Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-09-24 22:55 -0400 (Tue, 24 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4760 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4497 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4526 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4475 |
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 1495/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.22.0 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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: 1.22.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OUTRIDER_1.22.0.tar.gz |
StartedAt: 2024-09-23 02:04:32 -0400 (Mon, 23 Sep 2024) |
EndedAt: 2024-09-23 02:19:03 -0400 (Mon, 23 Sep 2024) |
EllapsedTime: 871.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OUTRIDER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OUTRIDER_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OUTRIDER.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.22.0’ * 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 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 13.465 0.343 13.764 OUTRIDER 10.490 3.297 12.258 findEncodingDim 10.808 0.404 11.212 * 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-3.19-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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, 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] "Mon Sep 23 02:13:28 2024: Initial PCA loss: 6.58014123080556" [1] "Mon Sep 23 02:13:29 2024: Iteration: 1 loss: 4.72422615741443" [1] "Mon Sep 23 02:13:29 2024: Iteration: 2 loss: 4.63642601655243" [1] "Mon Sep 23 02:13:30 2024: Iteration: 3 loss: 4.58797015553447" [1] "Mon Sep 23 02:13:31 2024: Iteration: 4 loss: 4.56761192180458" [1] "Mon Sep 23 02:13:31 2024: Iteration: 5 loss: 4.55602920162096" [1] "Mon Sep 23 02:13:32 2024: Iteration: 6 loss: 4.55180206850098" Time difference of 3.758647 secs [1] "Mon Sep 23 02:13:32 2024: 6 Final nb-AE loss: 4.55180206850098" [1] "Mon Sep 23 02:13:34 2024: Initial PCA loss: 6.58014123080556" [1] "Mon Sep 23 02:13:36 2024: Iteration: 1 loss: 4.72422615741443" [1] "Mon Sep 23 02:13:39 2024: Iteration: 2 loss: 4.63642601655243" [1] "Mon Sep 23 02:13:41 2024: Iteration: 3 loss: 4.58797015553447" [1] "Mon Sep 23 02:13:42 2024: Iteration: 4 loss: 4.56761192180458" [1] "Mon Sep 23 02:13:43 2024: Iteration: 5 loss: 4.55602920162096" [1] "Mon Sep 23 02:13:44 2024: Iteration: 6 loss: 4.55180206850098" Time difference of 8.987561 secs [1] "Mon Sep 23 02:13:44 2024: 6 Final nb-AE loss: 4.55180206850098" 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 Sep 23 02:14:03 2024: Initial PCA loss: 4.48586550230548" [1] "Mon Sep 23 02:14:05 2024: Iteration: 1 loss: 4.1424993108323" [1] "Mon Sep 23 02:14:06 2024: Iteration: 2 loss: 4.12419563642996" Time difference of 1.993786 secs [1] "Mon Sep 23 02:14:06 2024: 2 Final nb-AE loss: 4.12419563642996" [1] "Evaluation loss: 0.438981493765322 for q=3" [1] "Mon Sep 23 02:14:07 2024: Initial PCA loss: 4.44231986122511" [1] "Mon Sep 23 02:14:08 2024: Iteration: 1 loss: 4.07649715699974" [1] "Mon Sep 23 02:14:09 2024: Iteration: 2 loss: 4.06539998220339" Time difference of 1.371293 secs [1] "Mon Sep 23 02:14:09 2024: 2 Final nb-AE loss: 4.06539998220339" [1] "Evaluation loss: 0.332055893249971 for q=4" [1] "Mon Sep 23 02:14:11 2024: Initial PCA loss: 4.4221505819054" [1] "Mon Sep 23 02:14:13 2024: Iteration: 1 loss: 3.96128028563685" [1] "Mon Sep 23 02:14:13 2024: Iteration: 2 loss: 3.91897354075445" Time difference of 1.400451 secs [1] "Mon Sep 23 02:14:13 2024: 2 Final nb-AE loss: 3.91897354075445" [1] "Evaluation loss: 0.328801852848731 for q=5" [1] "Mon Sep 23 02:14:28 2024: Initial PCA loss: 7.16457134714849" [1] "Mon Sep 23 02:14:30 2024: Iteration: 1 loss: 6.82915165643358" [1] "Mon Sep 23 02:14:31 2024: Iteration: 2 loss: 6.82749554346071" Time difference of 2.130312 secs [1] "Mon Sep 23 02:14:31 2024: 2 Final nb-AE loss: 6.82749554346071" [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] > > proc.time() user system elapsed 105.403 3.191 113.444
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 10.490 | 3.297 | 12.258 | |
OutriderDataSet-class | 0.778 | 0.132 | 0.911 | |
aberrant | 1.662 | 0.945 | 1.687 | |
computeGeneLength | 1.360 | 0.195 | 1.556 | |
computeLatentSpace | 0.687 | 0.016 | 0.703 | |
computePvalues | 2.003 | 2.387 | 2.381 | |
computeZscores | 0.839 | 0.128 | 0.967 | |
controlForConfounders | 1.024 | 0.128 | 1.152 | |
counts | 0.527 | 0.044 | 0.570 | |
estimateBestQ | 0.384 | 0.036 | 0.420 | |
filterExpression | 1.388 | 0.048 | 1.435 | |
findEncodingDim | 10.808 | 0.404 | 11.212 | |
fit | 0.82 | 0.02 | 0.84 | |
fpkm | 0.648 | 0.016 | 0.664 | |
getter_setter_functions | 2.708 | 0.016 | 2.724 | |
makeExampleOutriderDataSet | 0.96 | 0.00 | 0.96 | |
normalizationFactors | 0.638 | 0.000 | 0.638 | |
plotFunctions | 13.465 | 0.343 | 13.764 | |
results | 3.514 | 0.020 | 3.534 | |
sampleExclusionMask | 0.440 | 0.000 | 0.439 | |
sizeFactors | 0.602 | 0.000 | 0.602 | |