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 11:59:07 -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: /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_1.6.1.tar.gz |
| StartedAt: 2020-10-14 04:36:54 -0400 (Wed, 14 Oct 2020) |
| EndedAt: 2020-10-14 04:47:49 -0400 (Wed, 14 Oct 2020) |
| EllapsedTime: 654.8 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_1.6.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/OUTRIDER.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findEncodingDim 24.919 0.071 25.085
plotFunctions 14.918 0.574 17.152
OUTRIDER 6.299 0.695 6.833
results 5.913 0.042 7.307
getter_setter_functions 5.714 0.012 5.729
* 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
‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’ * installing *source* package ‘OUTRIDER’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -mmacosx-version-min=10.13 -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 -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-darwin18/8.2.0 -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/4.0/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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 14 04:45:37 2020: Initial PCA loss: 6.08089564987666"
[1] "Wed Oct 14 04:45:40 2020: Iteration: 1 loss: 4.60975138193602"
[1] "Wed Oct 14 04:45:42 2020: Iteration: 2 loss: 4.51360142349333"
[1] "Wed Oct 14 04:45:44 2020: Iteration: 3 loss: 4.43409251013544"
[1] "Wed Oct 14 04:45:46 2020: Iteration: 4 loss: 4.35080956954133"
[1] "Wed Oct 14 04:45:48 2020: Iteration: 5 loss: 4.29595124293252"
[1] "Wed Oct 14 04:45:50 2020: Iteration: 6 loss: 4.26982013399639"
Time difference of 11.33831 secs
[1] "Wed Oct 14 04:45:50 2020: 6 Final nb-AE loss: 4.26982013399639"
[1] "Wed Oct 14 04:45:52 2020: Initial PCA loss: 6.08089564987666"
[1] "Wed Oct 14 04:45:56 2020: Iteration: 1 loss: 4.60975138193602"
[1] "Wed Oct 14 04:45:58 2020: Iteration: 2 loss: 4.51360142349333"
[1] "Wed Oct 14 04:46:00 2020: Iteration: 3 loss: 4.43409251013544"
[1] "Wed Oct 14 04:46:02 2020: Iteration: 4 loss: 4.35080956954133"
[1] "Wed Oct 14 04:46:04 2020: Iteration: 5 loss: 4.29595124293252"
[1] "Wed Oct 14 04:46:06 2020: Iteration: 6 loss: 4.26982013399639"
Time difference of 11.65416 secs
[1] "Wed Oct 14 04:46:06 2020: 6 Final nb-AE loss: 4.26982013399639"
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 04:46:39 2020: Initial PCA loss: 4.59683789134801"
[1] "Wed Oct 14 04:46:42 2020: Iteration: 1 loss: 4.25740500533551"
[1] "Wed Oct 14 04:46:44 2020: Iteration: 2 loss: 4.24030063295126"
Time difference of 3.602941 secs
[1] "Wed Oct 14 04:46:44 2020: 2 Final nb-AE loss: 4.24030063295126"
[1] "Evaluation loss: 0.63184979066753 for q=3"
[1] "Wed Oct 14 04:46:46 2020: Initial PCA loss: 4.54360924661606"
[1] "Wed Oct 14 04:46:50 2020: Iteration: 1 loss: 4.15386925750924"
[1] "Wed Oct 14 04:46:51 2020: Iteration: 2 loss: 4.13647911393216"
Time difference of 3.768075 secs
[1] "Wed Oct 14 04:46:51 2020: 2 Final nb-AE loss: 4.13647911393216"
[1] "Evaluation loss: 0.539926695676499 for q=4"
[1] "Wed Oct 14 04:46:54 2020: Initial PCA loss: 4.51281141021596"
[1] "Wed Oct 14 04:46:57 2020: Iteration: 1 loss: 4.06985757367822"
[1] "Wed Oct 14 04:46:59 2020: Iteration: 2 loss: 4.04888475136613"
Time difference of 3.641422 secs
[1] "Wed Oct 14 04:46:59 2020: 2 Final nb-AE loss: 4.04888475136613"
[1] "Evaluation loss: 0.507320534993459 for q=5"
[1] "Wed Oct 14 04:47:15 2020: Initial PCA loss: 6.46616282459584"
[1] "Wed Oct 14 04:47:18 2020: Iteration: 1 loss: 4.81518048146922"
[1] "Wed Oct 14 04:47:20 2020: Iteration: 2 loss: 4.78972706919211"
Time difference of 3.240604 secs
[1] "Wed Oct 14 04:47:20 2020: 2 Final nb-AE loss: 4.78972706919211"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 103 | SKIPPED: 0 | WARNINGS: 32 | FAILED: 0 ]
>
> proc.time()
user system elapsed
133.350 1.946 156.661
OUTRIDER.Rcheck/OUTRIDER-Ex.timings
| name | user | system | elapsed | |
| OUTRIDER | 6.299 | 0.695 | 6.833 | |
| OutriderDataSet-class | 1.556 | 0.027 | 1.654 | |
| aberrant | 3.538 | 0.550 | 3.303 | |
| computeGeneLength | 2.626 | 0.130 | 2.760 | |
| computeLatentSpace | 1.524 | 0.012 | 1.608 | |
| computePvalues | 1.860 | 0.291 | 1.994 | |
| computeZscores | 1.725 | 0.120 | 1.849 | |
| controlForConfounders | 2.336 | 0.037 | 2.613 | |
| counts | 0.880 | 0.005 | 0.885 | |
| estimateBestQ | 0.640 | 0.002 | 0.642 | |
| filterExpression | 2.682 | 0.020 | 2.704 | |
| findEncodingDim | 24.919 | 0.071 | 25.085 | |
| fit | 1.644 | 0.018 | 1.663 | |
| fpkm | 1.626 | 0.009 | 1.637 | |
| getter_setter_functions | 5.714 | 0.012 | 5.729 | |
| makeExampleOutriderDataSet | 2.093 | 0.006 | 2.102 | |
| normalizationFactors | 1.547 | 0.004 | 1.551 | |
| plotFunctions | 14.918 | 0.574 | 17.152 | |
| results | 5.913 | 0.042 | 7.307 | |
| sampleExclusionMask | 0.973 | 0.006 | 1.096 | |
| sizeFactors | 1.440 | 0.012 | 1.615 | |