Christian Mertes
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/OUTRIDER |
| Branch: RELEASE_3_10 |
| Last Commit: c1700e1 |
| Last Changed Date: 2020-04-14 02:19:33 -0400 (Tue, 14 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:49 -0400 (Wed, 15 Apr 2020).
| Package 1207/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OUTRIDER 1.4.2 Christian Mertes
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: OUTRIDER |
| Version: 1.4.2 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings OUTRIDER_1.4.2.tar.gz |
| StartedAt: 2020-04-15 05:17:39 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:35:19 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 1060.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings OUTRIDER_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/OUTRIDER.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OUTRIDER' version '1.4.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
plotAberrantPerSample: no visible binding for global variable 'y'
plotAberrantPerSample: no visible binding for global variable 'fill'
plotSizeFactors: no visible binding for global variable 'sizeFactor'
Undefined global functions or variables:
fill sizeFactor y
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/OUTRIDER/libs/i386/OUTRIDER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/OUTRIDER/libs/x64/OUTRIDER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findEncodingDim 25.58 0.01 25.69
plotFunctions 9.94 0.30 17.60
OUTRIDER 7.89 1.08 48.40
aberrant 4.53 0.07 46.75
computePvalues 3.02 0.04 42.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
findEncodingDim 36.69 0.03 36.72
plotFunctions 16.04 0.19 16.47
OUTRIDER 10.53 0.18 52.53
getter_setter_functions 7.94 0.00 7.94
results 7.13 0.04 7.15
aberrant 6.43 0.06 48.81
computePvalues 3.70 0.01 45.41
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.10-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.
OUTRIDER.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/OUTRIDER_1.4.2.tar.gz && rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OUTRIDER.buildbin-libdir OUTRIDER_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL OUTRIDER_1.4.2.zip && rm OUTRIDER_1.4.2.tar.gz OUTRIDER_1.4.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 711k 100 711k 0 0 16.7M 0 --:--:-- --:--:-- --:--:-- 18.7M
install for i386
* installing *source* package 'OUTRIDER' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mtune=core2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/OUTRIDER.buildbin-libdir/00LOCK-OUTRIDER/00new/OUTRIDER/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'OUTRIDER'
finding HTML links ... done
OUTRIDER html
OutriderDataSet-class html
aberrant html
computeGeneLength html
computeLatentSpace html
computePvalues html
computeZscores html
controlForConfounders html
counts html
estimateBestQ html
filterExpression html
findEncodingDim html
fit html
fpkm html
getter_setter_functions html
makeExampleOutriderDataSet html
normalizationFactors html
plotFunctions html
results html
sampleExclusionMask html
sizeFactors html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'OUTRIDER' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mtune=core2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/OUTRIDER.buildbin-libdir/OUTRIDER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OUTRIDER' as OUTRIDER_1.4.2.zip
* DONE (OUTRIDER)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'OUTRIDER' successfully unpacked and MD5 sums checked
|
OUTRIDER.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 Apr 15 05:31:42 2020: Initial PCA loss: 6.31706115782754"
[1] "Wed Apr 15 05:31:44 2020: Iteration: 1 loss: 4.44650304165844"
[1] "Wed Apr 15 05:31:45 2020: Iteration: 2 loss: 4.39411931712503"
[1] "Wed Apr 15 05:31:47 2020: Iteration: 3 loss: 4.37011990196398"
[1] "Wed Apr 15 05:31:48 2020: Iteration: 4 loss: 4.34912696184266"
[1] "Wed Apr 15 05:31:49 2020: Iteration: 5 loss: 4.33973361537641"
[1] "Wed Apr 15 05:31:50 2020: Iteration: 6 loss: 4.33114161854018"
Time difference of 6.515661 secs
[1] "Wed Apr 15 05:31:50 2020: 6 Final nb-AE loss: 4.33114161854018"
[1] "Wed Apr 15 05:31:52 2020: Initial PCA loss: 6.31706115782754"
[1] "Wed Apr 15 05:31:55 2020: Iteration: 1 loss: 4.44650304165844"
[1] "Wed Apr 15 05:31:56 2020: Iteration: 2 loss: 4.39411931712503"
[1] "Wed Apr 15 05:31:57 2020: Iteration: 3 loss: 4.37011990196398"
[1] "Wed Apr 15 05:31:58 2020: Iteration: 4 loss: 4.34912696184266"
[1] "Wed Apr 15 05:32:00 2020: Iteration: 5 loss: 4.33973361537641"
[1] "Wed Apr 15 05:32:01 2020: Iteration: 6 loss: 4.33114161854018"
Time difference of 7.812542 secs
