Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1988/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
slingshot 2.14.0 (landing page) Kelly Street
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the slingshot package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/slingshot.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: slingshot |
Version: 2.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:slingshot.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings slingshot_2.14.0.tar.gz |
StartedAt: 2024-12-20 09:51:39 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 09:59:08 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 449.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: slingshot.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:slingshot.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings slingshot_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/slingshot.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘slingshot/DESCRIPTION’ ... OK * this is package ‘slingshot’ version ‘2.14.0’ * 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 ‘slingshot’ 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) SlingshotDataSet-class.Rd:76-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:79-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:81-82: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:83-84: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:85-87: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:88-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:93-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:96-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:100-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:105-112: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:113-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:118-119: Lost braces in \itemize; meant \describe ? checkRd: (-1) SlingshotDataSet-class.Rd:119-121: Lost braces in \itemize; meant \describe ? checkRd: (-1) getCurves.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getCurves.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) newSlingshotDataSet.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:59-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:61-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:63-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:65-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:72-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:76-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:81-88: Lost braces in \itemize; meant \describe ? checkRd: (-1) newSlingshotDataSet.Rd:89-93: Lost braces in \itemize; meant \describe ? checkRd: (-1) slingParams.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:34-36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:45-48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:49-53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:54-61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:62-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) slingParams.Rd:68-70: Lost braces in \itemize; \value handles \item{}{} directly * 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/slingshot.Rcheck/00check.log’ for details.
slingshot.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL slingshot ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘slingshot’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘slingshot’ with signature ‘data="ClusterExperiment"’: no definition for class “ClusterExperiment” ** 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 (slingshot)
slingshot.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(slingshot) Loading required package: princurve Loading required package: TrajectoryUtils 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': 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, saveRDS, 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 > > test_check("slingshot") class: SlingshotDataSet Samples Dimensions 140 2 lineages: 2 Lineage1: 1 2 3 5 Lineage2: 1 2 3 4 curves: 2 Curve1: Length: 15.045 Samples: 100.61 Curve2: Length: 15.126 Samples: 103.49 [ FAIL 0 | WARN 0 | SKIP 1 | PASS 257 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On Mac (1): 'test_slingshot.R:536:5' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 257 ] > > proc.time() user system elapsed 86.840 2.645 90.790
slingshot.Rcheck/slingshot-Ex.timings
name | user | system | elapsed | |
SlingshotDataSet | 2.051 | 0.063 | 2.158 | |
as.PseudotimeOrdering | 2.300 | 0.067 | 2.402 | |
as.SlingshotDataSet | 0.639 | 0.015 | 0.659 | |
embedCurves | 0.713 | 0.016 | 0.805 | |
getCurves | 1.232 | 0.014 | 1.297 | |
getLineages | 0.147 | 0.009 | 0.156 | |
newSlingshotDataSet | 0.003 | 0.001 | 0.003 | |
pairs-SlingshotDataSet | 0.604 | 0.015 | 0.671 | |
plot-SlingshotDataSet | 0.639 | 0.038 | 0.688 | |
plot3d-SlingshotDataSet | 0.000 | 0.001 | 0.000 | |
predict.SlingshotDataSet | 0.656 | 0.012 | 0.675 | |
slingBranchGraph | 0.603 | 0.015 | 0.624 | |
slingBranchID | 0.608 | 0.017 | 0.634 | |
slingClusterLabels | 0.576 | 0.021 | 0.601 | |
slingCurves | 0.608 | 0.057 | 0.679 | |
slingLineages | 0.568 | 0.008 | 0.584 | |
slingMST | 0.573 | 0.014 | 0.590 | |
slingParams | 0.589 | 0.010 | 0.606 | |
slingPseudotime | 0.606 | 0.023 | 0.636 | |
slingReducedDim | 0.568 | 0.016 | 0.586 | |
slingshot | 0.613 | 0.013 | 0.638 | |
slingshotExample | 0.608 | 0.019 | 0.703 | |