Christian Mertes
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/OUTRIDER |
| git_branch: RELEASE_3_14 |
| git_last_commit: 2aa8599 |
| git_last_commit_date: 2021-10-26 12:45:42 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:02 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the OUTRIDER package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OUTRIDER.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1356/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.12.0 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OUTRIDER |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OUTRIDER_1.12.0.tar.gz |
| StartedAt: 2022-04-13 00:07:39 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 00:26:09 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 1109.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OUTRIDER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OUTRIDER_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/OUTRIDER.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.12.0'
* 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 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 ... NOTE
Namespace in Imports field not imported from: 'Rcpp'
All declared Imports should be used.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-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-3.14-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 (user + system) or elapsed time > 5s
user system elapsed
findEncodingDim 29.77 0.00 30.54
plotFunctions 14.10 0.54 15.86
getter_setter_functions 9.52 0.00 11.07
OUTRIDER 7.69 0.53 47.61
results 5.52 0.00 5.55
aberrant 4.23 0.01 53.69
computePvalues 3.58 0.02 35.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEncodingDim 21.38 0.00 21.37
plotFunctions 10.37 0.20 10.58
OUTRIDER 7.29 0.15 41.66
results 6.08 0.05 6.13
getter_setter_functions 5.77 0.00 5.77
aberrant 5.25 0.01 45.66
computePvalues 3.70 0.04 38.18
* 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-3.14-bioc/meat/OUTRIDER.Rcheck/00check.log'
for details.
OUTRIDER.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/OUTRIDER_1.12.0.tar.gz && rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OUTRIDER.buildbin-libdir OUTRIDER_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL OUTRIDER_1.12.0.zip && rm OUTRIDER_1.12.0.tar.gz OUTRIDER_1.12.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
2 711k 2 16083 0 0 134k 0 0:00:05 --:--:-- 0:00:05 134k
100 711k 100 711k 0 0 1166k 0 --:--:-- --:--:-- --:--:-- 1165k
install for i386
* installing *source* package 'OUTRIDER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o OUTRIDER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/OUTRIDER.buildbin-libdir/OUTRIDER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OUTRIDER' as OUTRIDER_1.12.0.zip
* DONE (OUTRIDER)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'OUTRIDER' successfully unpacked and MD5 sums checked
|
OUTRIDER.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
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, 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.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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: 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] "Wed Apr 13 00:22:15 2022: Initial PCA loss: 6.46733591201414"
[1] "Wed Apr 13 00:22:17 2022: Iteration: 1 loss: 4.62455398292301"
[1] "Wed Apr 13 00:22:19 2022: Iteration: 2 loss: 4.54479731925212"
[1] "Wed Apr 13 00:22:20 2022: Iteration: 3 loss: 4.52131450186376"
[1] "Wed Apr 13 00:22:22 2022: Iteration: 4 loss: 4.50560118627025"
[1] "Wed Apr 13 00:22:23 2022: Iteration: 5 loss: 4.49863635186188"
[1] "Wed Apr 13 00:22:24 2022: Iteration: 6 loss: 4.49266005657823"
Time difference of 8.43756 secs
[1] "Wed Apr 13 00:22:24 2022: 6 Final nb-AE loss: 4.49266005657823"
[1] "Wed Apr 13 00:22:27 2022: Initial PCA loss: 6.46733591201414"
[1] "Wed Apr 13 00:22:30 2022: Iteration: 1 loss: 4.62455398292301"
[1] "Wed Apr 13 00:22:32 2022: Iteration: 2 loss: 4.54479731925212"
[1] "Wed Apr 13 00:22:33 2022: Iteration: 3 loss: 4.52131450186376"
[1] "Wed Apr 13 00:22:35 2022: Iteration: 4 loss: 4.50560118627025"
[1] "Wed Apr 13 00:22:36 2022: Iteration: 5 loss: 4.49863635186188"
[1] "Wed Apr 13 00:22:37 2022: Iteration: 6 loss: 4.49266005657823"
Time difference of 9.421938 secs
[1] "Wed Apr 13 00:22:37 2022: 6 Final nb-AE loss: 4.49266005657823"
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 13 00:23:01 2022: Initial PCA loss: 4.4680283572348"
