Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:10 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 1448/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OUTRIDER 1.23.0 (landing page) Christian Mertes
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the OUTRIDER package: - 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: 2024-05-12 22:04:18 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 22:12:19 -0400 (Sun, 12 May 2024) |
EllapsedTime: 481.1 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/OUTRIDER.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.23.0’ * 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 15.0.0 (clang-1500.0.40.1)’ * 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 15.451 0.598 16.103 OUTRIDER 11.466 2.501 12.958 findEncodingDim 11.177 0.240 11.421 * 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-mac-arm64/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-arm64/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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] "Sun May 12 22:10:42 2024: Initial PCA loss: 6.20987928124715" [1] "Sun May 12 22:10:43 2024: Iteration: 1 loss: 4.60951817649755" [1] "Sun May 12 22:10:44 2024: Iteration: 2 loss: 4.52943908917772" [1] "Sun May 12 22:10:44 2024: Iteration: 3 loss: 4.4818707098359" [1] "Sun May 12 22:10:45 2024: Iteration: 4 loss: 4.44814852815747" [1] "Sun May 12 22:10:46 2024: Iteration: 5 loss: 4.43908106933092" [1] "Sun May 12 22:10:47 2024: Iteration: 6 loss: 4.43175059713278" Time difference of 4.910732 secs [1] "Sun May 12 22:10:47 2024: 6 Final nb-AE loss: 4.43175059713278" [1] "Sun May 12 22:10:50 2024: Initial PCA loss: 6.20987928124715" [1] "Sun May 12 22:10:52 2024: Iteration: 1 loss: 4.60951817649755" [1] "Sun May 12 22:10:54 2024: Iteration: 2 loss: 4.52943908917772" [1] "Sun May 12 22:10:55 2024: Iteration: 3 loss: 4.4818707098359" [1] "Sun May 12 22:10:56 2024: Iteration: 4 loss: 4.44814852815747" [1] "Sun May 12 22:10:58 2024: Iteration: 5 loss: 4.43908106933092" [1] "Sun May 12 22:10:59 2024: Iteration: 6 loss: 4.43175059713278" Time difference of 8.100334 secs [1] "Sun May 12 22:10:59 2024: 6 Final nb-AE loss: 4.43175059713278" 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] "Sun May 12 22:11:20 2024: Initial PCA loss: 4.49024154928438" [1] "Sun May 12 22:11:21 2024: Iteration: 1 loss: 4.17587787103811" [1] "Sun May 12 22:11:22 2024: Iteration: 2 loss: 4.16223457020287" Time difference of 1.31984 secs [1] "Sun May 12 22:11:22 2024: 2 Final nb-AE loss: 4.16223457020287" [1] "Evaluation loss: 0.576442941354598 for q=3" [1] "Sun May 12 22:11:23 2024: Initial PCA loss: 4.44885336307503" [1] "Sun May 12 22:11:25 2024: Iteration: 1 loss: 4.0878743782286" [1] "Sun May 12 22:11:27 2024: Iteration: 2 loss: 4.07254422919012" Time difference of 2.945559 secs [1] "Sun May 12 22:11:27 2024: 2 Final nb-AE loss: 4.07254422919012" [1] "Evaluation loss: 0.569460589967992 for q=4" [1] "Sun May 12 22:11:29 2024: Initial PCA loss: 4.42645498863736" [1] "Sun May 12 22:11:31 2024: Iteration: 1 loss: 4.04504753359821" [1] "Sun May 12 22:11:33 2024: Iteration: 2 loss: 4.03543195317705" Time difference of 2.965414 secs [1] "Sun May 12 22:11:33 2024: 2 Final nb-AE loss: 4.03543195317705" [1] "Evaluation loss: 0.605656469755381 for q=5" [1] "Sun May 12 22:11:47 2024: Initial PCA loss: 7.16457134714849" [1] "Sun May 12 22:11:48 2024: Iteration: 1 loss: 6.82914995400611" [1] "Sun May 12 22:11:49 2024: Iteration: 2 loss: 6.82750059615859" Time difference of 1.582805 secs [1] "Sun May 12 22:11:49 2024: 2 Final nb-AE loss: 6.82750059615859" Error in x$.self$finalize() : attempt to apply non-function [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] Warning message: call dbDisconnect() when finished working with a connection > > proc.time() user system elapsed 85.182 1.862 107.469
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 11.466 | 2.501 | 12.958 | |
OutriderDataSet-class | 0.801 | 0.099 | 0.901 | |
aberrant | 1.792 | 0.672 | 1.786 | |
computeGeneLength | 1.482 | 0.206 | 1.690 | |
computeLatentSpace | 0.689 | 0.008 | 0.698 | |
computePvalues | 2.118 | 1.386 | 2.439 | |
computeZscores | 0.824 | 0.156 | 0.980 | |
controlForConfounders | 1.033 | 0.052 | 1.085 | |
counts | 0.529 | 0.006 | 0.535 | |
estimateBestQ | 0.395 | 0.006 | 0.402 | |
filterExpression | 1.402 | 0.029 | 1.430 | |
findEncodingDim | 11.177 | 0.240 | 11.421 | |
fit | 0.908 | 0.010 | 0.919 | |
fpkm | 0.765 | 0.006 | 0.775 | |
getter_setter_functions | 3.080 | 0.015 | 3.107 | |
makeExampleOutriderDataSet | 1.124 | 0.010 | 1.137 | |
normalizationFactors | 0.740 | 0.005 | 0.746 | |
plotFunctions | 15.451 | 0.598 | 16.103 | |
results | 3.429 | 0.026 | 3.489 | |
sampleExclusionMask | 0.474 | 0.004 | 0.478 | |
sizeFactors | 0.631 | 0.005 | 0.636 | |