Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:40:07 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 2187/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
UMI4Cats 1.13.0 (landing page) Mireia Ramos-Rodriguez
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the UMI4Cats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/UMI4Cats.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: UMI4Cats |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UMI4Cats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UMI4Cats_1.13.0.tar.gz |
StartedAt: 2024-03-02 12:11:51 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 12:25:13 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 802.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: UMI4Cats.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UMI4Cats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UMI4Cats_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/UMI4Cats.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘UMI4Cats/DESCRIPTION’ ... OK * this is package ‘UMI4Cats’ 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 ‘UMI4Cats’ 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 R 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 ... 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 UMI4C 8.207 0.180 9.710 plotUMI4C 7.111 0.101 8.688 callInteractions 5.884 0.262 7.236 UMI4C-methods 5.136 0.295 6.372 waldUMI4C 5.066 0.085 5.910 plotDifferential 4.982 0.126 5.948 plotDomainogram 4.496 0.177 5.362 getSignInteractions 4.386 0.139 5.286 fisherUMI4C 4.270 0.081 5.048 digestGenome 4.087 0.249 5.155 * 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: FileForFormat > > test_check("UMI4Cats") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-statsUMI4C.R:8:3'): Stats plot output is correct ───────────── length(stats_plot) not equal to 9. 1/1 mismatches [1] 11 - 9 == 2 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] 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 See ‘/Users/biocbuild/bbs-3.19-bioc/meat/UMI4Cats.Rcheck/00check.log’ for details.
UMI4Cats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL UMI4Cats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘UMI4Cats’ ... ** 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 (UMI4Cats)
UMI4Cats.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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(UMI4Cats) 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 > library(BSgenome) Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat > > test_check("UMI4Cats") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-statsUMI4C.R:8:3'): Stats plot output is correct ───────────── length(stats_plot) not equal to 9. 1/1 mismatches [1] 11 - 9 == 2 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] Error: Test failures Execution halted
UMI4Cats.Rcheck/UMI4Cats-Ex.timings
name | user | system | elapsed | |
UMI4C-methods | 5.136 | 0.295 | 6.372 | |
UMI4C | 8.207 | 0.180 | 9.710 | |
addGrouping | 2.824 | 0.047 | 3.344 | |
alignmentUMI4C | 0.001 | 0.001 | 0.001 | |
callInteractions | 5.884 | 0.262 | 7.236 | |
combineUMI4C | 0.742 | 0.018 | 0.921 | |
contactsUMI4C | 0.004 | 0.002 | 0.007 | |
counterUMI4C | 0.002 | 0.001 | 0.004 | |
createGeneAnnotation | 2.725 | 0.155 | 3.439 | |
darken | 0.001 | 0.000 | 0.001 | |
demultiplexFastq | 0.000 | 0.001 | 0.001 | |
differentialNbinomWaldTestUMI4C | 0.000 | 0.002 | 0.002 | |
digestGenome | 4.087 | 0.249 | 5.155 | |
downloadUMI4CexampleData | 0.000 | 0.001 | 0.001 | |
fisherUMI4C | 4.270 | 0.081 | 5.048 | |
getSignInteractions | 4.386 | 0.139 | 5.286 | |
getViewpointCoordinates | 1.239 | 0.100 | 1.560 | |
makeWindowFragments | 0.770 | 0.023 | 0.935 | |
pipe | 0.008 | 0.002 | 0.010 | |
plotDifferential | 4.982 | 0.126 | 5.948 | |
plotDomainogram | 4.496 | 0.177 | 5.362 | |
plotGenes | 2.779 | 0.058 | 3.379 | |
plotTrend | 1.354 | 0.051 | 1.682 | |
plotUMI4C | 7.111 | 0.101 | 8.688 | |
prepUMI4C | 0.001 | 0.001 | 0.001 | |
splitUMI4C | 0.001 | 0.000 | 0.001 | |
statsUMI4C | 1.680 | 0.023 | 2.153 | |
theme | 0.247 | 0.006 | 0.323 | |
themeXYblank | 0.224 | 0.006 | 0.261 | |
themeXblank | 0.287 | 0.005 | 0.353 | |
themeYblank | 0.239 | 0.004 | 0.279 | |
waldUMI4C | 5.066 | 0.085 | 5.910 | |