Christian Mertes
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/OUTRIDER |
| Branch: RELEASE_3_12 |
| Last Commit: ab85565 |
| Last Changed Date: 2020-10-27 11:37:07 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:28 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the OUTRIDER package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1285/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OUTRIDER 1.8.0 (landing page) Christian Mertes
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OUTRIDER |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings OUTRIDER_1.8.0.tar.gz |
| StartedAt: 2021-05-06 04:15:30 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:25:38 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 608.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings OUTRIDER_1.8.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEncodingDim 29.328 0.116 29.509
plotFunctions 23.252 0.156 23.420
aberrant 7.948 1.508 4.684
getter_setter_functions 7.576 0.000 7.584
OUTRIDER 6.260 1.180 6.930
fit 5.916 0.004 5.927
results 5.548 0.000 5.557
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.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: 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] "Thu May 6 04:23:21 2021: Initial PCA loss: 6.10612672342372"
[1] "Thu May 6 04:23:25 2021: Iteration: 1 loss: 4.41027127393999"
[1] "Thu May 6 04:23:27 2021: Iteration: 2 loss: 4.36077015678829"
[1] "Thu May 6 04:23:30 2021: Iteration: 3 loss: 4.31093061664724"
[1] "Thu May 6 04:23:31 2021: Iteration: 4 loss: 4.2788300323228"
[1] "Thu May 6 04:23:34 2021: Iteration: 5 loss: 4.26822757375728"
[1] "Thu May 6 04:23:36 2021: Iteration: 6 loss: 4.26402641618342"
Time difference of 13.00272 secs
[1] "Thu May 6 04:23:36 2021: 6 Final nb-AE loss: 4.26402641618342"
[1] "Thu May 6 04:23:38 2021: Initial PCA loss: 6.10612672342372"
[1] "Thu May 6 04:23:42 2021: Iteration: 1 loss: 4.41027127393999"
[1] "Thu May 6 04:23:45 2021: Iteration: 2 loss: 4.36077015678829"
[1] "Thu May 6 04:23:46 2021: Iteration: 3 loss: 4.31093061664724"
[1] "Thu May 6 04:23:48 2021: Iteration: 4 loss: 4.2788300323228"
[1] "Thu May 6 04:23:50 2021: Iteration: 5 loss: 4.26822757375728"
[1] "Thu May 6 04:23:52 2021: Iteration: 6 loss: 4.26402641618342"
Time difference of 11.23219 secs
[1] "Thu May 6 04:23:52 2021: 6 Final nb-AE loss: 4.26402641618342"
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] "Thu May 6 04:24:13 2021: Initial PCA loss: 4.48257753657891"
[1] "Thu May 6 04:24:19 2021: Iteration: 1 loss: 4.13834793940632"
[1] "Thu May 6 04:24:21 2021: Iteration: 2 loss: 4.12433507738474"
Time difference of 5.019092 secs
[1] "Thu May 6 04:24:21 2021: 2 Final nb-AE loss: 4.12433507738474"
[1] "Evaluation loss: 0.286045553106254 for q=3"
[1] "Thu May 6 04:24:23 2021: Initial PCA loss: 4.46101006825542"
[1] "Thu May 6 04:24:27 2021: Iteration: 1 loss: 4.06759235129939"
[1] "Thu May 6 04:24:30 2021: Iteration: 2 loss: 4.05877406026205"
Time difference of 4.829603 secs
[1] "Thu May 6 04:24:30 2021: 2 Final nb-AE loss: 4.05877406026205"
[1] "Evaluation loss: 0.37016308797135 for q=4"
[1] "Thu May 6 04:24:32 2021: Initial PCA loss: 4.44094772612886"
[1] "Thu May 6 04:24:36 2021: Iteration: 1 loss: 3.99633133542729"
[1] "Thu May 6 04:24:39 2021: Iteration: 2 loss: 3.98251287794594"
Time difference of 4.593535 secs
[1] "Thu May 6 04:24:39 2021: 2 Final nb-AE loss: 3.98251287794594"
[1] "Evaluation loss: 0.378615198316967 for q=5"
[1] "Thu May 6 04:24:55 2021: Initial PCA loss: 6.46616282459584"
[1] "Thu May 6 04:25:06 2021: Iteration: 1 loss: 4.8154263846794"
[1] "Thu May 6 04:25:12 2021: Iteration: 2 loss: 4.79016305976782"
Time difference of 11.5569 secs
[1] "Thu May 6 04:25:12 2021: 2 Final nb-AE loss: 4.79016305976782"
[ FAIL 0 | WARN 32 | SKIP 0 | PASS 103 ]
>
> proc.time()
user system elapsed
152.940 1.144 155.845
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 6.26 | 1.18 | 6.93 | |
| OutriderDataSet-class | 1.272 | 0.016 | 1.307 | |
| aberrant | 7.948 | 1.508 | 4.684 | |
| computeGeneLength | 2.196 | 0.068 | 2.273 | |
| computeLatentSpace | 1.456 | 0.004 | 1.468 | |
| computePvalues | 2.208 | 0.884 | 2.172 | |
| computeZscores | 1.300 | 0.068 | 1.371 | |
| controlForConfounders | 1.78 | 0.02 | 1.80 | |
| counts | 0.780 | 0.004 | 0.786 | |
| estimateBestQ | 0.472 | 0.000 | 0.473 | |
| filterExpression | 1.780 | 0.008 | 1.788 | |
| findEncodingDim | 29.328 | 0.116 | 29.509 | |
| fit | 5.916 | 0.004 | 5.927 | |
| fpkm | 1.548 | 0.000 | 1.551 | |
| getter_setter_functions | 7.576 | 0.000 | 7.584 | |
| makeExampleOutriderDataSet | 1.940 | 0.000 | 1.942 | |
| normalizationFactors | 1.528 | 0.000 | 1.529 | |
| plotFunctions | 23.252 | 0.156 | 23.420 | |
| results | 5.548 | 0.000 | 5.557 | |
| sampleExclusionMask | 0.852 | 0.000 | 0.854 | |
| sizeFactors | 1.000 | 0.000 | 0.999 | |