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This page was generated on 2024-05-20 11:32:15 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 1220/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miaViz 1.13.0 (landing page) Tuomas Borman
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the miaViz package: - 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: miaViz |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miaViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miaViz_1.13.0.tar.gz |
StartedAt: 2024-05-19 18:57:29 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 19:07:05 -0400 (Sun, 19 May 2024) |
EllapsedTime: 575.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miaViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miaViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miaViz_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/miaViz.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘miaViz/DESCRIPTION’ ... OK * this is package ‘miaViz’ version ‘1.13.0’ * 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 ‘miaViz’ 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 ... NOTE .add_signif_to_vector_labels : <anonymous>: no visible global function definition for ‘italic’ .clean_tree_data: no visible global function definition for ‘all_of’ .get_prevalence_plot_matrix: no visible binding for global variable ‘ID’ .rda_plotter: no visible binding for global variable ‘color’ Undefined global functions or variables: ID all_of color italic * checking Rd files ... NOTE checkRd: (-1) plotAbundanceDensity.Rd:30-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:33-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:46-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:49-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotAbundanceDensity.Rd:52-53: Lost braces in \itemize; meant \describe ? * 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 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 plotTree 49.341 1.147 50.556 plotDMN 18.890 0.041 18.966 plotAbundanceDensity 13.238 1.238 16.880 plotAbundance 9.064 0.285 9.353 plotPrevalence 8.017 0.087 8.108 plotCCA 5.684 0.106 5.793 * 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-mac-arm64/meat/miaViz.Rcheck/00check.log’ for details.
miaViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miaViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘miaViz’ ... ** using staged installation ** R ** data ** 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 (miaViz)
miaViz.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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(miaViz) 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: TreeSummarizedExperiment Loading required package: SingleCellExperiment Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: mia Loading required package: MultiAssayExperiment Loading required package: ggplot2 Loading required package: ggraph > > test_check("miaViz") stringi (1.8.3 -> 1.8.4) [CRAN] farver (2.1.1 -> 2.1.2) [CRAN] systemfonts (1.0.6 -> 1.1.0) [CRAN] dqrng (0.3.2 -> 0.4.0) [CRAN] ragg (1.3.0 -> 1.3.2) [CRAN] fastmap (1.1.1 -> 1.2.0) [CRAN] cachem (1.0.8 -> 1.1.0) [CRAN] vegan (2.6-4 -> 2.6-6) [CRAN] trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/stringi_1.8.4.tgz' Content type 'application/x-gzip' length 14772477 bytes (14.1 MB) ================================================== downloaded 14.1 MB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/farver_2.1.2.tgz' Content type 'application/x-gzip' length 1968704 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/systemfonts_1.1.0.tgz' Content type 'application/x-gzip' length 6589647 bytes (6.3 MB) ================================================== downloaded 6.3 MB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/dqrng_0.4.0.tgz' Content type 'application/x-gzip' length 626105 bytes (611 KB) ================================================== downloaded 611 KB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/ragg_1.3.2.tgz' Content type 'application/x-gzip' length 10898401 bytes (10.4 MB) ================================================== downloaded 10.4 MB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/fastmap_1.2.0.tgz' Content type 'application/x-gzip' length 192461 bytes (187 KB) ================================================== downloaded 187 KB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/cachem_1.1.0.tgz' Content type 'application/x-gzip' length 69683 bytes (68 KB) ================================================== downloaded 68 KB trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/vegan_2.6-6.tgz' Content type 'application/x-gzip' length 3155010 bytes (3.0 MB) ================================================== downloaded 3.0 MB The downloaded binary packages are in /tmp/Rtmp0BBlkz/downloaded_packages ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/private/tmp/Rtmp0BBlkz/remotes1181f18849f3c/microbiome-miaTime-9fe9771/DESCRIPTION’ ... OK * preparing ‘miaTime’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘miaTime_0.1.21.tar.gz’ * installing *source* package ‘miaTime’ ... ** 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 (miaTime) [ FAIL 0 | WARN 11 | SKIP 0 | PASS 215 ] [ FAIL 0 | WARN 11 | SKIP 0 | PASS 215 ] > > proc.time() user system elapsed 143.518 18.446 181.179
miaViz.Rcheck/miaViz-Ex.timings
name | user | system | elapsed | |
plotAbundance | 9.064 | 0.285 | 9.353 | |
plotAbundanceDensity | 13.238 | 1.238 | 16.880 | |
plotCCA | 5.684 | 0.106 | 5.793 | |
plotColTile | 0.824 | 0.014 | 0.838 | |
plotDMN | 18.890 | 0.041 | 18.966 | |
plotGraph | 0 | 0 | 0 | |
plotPrevalence | 8.017 | 0.087 | 8.108 | |
plotSeries | 0.000 | 0.001 | 0.000 | |
plotTree | 49.341 | 1.147 | 50.556 | |
treeData | 0.875 | 0.033 | 0.909 | |