[1] "Wed Apr 15 05:32:01 2020: 6 Final nb-AE loss: 4.33114161854018"
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 Apr 15 05:32:22 2020: Initial PCA loss: 4.50586734153908"
[1] "Wed Apr 15 05:32:24 2020: Iteration: 1 loss: 4.18355395637231"
[1] "Wed Apr 15 05:32:25 2020: Iteration: 2 loss: 4.17108830939366"
Time difference of 2.421888 secs
[1] "Wed Apr 15 05:32:25 2020: 2 Final nb-AE loss: 4.17108830939366"
[1] "Evaluation loss: 0.47368104320725 for q=3"
[1] "Wed Apr 15 05:32:27 2020: Initial PCA loss: 4.46764641448793"
[1] "Wed Apr 15 05:32:28 2020: Iteration: 1 loss: 4.09146107625348"
[1] "Wed Apr 15 05:32:29 2020: Iteration: 2 loss: 4.02633254154785"
Time difference of 2.046885 secs
[1] "Wed Apr 15 05:32:29 2020: 2 Final nb-AE loss: 4.02633254154785"
[1] "Evaluation loss: 0.37238216182272 for q=4"
[1] "Wed Apr 15 05:32:31 2020: Initial PCA loss: 4.43770459562054"
[1] "Wed Apr 15 05:32:34 2020: Iteration: 1 loss: 3.99000352063997"
[1] "Wed Apr 15 05:32:35 2020: Iteration: 2 loss: 3.92504545360209"
Time difference of 3.062517 secs
[1] "Wed Apr 15 05:32:35 2020: 2 Final nb-AE loss: 3.92504545360209"
[1] "Evaluation loss: 0.294207496185275 for q=5"
[1] "Wed Apr 15 05:32:47 2020: Initial PCA loss: 6.46616282459584"
[1] "Wed Apr 15 05:32:50 2020: Iteration: 1 loss: 4.81569809301105"
[1] "Wed Apr 15 05:32:52 2020: Iteration: 2 loss: 4.78992131812697"
Time difference of 3.484396 secs
[1] "Wed Apr 15 05:32:52 2020: 2 Final nb-AE loss: 4.78992131812697"
== testthat results ===========================================================
[ OK: 102 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
111.87 2.89 114.29
|
OUTRIDER.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 Apr 15 05:33:35 2020: Initial PCA loss: 6.58279627485952"
[1] "Wed Apr 15 05:33:38 2020: Iteration: 1 loss: 4.83833206592075"
[1] "Wed Apr 15 05:33:39 2020: Iteration: 2 loss: 4.76698264755968"
[1] "Wed Apr 15 05:33:40 2020: Iteration: 3 loss: 4.72149111690763"
[1] "Wed Apr 15 05:33:41 2020: Iteration: 4 loss: 4.6894290266906"
[1] "Wed Apr 15 05:33:42 2020: Iteration: 5 loss: 4.66721412900698"
[1] "Wed Apr 15 05:33:43 2020: Iteration: 6 loss: 4.65926805010276"
Time difference of 6.953164 secs
[1] "Wed Apr 15 05:33:43 2020: 6 Final nb-AE loss: 4.65926805010276"
[1] "Wed Apr 15 05:33:46 2020: Initial PCA loss: 6.58279627485952"
[1] "Wed Apr 15 05:33:49 2020: Iteration: 1 loss: 4.83833206592075"
[1] "Wed Apr 15 05:33:50 2020: Iteration: 2 loss: 4.76698264755968"
[1] "Wed Apr 15 05:33:51 2020: Iteration: 3 loss: 4.72149111690763"
[1] "Wed Apr 15 05:33:53 2020: Iteration: 4 loss: 4.6894290266906"
[1] "Wed Apr 15 05:33:54 2020: Iteration: 5 loss: 4.66721412900698"
[1] "Wed Apr 15 05:33:56 2020: Iteration: 6 loss: 4.65926805010276"
Time difference of 8.73442 secs
[1] "Wed Apr 15 05:33:56 2020: 6 Final nb-AE loss: 4.65926805010276"
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 Apr 15 05:34:16 2020: Initial PCA loss: 4.47831010764575"
[1] "Wed Apr 15 05:34:18 2020: Iteration: 1 loss: 4.12457921733301"
[1] "Wed Apr 15 05:34:20 2020: Iteration: 2 loss: 4.0981854009558"
Time difference of 3.265644 secs
[1] "Wed Apr 15 05:34:20 2020: 2 Final nb-AE loss: 4.0981854009558"
[1] "Evaluation loss: 0.547354420861076 for q=3"
[1] "Wed Apr 15 05:34:21 2020: Initial PCA loss: 4.44303639609248"
[1] "Wed Apr 15 05:34:24 2020: Iteration: 1 loss: 4.05922639639716"
[1] "Wed Apr 15 05:34:25 2020: Iteration: 2 loss: 4.04343207413922"
Time difference of 2.375014 secs
[1] "Wed Apr 15 05:34:25 2020: 2 Final nb-AE loss: 4.04343207413922"
[1] "Evaluation loss: 0.473206999223512 for q=4"
[1] "Wed Apr 15 05:34:26 2020: Initial PCA loss: 4.41949124474033"
[1] "Wed Apr 15 05:34:28 2020: Iteration: 1 loss: 3.97641511395352"
[1] "Wed Apr 15 05:34:29 2020: Iteration: 2 loss: 3.96152621157727"
Time difference of 2.203137 secs
[1] "Wed Apr 15 05:34:29 2020: 2 Final nb-AE loss: 3.96152621157727"
[1] "Evaluation loss: 0.428257844250871 for q=5"
[1] "Wed Apr 15 05:34:42 2020: Initial PCA loss: 6.46616282459584"
[1] "Wed Apr 15 05:34:45 2020: Iteration: 1 loss: 4.81542744661623"
[1] "Wed Apr 15 05:34:46 2020: Iteration: 2 loss: 4.79019053974505"
Time difference of 2.687516 secs
[1] "Wed Apr 15 05:34:46 2020: 2 Final nb-AE loss: 4.79019053974505"
== testthat results ===========================================================
[ OK: 102 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
110.07 1.46 111.03
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OUTRIDER.Rcheck/examples_i386/OUTRIDER-Ex.timings
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OUTRIDER.Rcheck/examples_x64/OUTRIDER-Ex.timings
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