Christian Mertes
| Snapshot Date: 2020-10-13 14:50:23 -0400 (Tue, 13 Oct 2020) |
| URL: https://git.bioconductor.org/packages/OUTRIDER |
| Branch: RELEASE_3_11 |
| Last Commit: bef68ce |
| Last Changed Date: 2020-10-09 18:47:42 -0400 (Fri, 09 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-14 11:54:44 -0400 (Wed, 14 Oct 2020).
| 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 1253/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OUTRIDER 1.6.1 Christian Mertes
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: OUTRIDER |
| Version: 1.6.1 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings OUTRIDER_1.6.1.tar.gz |
| StartedAt: 2020-10-14 05:16:42 -0400 (Wed, 14 Oct 2020) |
| EndedAt: 2020-10-14 05:27:34 -0400 (Wed, 14 Oct 2020) |
| EllapsedTime: 651.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OUTRIDER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings OUTRIDER_1.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.6.1’
* 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 15.747 0.012 15.758
plotFunctions 11.158 0.163 10.585
OUTRIDER 5.154 0.982 5.818
* 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-3.11-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.
OUTRIDER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL OUTRIDER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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 14 05:26:29 2020: Initial PCA loss: 6.23482282850007"
[1] "Wed Oct 14 05:26:31 2020: Iteration: 1 loss: 4.70997716314341"
[1] "Wed Oct 14 05:26:32 2020: Iteration: 2 loss: 4.63251707110498"
[1] "Wed Oct 14 05:26:32 2020: Iteration: 3 loss: 4.55402189384039"
[1] "Wed Oct 14 05:26:33 2020: Iteration: 4 loss: 4.51450429172808"
[1] "Wed Oct 14 05:26:34 2020: Iteration: 5 loss: 4.49429203240507"
[1] "Wed Oct 14 05:26:35 2020: Iteration: 6 loss: 4.48464139824699"
Time difference of 4.813325 secs
[1] "Wed Oct 14 05:26:35 2020: 6 Final nb-AE loss: 4.48464139824699"
[1] "Wed Oct 14 05:26:36 2020: Initial PCA loss: 6.23482282850007"
[1] "Wed Oct 14 05:26:37 2020: Iteration: 1 loss: 4.70997716314341"
[1] "Wed Oct 14 05:26:38 2020: Iteration: 2 loss: 4.63251707110498"
[1] "Wed Oct 14 05:26:39 2020: Iteration: 3 loss: 4.55402189384039"
[1] "Wed Oct 14 05:26:40 2020: Iteration: 4 loss: 4.51450429172808"
[1] "Wed Oct 14 05:26:41 2020: Iteration: 5 loss: 4.49429203240507"
[1] "Wed Oct 14 05:26:42 2020: Iteration: 6 loss: 4.48464139824699"
Time difference of 4.97828 secs
[1] "Wed Oct 14 05:26:42 2020: 6 Final nb-AE loss: 4.48464139824699"
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 14 05:26:57 2020: Initial PCA loss: 4.46793536469941"
[1] "Wed Oct 14 05:26:58 2020: Iteration: 1 loss: 4.14249975451718"
[1] "Wed Oct 14 05:26:59 2020: Iteration: 2 loss: 4.12250911083302"
Time difference of 1.579726 secs
[1] "Wed Oct 14 05:26:59 2020: 2 Final nb-AE loss: 4.12250911083302"
[1] "Evaluation loss: 0.618369292685753 for q=3"
[1] "Wed Oct 14 05:27:01 2020: Initial PCA loss: 4.44466349784687"
[1] "Wed Oct 14 05:27:02 2020: Iteration: 1 loss: 4.08360215081782"
[1] "Wed Oct 14 05:27:03 2020: Iteration: 2 loss: 4.07435138266788"
Time difference of 1.557244 secs
[1] "Wed Oct 14 05:27:03 2020: 2 Final nb-AE loss: 4.07435138266788"
[1] "Evaluation loss: 0.464213809424744 for q=4"
[1] "Wed Oct 14 05:27:04 2020: Initial PCA loss: 4.41757661845091"
[1] "Wed Oct 14 05:27:06 2020: Iteration: 1 loss: 4.00907150192757"
[1] "Wed Oct 14 05:27:06 2020: Iteration: 2 loss: 3.99693286483901"
Time difference of 1.5827 secs
[1] "Wed Oct 14 05:27:06 2020: 2 Final nb-AE loss: 3.99693286483901"
[1] "Evaluation loss: 0.522008547092549 for q=5"
[1] "Wed Oct 14 05:27:16 2020: Initial PCA loss: 6.46616282459584"
[1] "Wed Oct 14 05:27:18 2020: Iteration: 1 loss: 4.8154263846794"
[1] "Wed Oct 14 05:27:19 2020: Iteration: 2 loss: 4.79016305976782"
Time difference of 2.304486 secs
[1] "Wed Oct 14 05:27:19 2020: 2 Final nb-AE loss: 4.79016305976782"
Error in x$.self$finalize() : attempt to apply non-function
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 103 | SKIPPED: 0 | WARNINGS: 32 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
77.264 0.897 80.854
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 5.154 | 0.982 | 5.818 | |
| OutriderDataSet-class | 0.900 | 0.008 | 0.919 | |
| aberrant | 2.073 | 0.576 | 1.971 | |
| computeGeneLength | 1.517 | 0.032 | 1.564 | |
| computeLatentSpace | 0.903 | 0.000 | 0.903 | |
| computePvalues | 1.209 | 0.505 | 1.417 | |
| computeZscores | 1.131 | 0.032 | 1.163 | |
| controlForConfounders | 1.344 | 0.012 | 1.356 | |
| counts | 0.638 | 0.000 | 0.639 | |
| estimateBestQ | 0.474 | 0.000 | 0.474 | |
| filterExpression | 1.583 | 0.008 | 1.590 | |
| findEncodingDim | 15.747 | 0.012 | 15.758 | |
| fit | 0.981 | 0.008 | 0.988 | |
| fpkm | 0.910 | 0.012 | 0.922 | |
| getter_setter_functions | 3.699 | 0.008 | 3.707 | |
| makeExampleOutriderDataSet | 1.170 | 0.000 | 1.171 | |
| normalizationFactors | 1.176 | 0.000 | 1.177 | |
| plotFunctions | 11.158 | 0.163 | 10.585 | |
| results | 4.314 | 0.000 | 4.315 | |
| sampleExclusionMask | 0.500 | 0.004 | 0.504 | |
| sizeFactors | 0.734 | 0.000 | 0.733 | |