Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 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" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 125/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Banksy 1.1.0 (landing page) Joseph Lee
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | TIMEOUT | skipped | skipped | |||||||||
To the developers/maintainers of the Banksy package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Banksy.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: Banksy |
Version: 1.1.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Banksy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Banksy_1.1.0.tar.gz |
StartedAt: 2024-06-10 00:01:06 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 00:09:12 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 485.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Banksy.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Banksy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Banksy_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Banksy.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Banksy/DESCRIPTION’ ... OK * this is package ‘Banksy’ version ‘1.1.0’ * 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 ‘Banksy’ 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 whether startup messages can be suppressed ... 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 ... NOTE checkRd: (-1) computeBanksy.Rd:81: 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 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/Banksy.Rcheck/00check.log’ for details.
Banksy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Banksy ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Banksy’ ... ** 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 (Banksy)
Banksy.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: 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(Banksy) > > test_check("Banksy") 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 Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Using seed=1000 Using seed=1000 Using seed=1000 Using seed=1000 clust_M1_lam0.2_k50_res1 --> cluster Iteration 1 Change: 25 Iteration 2 Change: 19 Iteration 3 Change: 13 Iteration 4 Change: 10 Iteration 5 Change: 1 Iteration 6 Change: 0 Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=30 Subsampling to 15 neighbors Using seed=1000 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=30 Subsampling to 15 neighbors Using seed=1000 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=309 Computing neighbors... Spatial mode is kNN_unif Parameters: k_geom = 15 Done Computing neighbors... Spatial mode is kNN_unif Parameters: k_geom = 15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_unif Parameters: k_geom = 309 Computing neighbors... Spatial mode is kNN_rn Parameters: k_geom=15, n=2 Done Computing neighbors... Spatial mode is kNN_rn Parameters: k_geom=15, n=2 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_rn Parameters: k_geom=309, n=2 Computing neighbors... Spatial mode is kNN_r Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_r Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_r Parameters: k_geom=309 Computing neighbors... Spatial mode is kNN_rank Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_rank Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_rank Parameters: k_geom=309 Computing neighbors... Spatial mode is rNN gaussian Parameters: sigma=1.5, k_spatial=100 Done Computing neighbors... Spatial mode is rNN gaussian Parameters: sigma=1.5, k_spatial=100 Done Computing harmonic m = 0 Using 9 neighbors Done Computing harmonic m = 1 Using 9 neighbors Centering Done Computing neighbors... Spatial mode is rNN gaussian Parameters: sigma=1.5, k_spatial=309 Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done Scaling counts Group: 1 Group: 2 Group: 3 Group: 4 Scaling harmonic m = 0 Group: 1 Group: 2 Group: 3 Group: 4 Scaling harmonic m = 1 Group: 1 Group: 2 Group: 3 Group: 4 Scaling counts Group: 1 Group: 2 Group: 3 Group: 4 Scaling harmonic m = 0 Group: 1 Group: 2 Group: 3 Group: 4 Scaling harmonic m = 1 Group: 1 Group: 2 Group: 3 Group: 4 Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Computing harmonic m = 0 Using 15 neighbors Done Computing harmonic m = 1 Using 15 neighbors Centering Done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 70 ] > > proc.time() user system elapsed 42.669 1.622 49.800
Banksy.Rcheck/Banksy-Ex.timings
name | user | system | elapsed | |
clusterBanksy | 2.674 | 0.056 | 3.067 | |
clusterNames | 1.564 | 0.035 | 1.845 | |
compareClusters | 1.232 | 0.031 | 1.414 | |
computeBanksy | 0.421 | 0.012 | 0.544 | |
connectClusters | 1.573 | 0.024 | 1.863 | |
getBanksyMatrix | 0.455 | 0.011 | 0.534 | |
runBanksyPCA | 0.585 | 0.010 | 0.690 | |
runBanksyUMAP | 4.253 | 0.033 | 4.835 | |
simulateDataset | 1.444 | 0.033 | 1.658 | |
smoothLabels | 1.711 | 0.109 | 2.048 | |