Christian Mertes
| Snapshot Date: 2020-01-05 16:45:23 -0500 (Sun, 05 Jan 2020) |
| URL: https://git.bioconductor.org/packages/OUTRIDER |
| Branch: master |
| Last Commit: 79afd86 |
| Last Changed Date: 2019-10-29 13:43:16 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-06 13:54:48 -0500 (Mon, 06 Jan 2020).
| Package 1199/1809 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OUTRIDER 1.5.0 Christian Mertes
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: OUTRIDER |
| Version: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2020-01-06 06:37:32 -0500 (Mon, 06 Jan 2020) |
| EndedAt: 2020-01-06 06:51:04 -0500 (Mon, 06 Jan 2020) |
| EllapsedTime: 812.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.5.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.5.0’
* 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 ... OK
* 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 51.407 0.582 51.768
plotFunctions 23.413 3.721 19.673
OUTRIDER 14.147 2.032 15.236
results 10.979 0.122 11.588
getter_setter_functions 10.527 0.020 10.604
aberrant 7.236 1.780 7.189
computeZscores 4.855 0.440 4.135
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -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 -fopenmp -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-darwin15/6.1.0 -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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
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 Jan 6 06:48:05 2020: Initial PCA loss: 6.52185856625207"
[1] "Mon Jan 6 06:48:10 2020: Iteration: 1 loss: 4.71084218077528"
[1] "Mon Jan 6 06:48:12 2020: Iteration: 2 loss: 4.64426496993884"
[1] "Mon Jan 6 06:48:15 2020: Iteration: 3 loss: 4.61595073734755"
[1] "Mon Jan 6 06:48:17 2020: Iteration: 4 loss: 4.59500523198472"
[1] "Mon Jan 6 06:48:19 2020: Iteration: 5 loss: 4.58241118319112"
[1] "Mon Jan 6 06:48:21 2020: Iteration: 6 loss: 4.57891273302692"
Time difference of 13.8497 secs
[1] "Mon Jan 6 06:48:21 2020: 6 Final nb-AE loss: 4.57891273302692"
[1] "Mon Jan 6 06:48:27 2020: Initial PCA loss: 6.52185856625207"
[1] "Mon Jan 6 06:48:32 2020: Iteration: 1 loss: 4.71084218077528"
[1] "Mon Jan 6 06:48:35 2020: Iteration: 2 loss: 4.64426496993884"
[1] "Mon Jan 6 06:48:38 2020: Iteration: 3 loss: 4.61595073734755"
[1] "Mon Jan 6 06:48:41 2020: Iteration: 4 loss: 4.59500523198472"
[1] "Mon Jan 6 06:48:43 2020: Iteration: 5 loss: 4.58241118319112"
[1] "Mon Jan 6 06:48:46 2020: Iteration: 6 loss: 4.57891273302692"
Time difference of 17.23127 secs
[1] "Mon Jan 6 06:48:46 2020: 6 Final nb-AE loss: 4.57891273302692"
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 Jan 6 06:49:20 2020: Initial PCA loss: 4.46922152411537"
[1] "Mon Jan 6 06:49:24 2020: Iteration: 1 loss: 4.12731222806311"
[1] "Mon Jan 6 06:49:26 2020: Iteration: 2 loss: 4.11057446562242"
Time difference of 4.531562 secs
[1] "Mon Jan 6 06:49:26 2020: 2 Final nb-AE loss: 4.11057446562242"
[1] "Evaluation loss: 0.700571230286714"
[1] "Mon Jan 6 06:49:29 2020: Initial PCA loss: 4.44355413439085"
[1] "Mon Jan 6 06:49:33 2020: Iteration: 1 loss: 4.05899726945472"
[1] "Mon Jan 6 06:49:35 2020: Iteration: 2 loss: 4.04773843654146"
Time difference of 4.605283 secs
[1] "Mon Jan 6 06:49:35 2020: 2 Final nb-AE loss: 4.04773843654146"
[1] "Evaluation loss: 0.706696580520206"
[1] "Mon Jan 6 06:49:39 2020: Initial PCA loss: 4.41950197320317"
[1] "Mon Jan 6 06:49:42 2020: Iteration: 1 loss: 3.96396409804806"
[1] "Mon Jan 6 06:49:45 2020: Iteration: 2 loss: 3.94303316346732"
Time difference of 4.417426 secs
[1] "Mon Jan 6 06:49:45 2020: 2 Final nb-AE loss: 3.94303316346732"
[1] "Evaluation loss: 0.720556501715461"
[1] "Mon Jan 6 06:50:08 2020: Initial PCA loss: 6.46616282459584"
Error in x$.self$finalize() : attempt to apply non-function
[1] "Mon Jan 6 06:50:12 2020: Iteration: 1 loss: 4.81518048146922"
[1] "Mon Jan 6 06:50:15 2020: Iteration: 2 loss: 4.78972706919211"
Time difference of 5.327087 secs
[1] "Mon Jan 6 06:50:15 2020: 2 Final nb-AE loss: 4.78972706919211"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 0 | WARNINGS: 36 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
256.571 49.863 198.415
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 14.147 | 2.032 | 15.236 | |
| OutriderDataSet-class | 1.894 | 0.050 | 1.946 | |
| aberrant | 7.236 | 1.780 | 7.189 | |
| computeGeneLength | 2.843 | 0.204 | 3.068 | |
| computeLatentSpace | 2.136 | 0.015 | 2.176 | |
| computePvalues | 3.399 | 0.708 | 3.807 | |
| computeZscores | 4.855 | 0.440 | 4.135 | |
| controlForConfounders | 3.569 | 0.137 | 3.712 | |
| counts | 1.902 | 0.081 | 2.056 | |
| estimateBestQ | 1.115 | 0.004 | 1.120 | |
| filterExpression | 4.285 | 0.121 | 3.565 | |
| findEncodingDim | 51.407 | 0.582 | 51.768 | |
| fit | 2.404 | 0.057 | 2.486 | |
| fpkm | 2.337 | 0.019 | 2.367 | |
| getter_setter_functions | 10.527 | 0.020 | 10.604 | |
| makeExampleOutriderDataSet | 2.678 | 0.008 | 2.686 | |
| normalizationFactors | 2.302 | 0.010 | 2.313 | |
| plotFunctions | 23.413 | 3.721 | 19.673 | |
| results | 10.979 | 0.122 | 11.588 | |
| sampleExclusionMask | 1.348 | 0.169 | 1.192 | |
| sizeFactors | 2.062 | 0.009 | 2.073 | |