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CHECK report for OUTRIDER on malbec1

This page was generated on 2019-04-16 11:53:40 -0400 (Tue, 16 Apr 2019).

Package 1108/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.0.4
Christian Mertes
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/OUTRIDER
Branch: RELEASE_3_8
Last Commit: 18fcd8e
Last Changed Date: 2019-03-18 14:04:22 -0400 (Mon, 18 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OUTRIDER
Version: 1.0.4
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings OUTRIDER_1.0.4.tar.gz
StartedAt: 2019-04-16 01:55:42 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:02:05 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 383.5 seconds
RetCode: 0
Status:  OK 
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings OUTRIDER_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/OUTRIDER.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.4’
* 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 ... NOTE
Authors@R field gives more than one person with maintainer role:
  Felix Brechtmann <brechtma@in.tum.de> [aut, cre]
  Christian Mertes <mertes@in.tum.de> [aut, cre]
* 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 ... OK
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotFunctions   6.308  0.128   4.183
findEncodingDim 5.540  0.008   4.856
* 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-3.8-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘OUTRIDER’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fpic  -g -O2 -Wall -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
loss_n_gradient_functions.cpp: In function ‘double truncLogLiklihoodD(arma::vec, arma::mat, arma::vec, arma::vec, arma::vec, double, arma::vec)’:
loss_n_gradient_functions.cpp:41:19: warning: unused variable ‘c’ [-Wunused-variable]
     double b, ll, c;
                   ^
loss_n_gradient_functions.cpp: In function ‘arma::vec gradientD(arma::vec, arma::mat, arma::vec, arma::vec, arma::vec, double, arma::vec)’:
loss_n_gradient_functions.cpp:68:15: warning: unused variable ‘c’ [-Wunused-variable]
     double b, c;
               ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (OUTRIDER)