[1] "Wed Apr 13 00:23:04 2022: Iteration: 1 loss: 4.12234441304723"
[1] "Wed Apr 13 00:23:05 2022: Iteration: 2 loss: 4.10563894159081"
Time difference of 2.609392 secs
[1] "Wed Apr 13 00:23:05 2022: 2 Final nb-AE loss: 4.10563894159081"
[1] "Evaluation loss: 0.465513288242005 for q=3"
[1] "Wed Apr 13 00:23:07 2022: Initial PCA loss: 4.44502661980547"
[1] "Wed Apr 13 00:23:10 2022: Iteration: 1 loss: 4.05497500969435"
[1] "Wed Apr 13 00:23:11 2022: Iteration: 2 loss: 4.03302630449862"
Time difference of 3.671902 secs
[1] "Wed Apr 13 00:23:11 2022: 2 Final nb-AE loss: 4.03302630449862"
[1] "Evaluation loss: 0.459503223915858 for q=4"
[1] "Wed Apr 13 00:23:13 2022: Initial PCA loss: 4.41877330208884"
[1] "Wed Apr 13 00:23:15 2022: Iteration: 1 loss: 3.98035946938947"
[1] "Wed Apr 13 00:23:16 2022: Iteration: 2 loss: 3.96485923642443"
Time difference of 2.625021 secs
[1] "Wed Apr 13 00:23:16 2022: 2 Final nb-AE loss: 3.96485923642443"
[1] "Evaluation loss: 0.474281945791018 for q=5"
Error in x$.self$finalize() : attempt to apply non-function
[1] "Wed Apr 13 00:23:31 2022: Initial PCA loss: 6.46616282459584"
[1] "Wed Apr 13 00:23:34 2022: Iteration: 1 loss: 4.81544153905003"
[1] "Wed Apr 13 00:23:35 2022: Iteration: 2 loss: 4.78966886254391"
Time difference of 3.625071 secs
[1] "Wed Apr 13 00:23:35 2022: 2 Final nb-AE loss: 4.78966886254391"
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
109.28 2.79 112.07
|
OUTRIDER.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
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, 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.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
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: 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] "Wed Apr 13 00:24:08 2022: Initial PCA loss: 6.41770055938261"
[1] "Wed Apr 13 00:24:11 2022: Iteration: 1 loss: 4.57096091846434"
[1] "Wed Apr 13 00:24:13 2022: Iteration: 2 loss: 4.52627991965021"
[1] "Wed Apr 13 00:24:14 2022: Iteration: 3 loss: 4.51277763134322"
[1] "Wed Apr 13 00:24:16 2022: Iteration: 4 loss: 4.50223776556933"
[1] "Wed Apr 13 00:24:17 2022: Iteration: 5 loss: 4.49803684272329"
[1] "Wed Apr 13 00:24:19 2022: Iteration: 6 loss: 4.49223130754841"
Time difference of 9.20319 secs
[1] "Wed Apr 13 00:24:19 2022: 6 Final nb-AE loss: 4.49223130754841"
[1] "Wed Apr 13 00:24:22 2022: Initial PCA loss: 6.41770055938261"
[1] "Wed Apr 13 00:24:25 2022: Iteration: 1 loss: 4.57096091846434"
[1] "Wed Apr 13 00:24:26 2022: Iteration: 2 loss: 4.52627991965021"
[1] "Wed Apr 13 00:24:28 2022: Iteration: 3 loss: 4.51277763134322"
[1] "Wed Apr 13 00:24:30 2022: Iteration: 4 loss: 4.50223776556933"
[1] "Wed Apr 13 00:24:32 2022: Iteration: 5 loss: 4.49803684272329"
[1] "Wed Apr 13 00:24:34 2022: Iteration: 6 loss: 4.49223130754841"
Time difference of 10.5157 secs
[1] "Wed Apr 13 00:24:34 2022: 6 Final nb-AE loss: 4.49223130754841"
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 13 00:24:58 2022: Initial PCA loss: 4.48990004709617"
[1] "Wed Apr 13 00:25:01 2022: Iteration: 1 loss: 4.17212108716617"
[1] "Wed Apr 13 00:25:02 2022: Iteration: 2 loss: 4.16071906278125"
Time difference of 3.171899 secs
[1] "Wed Apr 13 00:25:02 2022: 2 Final nb-AE loss: 4.16071906278125"
[1] "Evaluation loss: 0.745319753836641 for q=3"
[1] "Wed Apr 13 00:25:04 2022: Initial PCA loss: 4.46798789464478"
[1] "Wed Apr 13 00:25:07 2022: Iteration: 1 loss: 4.10806803697167"
[1] "Wed Apr 13 00:25:08 2022: Iteration: 2 loss: 4.09395722633209"
Time difference of 2.937551 secs
[1] "Wed Apr 13 00:25:08 2022: 2 Final nb-AE loss: 4.09395722633209"
[1] "Evaluation loss: 0.637786862645552 for q=4"
[1] "Wed Apr 13 00:25:10 2022: Initial PCA loss: 4.44280956510793"
[1] "Wed Apr 13 00:25:14 2022: Iteration: 1 loss: 4.04063059664207"
[1] "Wed Apr 13 00:25:16 2022: Iteration: 2 loss: 4.0287303631062"
Time difference of 3.406276 secs
[1] "Wed Apr 13 00:25:16 2022: 2 Final nb-AE loss: 4.0287303631062"
[1] "Evaluation loss: 0.58721287148844 for q=5"
[1] "Wed Apr 13 00:25:36 2022: Initial PCA loss: 6.46616282459584"
[1] "Wed Apr 13 00:25:39 2022: Iteration: 1 loss: 4.81544153905003"
[1] "Wed Apr 13 00:25:41 2022: Iteration: 2 loss: 4.78966886254391"
Time difference of 3.781286 secs
[1] "Wed Apr 13 00:25:41 2022: 2 Final nb-AE loss: 4.78966886254391"
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
127.54 1.28 128.92
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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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