Christian Mertes
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/OUTRIDER |
| Branch: RELEASE_3_9 |
| Last Commit: e925639 |
| Last Changed Date: 2019-10-12 17:17:18 -0400 (Sat, 12 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:02:53 -0400 (Wed, 16 Oct 2019).
| Package 1157/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OUTRIDER 1.2.4 Christian Mertes
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.2.4 |
| 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_1.2.4.tar.gz |
| StartedAt: 2019-10-16 05:18:30 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:28:23 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 592.7 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_1.2.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OUTRIDER.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.4’
* 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 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 or elapsed time > 5s
user system elapsed
plotFunctions 16.728 3.311 12.924
findEncodingDim 15.630 0.592 15.476
OUTRIDER 9.689 2.340 9.700
aberrant 5.613 2.611 6.276
computePvalues 4.068 1.977 5.366
* 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-3.9-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/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes"
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] "Wed Oct 16 05:26:59 2019: Initial PCA loss: 6.23328234088855"
[1] "Wed Oct 16 05:27:01 2019: Iteration: 1 loss: 4.57742466653428"
[1] "Wed Oct 16 05:27:02 2019: Iteration: 2 loss: 4.52441768507982"
[1] "Wed Oct 16 05:27:02 2019: Iteration: 3 loss: 4.50200402729927"
[1] "Wed Oct 16 05:27:03 2019: Iteration: 4 loss: 4.49087589832411"
[1] "Wed Oct 16 05:27:04 2019: Iteration: 5 loss: 4.48316300390326"
[1] "Wed Oct 16 05:27:05 2019: Iteration: 6 loss: 4.48058232796142"
Time difference of 4.850042 secs
[1] "Wed Oct 16 05:27:05 2019: 6 Final nb-AE loss: 4.48058232796142"
[1] "Wed Oct 16 05:27:06 2019: Initial PCA loss: 6.23328234088855"
[1] "Wed Oct 16 05:27:07 2019: Iteration: 1 loss: 4.57742466653428"
[1] "Wed Oct 16 05:27:08 2019: Iteration: 2 loss: 4.52441768507982"
[1] "Wed Oct 16 05:27:09 2019: Iteration: 3 loss: 4.50200402729927"
[1] "Wed Oct 16 05:27:10 2019: Iteration: 4 loss: 4.49087589832411"
[1] "Wed Oct 16 05:27:11 2019: Iteration: 5 loss: 4.48316300390326"
[1] "Wed Oct 16 05:27:12 2019: Iteration: 6 loss: 4.48058232796142"
Time difference of 4.960999 secs
[1] "Wed Oct 16 05:27:12 2019: 6 Final nb-AE loss: 4.48058232796142"
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] "Wed Oct 16 05:27:32 2019: Initial PCA loss: 4.49703284912145"
[1] "Wed Oct 16 05:27:34 2019: Iteration: 1 loss: 4.14892365370278"
[1] "Wed Oct 16 05:27:35 2019: Iteration: 2 loss: 4.13558342204501"
Time difference of 1.624891 secs
[1] "Wed Oct 16 05:27:35 2019: 2 Final nb-AE loss: 4.13558342204501"
[1] "Evaluation loss: 0.312509240637444"
[1] "Wed Oct 16 05:27:36 2019: Initial PCA loss: 4.45877467895188"
[1] "Wed Oct 16 05:27:37 2019: Iteration: 1 loss: 4.07528914761218"
[1] "Wed Oct 16 05:27:38 2019: Iteration: 2 loss: 4.0529490875435"
Time difference of 1.659028 secs
[1] "Wed Oct 16 05:27:38 2019: 2 Final nb-AE loss: 4.0529490875435"
[1] "Evaluation loss: 0.250019839126325"
[1] "Wed Oct 16 05:27:39 2019: Initial PCA loss: 4.42216809798661"
[1] "Wed Oct 16 05:27:41 2019: Iteration: 1 loss: 3.99487065006409"
[1] "Wed Oct 16 05:27:43 2019: Iteration: 2 loss: 3.97634969331179"
Time difference of 2.414748 secs
[1] "Wed Oct 16 05:27:43 2019: 2 Final nb-AE loss: 3.97634969331179"
[1] "Evaluation loss: 0.195246670059503"
[1] "Wed Oct 16 05:27:53 2019: Initial PCA loss: 6.46616282459584"
[1] "Wed Oct 16 05:27:55 2019: Iteration: 1 loss: 4.81518048146922"
[1] "Wed Oct 16 05:27:56 2019: Iteration: 2 loss: 4.78972706919211"
Time difference of 2.470052 secs
[1] "Wed Oct 16 05:27:56 2019: 2 Final nb-AE loss: 4.78972706919211"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 96 | SKIPPED: 0 | WARNINGS: 37 | FAILED: 0 ]
>
> proc.time()
user system elapsed
140.818 30.318 99.197
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 9.689 | 2.340 | 9.700 | |
| OutriderDataSet-class | 1.386 | 0.192 | 1.648 | |
| aberrant | 5.613 | 2.611 | 6.276 | |
| computeGeneLength | 3.200 | 0.409 | 3.653 | |
| computeLatentSpace | 0.808 | 0.012 | 0.820 | |
| computePvalues | 4.068 | 1.977 | 5.366 | |
| computeZscores | 1.771 | 0.580 | 1.775 | |
| controlForConfounders | 1.750 | 0.124 | 1.921 | |
| counts | 0.729 | 0.021 | 0.750 | |
| estimateBestQ | 0.485 | 0.004 | 0.489 | |
| filterExpression | 2.531 | 0.333 | 2.280 | |
| findEncodingDim | 15.630 | 0.592 | 15.476 | |
| fit | 1.353 | 0.048 | 1.402 | |
| fpkm | 1.081 | 0.016 | 1.097 | |
| getter_setter_functions | 3.207 | 0.009 | 3.217 | |
| makeExampleOutriderDataSet | 1.214 | 0.009 | 1.223 | |
| normalizationFactors | 0.836 | 0.012 | 0.847 | |
| plotFunctions | 16.728 | 3.311 | 12.924 | |
| results | 3.163 | 0.071 | 3.122 | |
| sampleExclusionMask | 0.769 | 0.234 | 0.533 | |
| sizeFactors | 0.854 | 0.007 | 0.861 | |