Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-19 12:05 -0400 (Tue, 19 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
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 1501/2317 | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.27.2.tar.gz |
StartedAt: 2025-08-18 23:05:09 -0400 (Mon, 18 Aug 2025) |
EndedAt: 2025-08-18 23:15:20 -0400 (Mon, 18 Aug 2025) |
EllapsedTime: 611.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OUTRIDER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OUTRIDER_1.27.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotFunctions 15.616 0.869 16.619 OUTRIDER 12.316 2.458 13.520 estimateBestQ 13.634 0.252 13.987 results 5.100 0.067 5.188 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** this is package ‘OUTRIDER’ version ‘1.27.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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(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] "Mon Aug 18 23:13:59 2025: Initial PCA loss: 6.13155221804268" [1] "Mon Aug 18 23:14:01 2025: Iteration: 1 loss: 4.36605227521053" [1] "Mon Aug 18 23:14:02 2025: Iteration: 2 loss: 4.29955956977034" [1] "Mon Aug 18 23:14:02 2025: Iteration: 3 loss: 4.27674067823598" [1] "Mon Aug 18 23:14:03 2025: Iteration: 4 loss: 4.26308238265888" [1] "Mon Aug 18 23:14:04 2025: Iteration: 5 loss: 4.25428750930756" [1] "Mon Aug 18 23:14:04 2025: Iteration: 6 loss: 4.24932354844554" Time difference of 4.530028 secs [1] "Mon Aug 18 23:14:04 2025: 6 Final nb-AE loss: 4.24932354844554" [1] "Mon Aug 18 23:14:06 2025: Initial PCA loss: 6.13155221804268" [1] "Mon Aug 18 23:14:07 2025: Iteration: 1 loss: 4.36605227521053" [1] "Mon Aug 18 23:14:08 2025: Iteration: 2 loss: 4.29955956977034" [1] "Mon Aug 18 23:14:09 2025: Iteration: 3 loss: 4.27674067823598" [1] "Mon Aug 18 23:14:09 2025: Iteration: 4 loss: 4.26308238265888" [1] "Mon Aug 18 23:14:10 2025: Iteration: 5 loss: 4.25428750930756" [1] "Mon Aug 18 23:14:11 2025: Iteration: 6 loss: 4.24932354844554" Time difference of 4.581938 secs [1] "Mon Aug 18 23:14:11 2025: 6 Final nb-AE loss: 4.24932354844554" 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] "Mon Aug 18 23:14:17 2025: Initial PCA loss: 4.47811317395699" [1] "Mon Aug 18 23:14:19 2025: Iteration: 1 loss: 4.11977399054898" [1] "Mon Aug 18 23:14:19 2025: Iteration: 2 loss: 4.10953023679592" Time difference of 1.435535 secs [1] "Mon Aug 18 23:14:19 2025: 2 Final nb-AE loss: 4.10953023679592" [1] "Evaluation loss: 0.342565467420194 for q=3" [1] "Mon Aug 18 23:14:20 2025: Initial PCA loss: 4.44889549837298" [1] "Mon Aug 18 23:14:22 2025: Iteration: 1 loss: 4.04372200966076" [1] "Mon Aug 18 23:14:23 2025: Iteration: 2 loss: 4.02233999559359" Time difference of 1.619079 secs [1] "Mon Aug 18 23:14:23 2025: 2 Final nb-AE loss: 4.02233999559359" [1] "Evaluation loss: 0.376468940389151 for q=4" [1] "Mon Aug 18 23:14:24 2025: Initial PCA loss: 4.42748829968766" [1] "Mon Aug 18 23:14:25 2025: Iteration: 1 loss: 3.96118390485688" [1] "Mon Aug 18 23:14:26 2025: Iteration: 2 loss: 3.93114632144612" Time difference of 1.458575 secs [1] "Mon Aug 18 23:14:26 2025: 2 Final nb-AE loss: 3.93114632144612" [1] "Evaluation loss: 0.337794461405286 for q=5" Optimal encoding dimension: 4 Optimal encoding dimension: 50 Optimal encoding dimension: 20 Optimal encoding dimension: 2 Optimal encoding dimension: 4 [1] "Mon Aug 18 23:14:49 2025: Initial PCA loss: 7.16457134714849" [1] "Mon Aug 18 23:14:51 2025: Iteration: 1 loss: 6.82913712406641" [1] "Mon Aug 18 23:14:52 2025: Iteration: 2 loss: 6.82748357330359" Time difference of 1.710256 secs [1] "Mon Aug 18 23:14:52 2025: 2 Final nb-AE loss: 6.82748357330359" [ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ] [ FAIL 0 | WARN 11 | SKIP 0 | PASS 131 ] > > proc.time() user system elapsed 90.047 2.300 92.778
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 12.316 | 2.458 | 13.520 | |
OutriderDataSet-class | 0.956 | 0.063 | 1.027 | |
aberrant | 2.101 | 0.733 | 2.023 | |
computeGeneLength | 1.599 | 0.135 | 1.743 | |
computeLatentSpace | 0.830 | 0.007 | 0.841 | |
computePvalues | 2.602 | 1.510 | 2.866 | |
computeZscores | 1.129 | 0.315 | 1.390 | |
controlForConfounders | 1.319 | 0.060 | 1.390 | |
counts | 0.634 | 0.009 | 0.646 | |
estimateBestQ | 13.634 | 0.252 | 13.987 | |
filterExpression | 1.630 | 0.015 | 1.652 | |
fit | 1.009 | 0.013 | 1.029 | |
fpkm | 0.896 | 0.011 | 0.909 | |
getter_setter_functions | 3.211 | 0.021 | 3.245 | |
makeExampleOutriderDataSet | 1.196 | 0.009 | 1.210 | |
normalizationFactors | 0.720 | 0.005 | 0.729 | |
plotFunctions | 15.616 | 0.869 | 16.619 | |
results | 5.100 | 0.067 | 5.188 | |
sampleExclusionMask | 0.457 | 0.038 | 0.497 | |
sizeFactors | 0.693 | 0.029 | 0.725 | |