Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-21 13:23 -0400 (Fri, 21 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 1223/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mia 1.13.23 (landing page) Tuomas Borman
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.13.23 |
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_1.13.23.tar.gz |
StartedAt: 2024-06-20 22:09:18 -0400 (Thu, 20 Jun 2024) |
EndedAt: 2024-06-20 22:16:35 -0400 (Thu, 20 Jun 2024) |
EllapsedTime: 436.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.13.23.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mia’ version ‘1.13.23’ * 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 ... 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 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 runCCA 29.394 0.091 29.488 calculateDMN 26.973 0.012 26.989 hierarchy-tree 6.387 0.351 6.738 agglomerate-methods 6.513 0.048 6.561 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck/00check.log’ for details.
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-arm64/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 version 4.4.1 RC (2024-06-06 r86719) -- "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. > 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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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': expand.grid, I, 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 3.38 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. initial value 0.383462 iter 5 value 0.161655 iter 10 value 0.113278 final value 0.003270 converged initial value 0.000000 final value 0.000000 converged initial value 0.000000 final value 0.000000 converged [ FAIL 0 | WARN 5 | SKIP 3 | PASS 961 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • require("miaTime", quietly = TRUE) is not TRUE (3): 'test-2mergeSEs.R:382:5', 'test-3agglomerate.R:155:5', 'test-mediate.R:3:3' [ FAIL 0 | WARN 5 | SKIP 3 | PASS 961 ] > > proc.time() user system elapsed 208.647 32.959 230.944
mia.Rcheck/mia-Ex.timings
name | user | system | elapsed | |
addCluster | 0.215 | 0.005 | 0.220 | |
addDivergence | 0.859 | 0.019 | 0.878 | |
agglomerate-methods | 6.513 | 0.048 | 6.561 | |
calculateDMN | 26.973 | 0.012 | 26.989 | |
calculateJSD | 1.609 | 0.316 | 1.926 | |
calculateOverlap | 0.047 | 0.003 | 0.050 | |
calculateUnifrac | 0.094 | 0.006 | 0.101 | |
estimateDiversity | 4.289 | 0.401 | 4.695 | |
estimateDominance | 0.079 | 0.002 | 0.082 | |
estimateEvenness | 0.022 | 0.002 | 0.022 | |
estimateRichness | 0.095 | 0.005 | 0.100 | |
getCrossAssociation | 1.634 | 0.010 | 1.644 | |
getDominant | 0.728 | 0.007 | 0.735 | |
getMediation | 0.000 | 0.000 | 0.001 | |
getPrevalence | 1.781 | 0.039 | 1.819 | |
hierarchy-tree | 6.387 | 0.351 | 6.738 | |
importHUMAnN | 0.089 | 0.000 | 0.091 | |
importMetaPhlAn | 1.392 | 0.017 | 1.413 | |
importMothur | 0.075 | 0.001 | 0.076 | |
importQIIME2 | 0.334 | 0.045 | 0.379 | |
isContaminant | 0.119 | 0.002 | 0.121 | |
makePhyloseqFromTreeSE | 0.617 | 0.028 | 0.646 | |
makeTreeSEFromBiom | 0.199 | 0.002 | 0.202 | |
makeTreeSEFromDADA2 | 2.674 | 0.082 | 2.755 | |
makeTreeSEFromPhyloseq | 0.453 | 0.024 | 0.479 | |
meltSE | 0.353 | 0.025 | 0.378 | |
mergeSEs | 1.955 | 0.080 | 2.036 | |
mia-datasets | 0.186 | 0.003 | 0.189 | |
rarefyAssay | 0.570 | 0.021 | 0.590 | |
relabundance | 0.167 | 0.007 | 0.175 | |
runCCA | 29.394 | 0.091 | 29.488 | |
runDPCoA | 0.121 | 0.005 | 0.126 | |
runNMDS | 0.082 | 0.003 | 0.085 | |
splitOn | 1.795 | 0.034 | 1.831 | |
subsetSamples | 0.268 | 0.005 | 0.274 | |
summaries | 1.076 | 0.013 | 1.089 | |
taxonomy-methods | 0.360 | 0.003 | 0.364 | |
transformAssay | 0.053 | 0.001 | 0.053 | |