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 12:04 -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 1483/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.24.0 (landing page) Christian Mertes
| 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 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: 1.24.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OUTRIDER_1.24.0.tar.gz |
StartedAt: 2024-12-20 03:56:25 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:10:45 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 859.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OUTRIDER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OUTRIDER_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.24.0’ * 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 ‘OUTRIDER’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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. * 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) results.Rd:48-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) results.Rd:68-71: 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 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 19.842 0.488 20.928 OUTRIDER 11.957 3.491 13.484 findEncodingDim 11.220 0.537 11.789 results 9.495 0.247 9.807 getter_setter_functions 6.563 0.057 7.846 * 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: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.20-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 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 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: GenomeInfoDb 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] "Fri Dec 20 04:05:36 2024: Initial PCA loss: 6.59081843406025" [1] "Fri Dec 20 04:05:40 2024: Iteration: 1 loss: 4.90001772457774" [1] "Fri Dec 20 04:05:43 2024: Iteration: 2 loss: 4.82691518955841" [1] "Fri Dec 20 04:05:44 2024: Iteration: 3 loss: 4.78884736511531" [1] "Fri Dec 20 04:05:45 2024: Iteration: 4 loss: 4.76938866574421" [1] "Fri Dec 20 04:05:46 2024: Iteration: 5 loss: 4.75865351791402" [1] "Fri Dec 20 04:05:47 2024: Iteration: 6 loss: 4.75521340556111" Time difference of 8.785697 secs [1] "Fri Dec 20 04:05:47 2024: 6 Final nb-AE loss: 4.75521340556111" [1] "Fri Dec 20 04:05:50 2024: Initial PCA loss: 6.59081843406025" [1] "Fri Dec 20 04:05:53 2024: Iteration: 1 loss: 4.90001772457774" [1] "Fri Dec 20 04:05:55 2024: Iteration: 2 loss: 4.82691518955841" [1] "Fri Dec 20 04:05:56 2024: Iteration: 3 loss: 4.78884736511531" [1] "Fri Dec 20 04:05:57 2024: Iteration: 4 loss: 4.76938866574421" [1] "Fri Dec 20 04:05:58 2024: Iteration: 5 loss: 4.75865351791402" [1] "Fri Dec 20 04:05:59 2024: Iteration: 6 loss: 4.75521340556111" Time difference of 7.210284 secs [1] "Fri Dec 20 04:05:59 2024: 6 Final nb-AE loss: 4.75521340556111" 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] "Fri Dec 20 04:06:13 2024: Initial PCA loss: 4.4812509618378" [1] "Fri Dec 20 04:06:14 2024: Iteration: 1 loss: 4.14473017971666" [1] "Fri Dec 20 04:06:14 2024: Iteration: 2 loss: 4.12681727950227" Time difference of 1.306561 secs [1] "Fri Dec 20 04:06:14 2024: 2 Final nb-AE loss: 4.12681727950227" [1] "Evaluation loss: 0.665953508753008 for q=3" [1] "Fri Dec 20 04:06:15 2024: Initial PCA loss: 4.45161029233932" [1] "Fri Dec 20 04:06:16 2024: Iteration: 1 loss: 4.07112198664084" [1] "Fri Dec 20 04:06:17 2024: Iteration: 2 loss: 4.06034682077759" Time difference of 1.209326 secs [1] "Fri Dec 20 04:06:17 2024: 2 Final nb-AE loss: 4.06034682077759" [1] "Evaluation loss: 0.606938714269111 for q=4" [1] "Fri Dec 20 04:06:18 2024: Initial PCA loss: 4.4286422491779" [1] "Fri Dec 20 04:06:19 2024: Iteration: 1 loss: 3.99122416140893" [1] "Fri Dec 20 04:06:19 2024: Iteration: 2 loss: 3.9697655715224" Time difference of 1.269724 secs [1] "Fri Dec 20 04:06:19 2024: 2 Final nb-AE loss: 3.9697655715224" [1] "Evaluation loss: 0.57254336276334 for q=5" [1] "Fri Dec 20 04:06:27 2024: Initial PCA loss: 7.16457134714849" [1] "Fri Dec 20 04:06:29 2024: Iteration: 1 loss: 6.82915922411761" [1] "Fri Dec 20 04:06:29 2024: Iteration: 2 loss: 6.82750047452709" Time difference of 1.625522 secs [1] "Fri Dec 20 04:06:29 2024: 2 Final nb-AE loss: 6.82750047452709" [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] > > proc.time() user system elapsed 91.472 2.485 98.251
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 11.957 | 3.491 | 13.484 | |
OutriderDataSet-class | 0.797 | 0.094 | 0.891 | |
aberrant | 1.874 | 1.085 | 1.882 | |
computeGeneLength | 1.462 | 0.257 | 1.720 | |
computeLatentSpace | 0.686 | 0.024 | 0.711 | |
computePvalues | 2.007 | 2.490 | 2.562 | |
computeZscores | 0.873 | 0.158 | 1.031 | |
controlForConfounders | 1.068 | 0.143 | 1.213 | |
counts | 0.527 | 0.012 | 0.540 | |
estimateBestQ | 0.374 | 0.019 | 0.394 | |
filterExpression | 1.538 | 0.128 | 1.666 | |
findEncodingDim | 11.220 | 0.537 | 11.789 | |
fit | 0.949 | 0.046 | 0.995 | |
fpkm | 0.871 | 0.021 | 0.892 | |
getter_setter_functions | 6.563 | 0.057 | 7.846 | |
makeExampleOutriderDataSet | 2.032 | 0.009 | 2.041 | |
normalizationFactors | 0.731 | 0.002 | 0.732 | |
plotFunctions | 19.842 | 0.488 | 20.928 | |
results | 9.495 | 0.247 | 9.807 | |
sampleExclusionMask | 0.575 | 0.117 | 0.698 | |
sizeFactors | 0.755 | 0.073 | 0.828 | |