Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 277/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CATALYST 1.28.0 (landing page) Helena L. Crowell
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the CATALYST 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: CATALYST |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.28.0.tar.gz |
StartedAt: 2024-05-06 20:10:30 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 20:14:01 -0400 (Mon, 06 May 2024) |
EllapsedTime: 210.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: CATALYST.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CATALYST.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘CATALYST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CATALYST’ version ‘1.28.0’ * 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 ‘CATALYST’ 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 ... NOTE checkRd: (-1) plotDiffHeatmap.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotDiffHeatmap.Rd:88: 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 LazyData ... 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’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: c(y) not identical to c(ms). Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CATALYST.Rcheck/00check.log’ for details.
CATALYST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CATALYST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘CATALYST’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CATALYST)
CATALYST.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24) -- "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(CATALYST) Loading required package: SingleCellExperiment 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 > > test_check("CATALYST") [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_plotDiffHeatmap.R:36:5'): plotDiffHeatmap() - DA ───────────── all(colSums(y) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_plotMultiHeatmap.R:26:5'): plotMultiHeatmap() - hm2 = 'abundances' ── all(colSums(y) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_plotMultiHeatmap.R:43:5'): plotMultiHeatmap() - hm2 = 'state' ── c(y) not identical to c(ms). Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ── p@ht_list[[i + 1]]@matrix not identical to meds[[i]]. Objects equal but not identical [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ] Error: Test failures Execution halted
CATALYST.Rcheck/CATALYST-Ex.timings
name | user | system | elapsed | |
SCE-accessors | 2.259 | 0.124 | 2.386 | |
adaptSpillmat | 1.123 | 0.087 | 1.213 | |
applyCutoffs | 0.957 | 0.044 | 1.003 | |
assignPrelim | 0.514 | 0.012 | 0.527 | |
clrDR | 1.978 | 0.112 | 2.110 | |
cluster | 2.033 | 0.135 | 2.169 | |
compCytof | 2.018 | 0.135 | 2.154 | |
computeSpillmat | 0.993 | 0.044 | 1.038 | |
data | 0.001 | 0.006 | 0.007 | |
estCutoffs | 1.128 | 0.044 | 1.174 | |
extractClusters | 1.331 | 0.127 | 1.461 | |
filterSCE | 1.839 | 0.176 | 2.016 | |
guessPanel | 0.011 | 0.001 | 0.013 | |
mergeClusters | 1.716 | 0.136 | 1.854 | |
normCytof | 0.778 | 0.019 | 0.797 | |
pbMDS | 2.089 | 0.288 | 2.380 | |
plotAbundances | 2.074 | 0.157 | 2.238 | |
plotClusterExprs | 2.425 | 0.164 | 2.592 | |
plotCodes | 1.957 | 0.085 | 2.043 | |
plotCounts | 0.299 | 0.005 | 0.303 | |
plotDR | 4.555 | 0.312 | 4.867 | |
plotDiffHeatmap | 3.435 | 0.192 | 3.634 | |
plotEvents | 0.559 | 0.009 | 0.569 | |
plotExprHeatmap | 2.986 | 0.127 | 3.115 | |
plotExprs | 1.063 | 0.055 | 1.119 | |
plotFreqHeatmap | 2.552 | 0.128 | 2.685 | |
plotMahal | 1.571 | 0.020 | 1.591 | |
plotMultiHeatmap | 4.182 | 0.091 | 4.275 | |
plotNRS | 0.381 | 0.005 | 0.387 | |
plotPbExprs | 3.611 | 0.074 | 3.687 | |
plotScatter | 1.476 | 0.035 | 1.514 | |
plotSpillmat | 1.704 | 0.074 | 1.779 | |
plotYields | 1.130 | 0.052 | 1.182 | |
prepData | 0.515 | 0.014 | 0.529 | |
runDR | 2.336 | 0.008 | 2.342 | |
sce2fcs | 3.265 | 0.114 | 3.380 | |