Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-27 11:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1463/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.23.0 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-08-26 22:18:41 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:28:42 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 601.0 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OUTRIDER.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.23.0’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 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 15.492 0.902 16.558 OUTRIDER 12.429 2.691 13.909 findEncodingDim 13.102 0.224 13.386 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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++11 -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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(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 Aug 26 22:27:24 2024: Initial PCA loss: 6.41165239687408" [1] "Mon Aug 26 22:27:26 2024: Iteration: 1 loss: 4.55404598621925" [1] "Mon Aug 26 22:27:27 2024: Iteration: 2 loss: 4.50372740646073" [1] "Mon Aug 26 22:27:27 2024: Iteration: 3 loss: 4.48633702990051" [1] "Mon Aug 26 22:27:28 2024: Iteration: 4 loss: 4.47675648193484" [1] "Mon Aug 26 22:27:29 2024: Iteration: 5 loss: 4.46588688753117" [1] "Mon Aug 26 22:27:30 2024: Iteration: 6 loss: 4.45777975255916" Time difference of 4.614315 secs [1] "Mon Aug 26 22:27:30 2024: 6 Final nb-AE loss: 4.45777975255916" [1] "Mon Aug 26 22:27:31 2024: Initial PCA loss: 6.41165239687408" [1] "Mon Aug 26 22:27:32 2024: Iteration: 1 loss: 4.55404598621925" [1] "Mon Aug 26 22:27:33 2024: Iteration: 2 loss: 4.50372740646073" [1] "Mon Aug 26 22:27:34 2024: Iteration: 3 loss: 4.48633702990051" [1] "Mon Aug 26 22:27:34 2024: Iteration: 4 loss: 4.47675648193484" [1] "Mon Aug 26 22:27:35 2024: Iteration: 5 loss: 4.46588688753117" [1] "Mon Aug 26 22:27:36 2024: Iteration: 6 loss: 4.45777975255916" Time difference of 4.293995 secs [1] "Mon Aug 26 22:27:36 2024: 6 Final nb-AE loss: 4.45777975255916" 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 26 22:27:51 2024: Initial PCA loss: 4.52459032260352" [1] "Mon Aug 26 22:27:53 2024: Iteration: 1 loss: 4.16312071878356" [1] "Mon Aug 26 22:27:53 2024: Iteration: 2 loss: 4.15123560227318" Time difference of 1.443414 secs [1] "Mon Aug 26 22:27:53 2024: 2 Final nb-AE loss: 4.15123560227318" [1] "Evaluation loss: 0.56395949959585 for q=3" [1] "Mon Aug 26 22:27:54 2024: Initial PCA loss: 4.49462588441018" [1] "Mon Aug 26 22:27:56 2024: Iteration: 1 loss: 4.1048087003128" [1] "Mon Aug 26 22:27:56 2024: Iteration: 2 loss: 4.09503868365568" Time difference of 1.478351 secs [1] "Mon Aug 26 22:27:56 2024: 2 Final nb-AE loss: 4.09503868365568" [1] "Evaluation loss: 0.502638172647404 for q=4" [1] "Mon Aug 26 22:27:57 2024: Initial PCA loss: 4.45703378530061" [1] "Mon Aug 26 22:27:59 2024: Iteration: 1 loss: 3.99623175710309" [1] "Mon Aug 26 22:27:59 2024: Iteration: 2 loss: 3.96938275881799" Time difference of 1.471276 secs [1] "Mon Aug 26 22:27:59 2024: 2 Final nb-AE loss: 3.96938275881799" [1] "Evaluation loss: 0.414258973449991 for q=5" [1] "Mon Aug 26 22:28:10 2024: Initial PCA loss: 7.16457134714849" [1] "Mon Aug 26 22:28:12 2024: Iteration: 1 loss: 6.82914691619536" [1] "Mon Aug 26 22:28:13 2024: Iteration: 2 loss: 6.82749571057606" Time difference of 1.846466 secs [1] "Mon Aug 26 22:28:13 2024: 2 Final nb-AE loss: 6.82749571057606" [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] > > proc.time() user system elapsed 86.838 2.362 89.791
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 12.429 | 2.691 | 13.909 | |
OutriderDataSet-class | 0.999 | 0.067 | 1.075 | |
aberrant | 2.208 | 0.775 | 2.154 | |
computeGeneLength | 1.699 | 0.135 | 1.840 | |
computeLatentSpace | 0.815 | 0.009 | 0.827 | |
computePvalues | 2.667 | 1.736 | 3.117 | |
computeZscores | 1.044 | 0.093 | 1.142 | |
controlForConfounders | 1.286 | 0.136 | 1.562 | |
counts | 0.618 | 0.007 | 0.628 | |
estimateBestQ | 0.470 | 0.007 | 0.480 | |
filterExpression | 1.707 | 0.035 | 1.765 | |
findEncodingDim | 13.102 | 0.224 | 13.386 | |
fit | 1.022 | 0.012 | 1.038 | |
fpkm | 0.852 | 0.009 | 0.865 | |
getter_setter_functions | 3.393 | 0.024 | 3.431 | |
makeExampleOutriderDataSet | 1.286 | 0.009 | 1.297 | |
normalizationFactors | 0.828 | 0.006 | 0.836 | |
plotFunctions | 15.492 | 0.902 | 16.558 | |
results | 4.059 | 0.119 | 4.338 | |
sampleExclusionMask | 0.517 | 0.006 | 0.528 | |
sizeFactors | 1.932 | 0.020 | 1.975 | |