfConsist step 1 . selfConsist step 2 selfConsist step 3 selfConsist step 4 Convergence after 4 rounds.
mia.Rcheck/mia-Ex.timings
name | user | system | elapsed | |
agglomerate-methods | 30.280 | 0.715 | 37.970 | |
calculateDMN | 101.211 | 0.651 | 123.328 | |
calculateJSD | 7.121 | 0.650 | 9.148 | |
calculateOverlap | 0.410 | 0.012 | 0.481 | |
calculateUnifrac | 0.892 | 0.020 | 1.051 | |
cluster | 1.159 | 0.029 | 1.389 | |
estimateDivergence | 4.309 | 0.131 | 5.207 | |
estimateDiversity | 19.470 | 1.149 | 25.456 | |
estimateDominance | 0.701 | 0.038 | 0.956 | |
estimateEvenness | 0.204 | 0.016 | 0.290 | |
estimateRichness | 0.901 | 0.036 | 1.186 | |
getExperimentCrossAssociation | 9.950 | 0.090 | 12.956 | |
getPrevalence | 16.045 | 0.176 | 20.387 | |
isContaminant | 0.926 | 0.019 | 1.162 | |
loadFromHumann | 0.73 | 0.01 | 0.93 | |
loadFromMetaphlan | 8.327 | 0.082 | 10.724 | |
loadFromMothur | 0.617 | 0.011 | 0.744 | |
loadFromQIIME2 | 2.301 | 0.254 | 3.191 | |
makePhyloseqFromTreeSE | 4.377 | 0.104 | 5.332 | |
makeTreeSEFromBiom | 1.526 | 0.019 | 1.760 | |
makeTreeSEFromDADA2 | 11.454 | 0.458 | 14.073 | |
makeTreeSEFromPhyloseq | 3.021 | 0.043 | 3.475 | |
meltAssay | 1.598 | 0.066 | 1.948 | |
merge-methods | 3.324 | 0.066 | 4.254 | |
mergeSEs | 17.056 | 0.170 | 20.025 | |
mia-datasets | 1.095 | 0.016 | 1.304 | |
perSampleDominantTaxa | 5.572 | 0.105 | 6.580 | |
relabundance | 0.867 | 0.017 | 1.042 | |
runCCA | 87.875 | 1.020 | 99.389 | |
runDPCoA | 1.031 | 0.021 | 1.202 | |
runNMDS | 0.829 | 0.064 | 1.020 | |
splitByRanks | 20.563 | 0.364 | 24.196 | |
splitOn | 99.936 | 2.821 | 122.832 | |
subsampleCounts | 2.993 | 0.060 | 3.642 | |
subsetSamples | 2.113 | 0.041 | 2.552 | |
summaries | 8.455 | 0.102 | 10.147 | |
taxonomy-methods | 34.218 | 0.791 | 41.060 | |
transformAssay | 0.517 | 0.015 | 0.621 | |