Tests output

OUTRIDER.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

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] "Initial PCA loss: 6.2247763613379"
[1] "Tue Apr 16 02:00:33 2019: Iteration: 1 loss: 4.57829156695037"
[1] "Tue Apr 16 02:00:35 2019: Iteration: 2 loss: 4.45668755271273"
[1] "Tue Apr 16 02:00:37 2019: Iteration: 3 loss: 4.40710888540369"
[1] "Tue Apr 16 02:00:38 2019: Iteration: 4 loss: 4.38790873048755"
[1] "Tue Apr 16 02:00:40 2019: Iteration: 5 loss: 4.37526986427832"
[1] "Tue Apr 16 02:00:41 2019: Iteration: 6 loss: 4.36876984668577"
Time difference of 9.266305 secs
[1] "6 Final nb-AE loss: 4.36876984668577"
[1] "Initial PCA loss: 6.2247763613379"
[1] "Tue Apr 16 02:00:44 2019: Iteration: 1 loss: 4.57829156695037"
[1] "Tue Apr 16 02:00:46 2019: Iteration: 2 loss: 4.45668755271273"
[1] "Tue Apr 16 02:00:48 2019: Iteration: 3 loss: 4.40710888540369"
[1] "Tue Apr 16 02:00:50 2019: Iteration: 4 loss: 4.38790873048755"
[1] "Tue Apr 16 02:00:52 2019: Iteration: 5 loss: 4.37526986427832"
[1] "Tue Apr 16 02:00:53 2019: Iteration: 6 loss: 4.36876984668577"
Time difference of 10.87686 secs
[1] "6 Final nb-AE loss: 4.36876984668577"
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] "Initial PCA loss: 4.46148976142138"
[1] "Tue Apr 16 02:01:05 2019: Iteration: 1 loss: 4.08972331581224"
[1] "Tue Apr 16 02:01:05 2019: Iteration: 2 loss: 4.06776149291593"
[1] "Tue Apr 16 02:01:06 2019: Iteration: 3 loss: 4.05230677464077"
[1] "Tue Apr 16 02:01:07 2019: Iteration: 4 loss: 4.02912254587462"
[1] "Tue Apr 16 02:01:08 2019: Iteration: 5 loss: 4.00900976499821"
[1] "Tue Apr 16 02:01:10 2019: Iteration: 6 loss: 4.00639153478246"
[1] "Tue Apr 16 02:01:12 2019: Iteration: 7 loss: 4.00355151457826"
[1] "Tue Apr 16 02:01:13 2019: Iteration: 8 loss: 3.9995885899756"
[1] "Tue Apr 16 02:01:14 2019: Iteration: 9 loss: 3.99767032116339"
[1] "Tue Apr 16 02:01:15 2019: Iteration: 10 loss: 3.99734646038322"
[1] "Tue Apr 16 02:01:15 2019: Iteration: 11 loss: 3.99730207803732"
[1] "Tue Apr 16 02:01:16 2019: Iteration: 12 loss: 3.99728592026719"
[1] "Tue Apr 16 02:01:16 2019: Iteration: 13 loss: 3.99728057283333"
Time difference of 12.83465 secs
[1] "13 Final nb-AE loss: 3.99728057283333"
[1] "Evaluation loss: 0.55276757207154"
[1] "Initial PCA loss: 4.4330027343713"
[1] "Tue Apr 16 02:01:18 2019: Iteration: 1 loss: 4.01207261535758"
[1] "Tue Apr 16 02:01:19 2019: Iteration: 2 loss: 3.99471035488846"
[1] "Tue Apr 16 02:01:20 2019: Iteration: 3 loss: 3.98423111213513"
[1] "Tue Apr 16 02:01:21 2019: Iteration: 4 loss: 3.9702502305515"
[1] "Tue Apr 16 02:01:22 2019: Iteration: 5 loss: 3.94289713686934"
[1] "Tue Apr 16 02:01:24 2019: Iteration: 6 loss: 3.93158895127863"
[1] "Tue Apr 16 02:01:25 2019: Iteration: 7 loss: 3.92721659912569"
[1] "Tue Apr 16 02:01:28 2019: Iteration: 8 loss: 3.9205670968784"
[1] "Tue Apr 16 02:01:29 2019: Iteration: 9 loss: 3.91713361151344"
[1] "Tue Apr 16 02:01:30 2019: Iteration: 10 loss: 3.91412922506586"
[1] "Tue Apr 16 02:01:31 2019: Iteration: 11 loss: 3.91315051872421"
[1] "Tue Apr 16 02:01:31 2019: Iteration: 12 loss: 3.91311007795669"
[1] "Tue Apr 16 02:01:32 2019: Iteration: 13 loss: 3.91308033542948"
[1] "Tue Apr 16 02:01:32 2019: Iteration: 14 loss: 3.91307241532011"
Time difference of 14.95424 secs
[1] "14 Final nb-AE loss: 3.91307241532011"
[1] "Evaluation loss: 0.5410397063901"
[1] "Initial PCA loss: 4.41362267470606"
[1] "Tue Apr 16 02:01:34 2019: Iteration: 1 loss: 3.94795870998893"
[1] "Tue Apr 16 02:01:36 2019: Iteration: 2 loss: 3.9276191371008"
[1] "Tue Apr 16 02:01:37 2019: Iteration: 3 loss: 3.9149552659075"
[1] "Tue Apr 16 02:01:37 2019: Iteration: 4 loss: 3.9053440680996"
[1] "Tue Apr 16 02:01:38 2019: Iteration: 5 loss: 3.89283186660047"
[1] "Tue Apr 16 02:01:39 2019: Iteration: 6 loss: 3.87020583916921"
[1] "Tue Apr 16 02:01:40 2019: Iteration: 7 loss: 3.84267994249911"
[1] "Tue Apr 16 02:01:42 2019: Iteration: 8 loss: 3.8182539285327"
[1] "Tue Apr 16 02:01:43 2019: Iteration: 9 loss: 3.80524850493526"
[1] "Tue Apr 16 02:01:44 2019: Iteration: 10 loss: 3.80501828158425"
[1] "Tue Apr 16 02:01:44 2019: Iteration: 11 loss: 3.80501454817465"
Time difference of 11.43472 secs
[1] "11 Final nb-AE loss: 3.80501454817465"
[1] "Evaluation loss: 0.566333933214007"
[1] "Initial PCA loss: 6.46616282459584"
[1] "Tue Apr 16 02:01:53 2019: Iteration: 1 loss: 4.8154263846794"
[1] "Tue Apr 16 02:01:55 2019: Iteration: 2 loss: 4.79016305976782"
Time difference of 4.147903 secs
[1] "2 Final nb-AE loss: 4.79016305976782"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 108 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
361.048   1.612 103.808

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER2.5640.6762.560
OutriderDataSet-class0.6400.0080.659
aberrant1.9680.6841.899
computeGeneLength2.0160.1042.136
computeLatentSpace0.2960.0480.344
computePvalues0.5640.5120.882
computeZscores0.6680.0480.691
controlForConfounders0.5040.0040.506
counts0.3080.0000.309
estimateBestQ0.1880.0000.188
filterExpression1.2640.0081.278
findEncodingDim5.5400.0084.856
fit0.5520.0040.589
fpkm0.6080.0040.613
getter_setter_functions1.3600.0041.366
makeExampleOutriderDataSet0.4760.0040.479
normalizationFactors0.3160.0000.317
plotFunctions6.3080.1284.183
results1.6480.0041.228
sampleExclusionMask0.3480.0000.349
sizeFactors0.4240.0000.425