Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the OUTRIDER package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1330/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.10.0 (landing page) Christian Mertes
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: OUTRIDER |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OUTRIDER_1.10.0.tar.gz |
StartedAt: 2021-10-14 22:01:58 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:14:42 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 763.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OUTRIDER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OUTRIDER_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/OUTRIDER.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.10.0’ * 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 * 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 R 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 Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used. * 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 ... OK * 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 findEncodingDim 45.792 0.264 46.106 plotFunctions 25.280 0.422 25.744 aberrant 9.698 2.282 6.260 getter_setter_functions 11.571 0.035 11.632 OUTRIDER 8.735 1.119 9.025 results 9.427 0.069 9.505 fit 6.078 0.106 6.188 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/OUTRIDER.Rcheck/00check.log’ for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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] "Thu Oct 14 22:11:31 2021: Initial PCA loss: 6.52820461605301" [1] "Thu Oct 14 22:11:36 2021: Iteration: 1 loss: 4.63297178626901" [1] "Thu Oct 14 22:11:39 2021: Iteration: 2 loss: 4.55234173455206" [1] "Thu Oct 14 22:11:42 2021: Iteration: 3 loss: 4.51899616672322" [1] "Thu Oct 14 22:11:45 2021: Iteration: 4 loss: 4.49726795737891" [1] "Thu Oct 14 22:11:48 2021: Iteration: 5 loss: 4.48712179628123" [1] "Thu Oct 14 22:11:51 2021: Iteration: 6 loss: 4.4855176435821" Time difference of 17.62503 secs [1] "Thu Oct 14 22:11:51 2021: 6 Final nb-AE loss: 4.4855176435821" [1] "Thu Oct 14 22:11:54 2021: Initial PCA loss: 6.52820461605301" [1] "Thu Oct 14 22:12:00 2021: Iteration: 1 loss: 4.63297178626901" [1] "Thu Oct 14 22:12:03 2021: Iteration: 2 loss: 4.55234173455206" [1] "Thu Oct 14 22:12:06 2021: Iteration: 3 loss: 4.51899616672322" [1] "Thu Oct 14 22:12:09 2021: Iteration: 4 loss: 4.49726795737891" [1] "Thu Oct 14 22:12:12 2021: Iteration: 5 loss: 4.48712179628123" [1] "Thu Oct 14 22:12:15 2021: Iteration: 6 loss: 4.4855176435821" Time difference of 17.77195 secs [1] "Thu Oct 14 22:12:15 2021: 6 Final nb-AE loss: 4.4855176435821" 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] "Thu Oct 14 22:12:45 2021: Initial PCA loss: 4.44901974982455" [1] "Thu Oct 14 22:12:52 2021: Iteration: 1 loss: 4.13588958470146" [1] "Thu Oct 14 22:12:55 2021: Iteration: 2 loss: 4.12842508846871" Time difference of 6.781232 secs [1] "Thu Oct 14 22:12:55 2021: 2 Final nb-AE loss: 4.12842508846871" [1] "Evaluation loss: 0.349664859208444 for q=3" [1] "Thu Oct 14 22:12:58 2021: Initial PCA loss: 4.42436019015585" [1] "Thu Oct 14 22:13:05 2021: Iteration: 1 loss: 4.05226640142655" [1] "Thu Oct 14 22:13:08 2021: Iteration: 2 loss: 4.0402760863617" Time difference of 7.203056 secs [1] "Thu Oct 14 22:13:08 2021: 2 Final nb-AE loss: 4.0402760863617" [1] "Evaluation loss: 0.334758330229599 for q=4" [1] "Thu Oct 14 22:13:11 2021: Initial PCA loss: 4.40145640895893" [1] "Thu Oct 14 22:13:17 2021: Iteration: 1 loss: 3.9744594315801" [1] "Thu Oct 14 22:13:21 2021: Iteration: 2 loss: 3.96167869389219" Time difference of 6.591168 secs [1] "Thu Oct 14 22:13:21 2021: 2 Final nb-AE loss: 3.96167869389219" [1] "Evaluation loss: 0.382425131359587 for q=5" [1] "Thu Oct 14 22:13:44 2021: Initial PCA loss: 6.46616282459588" [1] "Thu Oct 14 22:13:57 2021: Iteration: 1 loss: 4.81534335542007" [1] "Thu Oct 14 22:14:04 2021: Iteration: 2 loss: 4.78989160274581" Time difference of 13.39809 secs [1] "Thu Oct 14 22:14:04 2021: 2 Final nb-AE loss: 4.78989160274581" [ FAIL 0 | WARN 36 | SKIP 0 | PASS 103 ] > > proc.time() user system elapsed 202.097 1.728 204.030
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 8.735 | 1.119 | 9.025 | |
OutriderDataSet-class | 2.471 | 0.023 | 2.496 | |
aberrant | 9.698 | 2.282 | 6.260 | |
computeGeneLength | 2.984 | 0.074 | 3.083 | |
computeLatentSpace | 2.148 | 0.007 | 2.155 | |
computePvalues | 3.022 | 0.906 | 2.923 | |
computeZscores | 2.234 | 0.082 | 2.320 | |
controlForConfounders | 2.982 | 0.026 | 3.011 | |
counts | 1.624 | 0.010 | 1.638 | |
estimateBestQ | 0.931 | 0.003 | 0.937 | |
filterExpression | 3.514 | 0.023 | 3.541 | |
findEncodingDim | 45.792 | 0.264 | 46.106 | |
fit | 6.078 | 0.106 | 6.188 | |
fpkm | 2.221 | 0.033 | 2.256 | |
getter_setter_functions | 11.571 | 0.035 | 11.632 | |
makeExampleOutriderDataSet | 3.383 | 0.040 | 3.431 | |
normalizationFactors | 2.048 | 0.005 | 2.055 | |
plotFunctions | 25.280 | 0.422 | 25.744 | |
results | 9.427 | 0.069 | 9.505 | |
sampleExclusionMask | 1.296 | 0.018 | 1.317 | |
sizeFactors | 1.755 | 0.017 | 1.776 | |