Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:40 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 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: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2024-05-06 23:35:39 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 23:38:04 -0400 (Mon, 06 May 2024) |
EllapsedTime: 144.6 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/OUTRIDER.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OUTRIDER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OUTRIDER’ version ‘1.22.0’ * 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 * 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-3.19-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-1500.1.0.2.5)’ 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 (2024-04-24) -- "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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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': expand.grid, I, 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 May 6 23:37:44 2024: Initial PCA loss: 4.49480338098309" [1] "Mon May 6 23:37:44 2024: Iteration: 1 loss: 4.14778367602881" [1] "Mon May 6 23:37:44 2024: Iteration: 2 loss: 4.12853146702259" Time difference of 0.7148509 secs [1] "Mon May 6 23:37:44 2024: 2 Final nb-AE loss: 4.12853146702259" [1] "Evaluation loss: 0.530619373183546 for q=3" [1] "Mon May 6 23:37:45 2024: Initial PCA loss: 4.45717839468628" [1] "Mon May 6 23:37:45 2024: Iteration: 1 loss: 4.05826116984482" [1] "Mon May 6 23:37:45 2024: Iteration: 2 loss: 4.04568724999612" Time difference of 0.314539 secs [1] "Mon May 6 23:37:45 2024: 2 Final nb-AE loss: 4.04568724999612" [1] "Evaluation loss: 0.458331200435315 for q=4" [1] "Mon May 6 23:37:45 2024: Initial PCA loss: 4.43094639706086" [1] "Mon May 6 23:37:46 2024: Iteration: 1 loss: 3.96287017329588" [1] "Mon May 6 23:37:46 2024: Iteration: 2 loss: 3.94787951749243" Time difference of 0.321389 secs [1] "Mon May 6 23:37:46 2024: 2 Final nb-AE loss: 3.94787951749243" [1] "Evaluation loss: 0.361553940692389 for q=5" [1] "Mon May 6 23:37:48 2024: Initial PCA loss: 7.16457134714849" [1] "Mon May 6 23:37:48 2024: Iteration: 1 loss: 6.82914995400611" [1] "Mon May 6 23:37:48 2024: Iteration: 2 loss: 6.82750059615859" Time difference of 0.3926878 secs [1] "Mon May 6 23:37:48 2024: 2 Final nb-AE loss: 6.82750059615859" 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 May 6 23:37:50 2024: Initial PCA loss: 5.98905731951991" [1] "Mon May 6 23:37:50 2024: Iteration: 1 loss: 4.53705815693666" [1] "Mon May 6 23:37:50 2024: Iteration: 2 loss: 4.43702218749881" [1] "Mon May 6 23:37:50 2024: Iteration: 3 loss: 4.40962729380234" [1] "Mon May 6 23:37:50 2024: Iteration: 4 loss: 4.39352205591229" [1] "Mon May 6 23:37:51 2024: Iteration: 5 loss: 4.37755743998482" [1] "Mon May 6 23:37:51 2024: Iteration: 6 loss: 4.36483227222613" Time difference of 0.963459 secs [1] "Mon May 6 23:37:51 2024: 6 Final nb-AE loss: 4.36483227222613" [1] "Mon May 6 23:37:51 2024: Initial PCA loss: 5.98905731951991" [1] "Mon May 6 23:37:51 2024: Iteration: 1 loss: 4.53705815693666" [1] "Mon May 6 23:37:52 2024: Iteration: 2 loss: 4.43702218749881" [1] "Mon May 6 23:37:52 2024: Iteration: 3 loss: 4.40962729380234" [1] "Mon May 6 23:37:52 2024: Iteration: 4 loss: 4.39352205591229" [1] "Mon May 6 23:37:52 2024: Iteration: 5 loss: 4.37755743998482" [1] "Mon May 6 23:37:52 2024: Iteration: 6 loss: 4.36483227222613" Time difference of 0.9841139 secs [1] "Mon May 6 23:37:52 2024: 6 Final nb-AE loss: 4.36483227222613" [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] [ FAIL 0 | WARN 10 | SKIP 0 | PASS 115 ] > > proc.time() user system elapsed 23.919 0.502 25.415
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
name | user | system | elapsed | |
OUTRIDER | 3.514 | 0.770 | 3.931 | |
OutriderDataSet-class | 0.225 | 0.025 | 0.251 | |
aberrant | 0.483 | 0.190 | 0.521 | |
computeGeneLength | 0.415 | 0.101 | 0.517 | |
computeLatentSpace | 0.200 | 0.001 | 0.201 | |
computePvalues | 0.618 | 0.466 | 0.693 | |
computeZscores | 0.222 | 0.052 | 0.275 | |
controlForConfounders | 0.278 | 0.021 | 0.299 | |
counts | 0.149 | 0.005 | 0.154 | |
estimateBestQ | 0.095 | 0.001 | 0.095 | |
filterExpression | 0.358 | 0.008 | 0.366 | |
findEncodingDim | 3.077 | 0.128 | 3.264 | |
fit | 0.237 | 0.005 | 0.248 | |
fpkm | 0.202 | 0.003 | 0.205 | |
getter_setter_functions | 0.762 | 0.002 | 0.763 | |
makeExampleOutriderDataSet | 0.289 | 0.001 | 0.291 | |
normalizationFactors | 0.187 | 0.001 | 0.188 | |
plotFunctions | 4.414 | 0.166 | 4.594 | |
results | 1.001 | 0.007 | 1.010 | |
sampleExclusionMask | 0.125 | 0.001 | 0.126 | |
sizeFactors | 0.677 | 0.003 | 0.681 | |