Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1522/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.27.2 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the OUTRIDER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.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: OUTRIDER |
Version: 1.27.2 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OUTRIDER_1.27.2.tar.gz |
StartedAt: 2025-10-11 02:49:34 -0400 (Sat, 11 Oct 2025) |
EndedAt: 2025-10-11 03:04:59 -0400 (Sat, 11 Oct 2025) |
EllapsedTime: 925.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OUTRIDER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OUTRIDER_1.27.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.27.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘OUTRIDER’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'ggbio:::.buildFacetsFromArgs' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'checkOutriderDataSet' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE estimateBestQ: no visible binding for global variable ‘oht’ plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘oht’ plotEncDimSearch.OUTRIDER: no visible binding for global variable ‘singular_values’ plotEncDimSearch,OutriderDataSet: no visible binding for global variable ‘oht’ plotEncDimSearch,OutriderDataSet: no visible binding for global variable ‘singular_values’ Undefined global functions or variables: oht singular_values * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'getter_setter_functions.Rd': ‘[DESeq2]{estimateDispersions}’ Non-topic package-anchored link(s) in Rd file 'sizeFactors.Rd': ‘[DESeq2]{estimateSizeFactors}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotFunctions 32.461 1.176 30.525 estimateBestQ 21.645 1.018 24.695 OUTRIDER 11.284 3.528 12.997 results 7.640 0.350 8.708 computePvalues 2.180 2.872 2.840 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘OUTRIDER’ ... ** this is package ‘OUTRIDER’ version ‘1.27.2’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -Werror=format-security -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OUTRIDER/00new/OUTRIDER/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OUTRIDER)
OUTRIDER.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(OUTRIDER) Loading required package: BiocParallel Loading required package: GenomicFeatures Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 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: Seqinfo Loading required package: GenomicRanges Loading required package: AnnotationDbi 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")'. Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:SummarizedExperiment': shift The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second > > register(SerialParam()) > > test_check("OUTRIDER") [1] "Sat Oct 11 02:59:45 2025: Initial PCA loss: 6.01378526312835" [1] "Sat Oct 11 02:59:46 2025: Iteration: 1 loss: 4.30597708836917" [1] "Sat Oct 11 02:59:47 2025: Iteration: 2 loss: 4.26433036184216" [1] "Sat Oct 11 02:59:47 2025: Iteration: 3 loss: 4.25308004192391" [1] "Sat Oct 11 02:59:48 2025: Iteration: 4 loss: 4.24410982224386" [1] "Sat Oct 11 02:59:49 2025: Iteration: 5 loss: 4.23109611231499" [1] "Sat Oct 11 02:59:49 2025: Iteration: 6 loss: 4.22516408365566" Time difference of 3.904401 secs [1] "Sat Oct 11 02:59:49 2025: 6 Final nb-AE loss: 4.22516408365566" [1] "Sat Oct 11 02:59:50 2025: Initial PCA loss: 6.01378526312835" [1] "Sat Oct 11 02:59:51 2025: Iteration: 1 loss: 4.30597708836917" [1] "Sat Oct 11 02:59:52 2025: Iteration: 2 loss: 4.26433036184216" [1] "Sat Oct 11 02:59:53 2025: Iteration: 3 loss: 4.25308004192391" [1] "Sat Oct 11 02:59:53 2025: Iteration: 4 loss: 4.24410982224386" [1] "Sat Oct 11 02:59:54 2025: Iteration: 5 loss: 4.23109611231499" [1] "Sat Oct 11 02:59:54 2025: Iteration: 6 loss: 4.22516408365566" Time difference of 3.665596 secs [1] "Sat Oct 11 02:59:54 2025: 6 Final nb-AE loss: 4.22516408365566" class: OutriderDataSet class: RangedSummarizedExperiment dim: 100 50 metadata(1): version assays(1): counts rownames(100): ENSG00000223972.4 ENSG00000227232.4 ... ENSG00000107404.13 ENSG00000162576.12 rowData names(0): colnames(50): GTEX.UPK5.0426.SM.3GAEK GTEX.WFG7.2026.SM.3GIL7 ... GTEX.11UD2.2526.SM.5CVNU GTEX.13O61.1426.SM.5KM3D colData names(1): sampleID [1] "Sat Oct 11 03:00:00 2025: Initial PCA loss: 4.44593225407183" [1] "Sat Oct 11 03:00:01 2025: Iteration: 1 loss: 4.07529220856415" [1] "Sat Oct 11 03:00:02 2025: Iteration: 2 loss: 4.06393646301289" Time difference of 1.275239 secs [1] "Sat Oct 11 03:00:02 2025: 2 Final nb-AE loss: 4.06393646301289" [1] "Evaluation loss: 0.158348989269851 for q=3" [1] "Sat Oct 11 03:00:02 2025: Initial PCA loss: 4.41838724853205" [1] "Sat Oct 11 03:00:03 2025: Iteration: 1 loss: 4.01779331591635" [1] "Sat Oct 11 03:00:04 2025: Iteration: 2 loss: 4.00422694638347" Time difference of 1.211627 secs [1] "Sat Oct 11 03:00:04 2025: 2 Final nb-AE loss: 4.00422694638347" [1] "Evaluation loss: 0.160521465721718 for q=4" [1] "Sat Oct 11 03:00:05 2025: Initial PCA loss: 4.39769628196885" [1] "Sat Oct 11 03:00:06 2025: Iteration: 1 loss: 3.93764335667627" [1] "Sat Oct 11 03:00:06 2025: Iteration: 2 loss: 3.91756871704361" Time difference of 1.238494 secs [1] "Sat Oct 11 03:00:06 2025: 2 Final nb-AE loss: 3.91756871704361" [1] "Evaluation loss: 0.0484218787613502 for q=5" Optimal encoding dimension: 4 Optimal encoding dimension: 50 Optimal encoding dimension: 20 Optimal encoding dimension: 2 Optimal encoding dimension: 4 [1] "Sat Oct 11 03:00:34 2025: Initial PCA loss: 7.16457134714849" [1] "Sat Oct 11 03:00:36 2025: Iteration: 1 loss: 6.82914112812595" [1] "Sat Oct 11 03:00:36 2025: Iteration: 2 loss: 6.82749097859465" Time difference of 1.478806 secs [1] "Sat Oct 11 03:00:36 2025: 2 Final nb-AE loss: 6.82749097859465" [ FAIL 0 | WARN 12 | SKIP 0 | PASS 131 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 131 ] > > proc.time() user system elapsed 98.908 2.863 104.706
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 11.284 | 3.528 | 12.997 | |
OutriderDataSet-class | 0.789 | 0.121 | 0.911 | |
aberrant | 1.787 | 1.230 | 2.022 | |
computeGeneLength | 1.586 | 0.332 | 1.919 | |
computeLatentSpace | 0.852 | 0.260 | 1.113 | |
computePvalues | 2.180 | 2.872 | 2.840 | |
computeZscores | 0.941 | 0.184 | 1.125 | |
controlForConfounders | 1.091 | 0.187 | 1.279 | |
counts | 0.593 | 0.057 | 0.650 | |
estimateBestQ | 21.645 | 1.018 | 24.695 | |
filterExpression | 1.525 | 0.014 | 1.560 | |
fit | 0.828 | 0.025 | 0.854 | |
fpkm | 0.755 | 0.031 | 0.785 | |
getter_setter_functions | 3.122 | 0.084 | 3.207 | |
makeExampleOutriderDataSet | 1.390 | 0.010 | 1.402 | |
normalizationFactors | 1.342 | 0.002 | 1.345 | |
plotFunctions | 32.461 | 1.176 | 30.525 | |
results | 7.640 | 0.350 | 8.708 | |
sampleExclusionMask | 1.049 | 0.018 | 1.108 | |
sizeFactors | 2.105 | 0.035 | 2.140 | |