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CHECK report for OUTRIDER on malbec2

This page was generated on 2019-04-09 11:51:32 -0400 (Tue, 09 Apr 2019).

Package 1134/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OUTRIDER 1.1.4
Christian Mertes
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/OUTRIDER
Branch: master
Last Commit: 5245580
Last Changed Date: 2019-03-18 13:51:05 -0400 (Mon, 18 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: OUTRIDER
Version: 1.1.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings OUTRIDER_1.1.4.tar.gz
StartedAt: 2019-04-09 02:31:39 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:38:37 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 418.1 seconds
RetCode: 0
Status:  OK 
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:OUTRIDER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings OUTRIDER_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.4’
* 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
findEncodingDim 10.011  0.015   9.610
aberrant         5.953  3.282   4.238
plotFunctions    6.630  0.100   4.871
* 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-3.9-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

Installation output

OUTRIDER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL OUTRIDER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)

Tests output

OUTRIDER.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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, 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] "Initial PCA loss: 7.02901109954309"
[1] "Tue Apr  9 02:36:54 2019: Iteration: 1 loss: 5.04374415632323"
[1] "Tue Apr  9 02:36:56 2019: Iteration: 2 loss: 4.94827974912167"
[1] "Tue Apr  9 02:36:58 2019: Iteration: 3 loss: 4.92152153560946"
[1] "Tue Apr  9 02:37:00 2019: Iteration: 4 loss: 4.91143835026524"
[1] "Tue Apr  9 02:37:02 2019: Iteration: 5 loss: 4.90594309519595"
[1] "Tue Apr  9 02:37:03 2019: Iteration: 6 loss: 4.90460517091562"
Time difference of 12.06673 secs
[1] "6 Final nb-AE loss: 4.90460517091562"
[1] "Initial PCA loss: 7.02901109954309"
[1] "Tue Apr  9 02:37:06 2019: Iteration: 1 loss: 5.04374415632323"
[1] "Tue Apr  9 02:37:08 2019: Iteration: 2 loss: 4.94827974912167"
[1] "Tue Apr  9 02:37:11 2019: Iteration: 3 loss: 4.92152153560946"
[1] "Tue Apr  9 02:37:13 2019: Iteration: 4 loss: 4.91143835026524"
[1] "Tue Apr  9 02:37:15 2019: Iteration: 5 loss: 4.90594309519595"
[1] "Tue Apr  9 02:37:16 2019: Iteration: 6 loss: 4.90460517091562"
Time difference of 11.34608 secs
[1] "6 Final nb-AE loss: 4.90460517091562"
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: 4.48542880610758"
[1] "Tue Apr  9 02:37:26 2019: Iteration: 1 loss: 4.12704263104361"
[1] "Tue Apr  9 02:37:26 2019: Iteration: 2 loss: 4.10505581746734"
[1] "Tue Apr  9 02:37:28 2019: Iteration: 3 loss: 4.08614385529874"
[1] "Tue Apr  9 02:37:29 2019: Iteration: 4 loss: 4.06132156699896"
[1] "Tue Apr  9 02:37:30 2019: Iteration: 5 loss: 4.02619606771475"
[1] "Tue Apr  9 02:37:32 2019: Iteration: 6 loss: 3.99328075440565"
[1] "Tue Apr  9 02:37:33 2019: Iteration: 7 loss: 3.99248530415327"
[1] "Tue Apr  9 02:37:33 2019: Iteration: 8 loss: 3.99248095479095"
Time difference of 9.047294 secs
[1] "8 Final nb-AE loss: 3.99248095479095"
[1] "Evaluation loss: 0.360933441851756"
[1] "Initial PCA loss: 4.43841028295205"
[1] "Tue Apr  9 02:37:36 2019: Iteration: 1 loss: 3.9872149715776"
[1] "Tue Apr  9 02:37:38 2019: Iteration: 2 loss: 3.94881723268608"
[1] "Tue Apr  9 02:37:40 2019: Iteration: 3 loss: 3.93147364254856"
[1] "Tue Apr  9 02:37:42 2019: Iteration: 4 loss: 3.91622466461578"
[1] "Tue Apr  9 02:37:44 2019: Iteration: 5 loss: 3.90631808307816"
[1] "Tue Apr  9 02:37:47 2019: Iteration: 6 loss: 3.90254248296329"
[1] "Tue Apr  9 02:37:47 2019: Iteration: 7 loss: 3.9016652889122"
[1] "Tue Apr  9 02:37:48 2019: Iteration: 8 loss: 3.90113489964535"
[1] "Tue Apr  9 02:37:50 2019: Iteration: 9 loss: 3.90076259576211"
[1] "Tue Apr  9 02:37:51 2019: Iteration: 10 loss: 3.90015982161387"
[1] "Tue Apr  9 02:37:52 2019: Iteration: 11 loss: 3.89988357215169"
[1] "Tue Apr  9 02:37:53 2019: Iteration: 12 loss: 3.89844913839444"
[1] "Tue Apr  9 02:37:54 2019: Iteration: 13 loss: 3.89566401148318"
[1] "Tue Apr  9 02:37:56 2019: Iteration: 14 loss: 3.88992146228139"
[1] "Tue Apr  9 02:37:57 2019: Iteration: 15 loss: 3.87946607945237"
Time difference of 22.71642 secs
[1] "15 Final nb-AE loss: 3.87946607945237"
[1] "Evaluation loss: 0.25569446384975"
[1] "Initial PCA loss: 4.41505416292337"
[1] "Tue Apr  9 02:38:00 2019: Iteration: 1 loss: 3.90963127749208"
[1] "Tue Apr  9 02:38:02 2019: Iteration: 2 loss: 3.87396816554174"
[1] "Tue Apr  9 02:38:04 2019: Iteration: 3 loss: 3.86046857600024"
[1] "Tue Apr  9 02:38:05 2019: Iteration: 4 loss: 3.84911308241814"
[1] "Tue Apr  9 02:38:07 2019: Iteration: 5 loss: 3.84150032099833"
[1] "Tue Apr  9 02:38:08 2019: Iteration: 6 loss: 3.83810198725753"
[1] "Tue Apr  9 02:38:09 2019: Iteration: 7 loss: 3.83729403776746"
[1] "Tue Apr  9 02:38:11 2019: Iteration: 8 loss: 3.83597615602721"
[1] "Tue Apr  9 02:38:11 2019: Iteration: 9 loss: 3.8345325867978"
[1] "Tue Apr  9 02:38:13 2019: Iteration: 10 loss: 3.83173870299429"
[1] "Tue Apr  9 02:38:13 2019: Iteration: 11 loss: 3.82962172228203"
[1] "Tue Apr  9 02:38:14 2019: Iteration: 12 loss: 3.8281314491782"
[1] "Tue Apr  9 02:38:15 2019: Iteration: 13 loss: 3.82721695423739"
[1] "Tue Apr  9 02:38:16 2019: Iteration: 14 loss: 3.82551826613269"
[1] "Tue Apr  9 02:38:17 2019: Iteration: 15 loss: 3.82417468759316"
Time difference of 18.71572 secs
[1] "15 Final nb-AE loss: 3.82417468759316"
[1] "Evaluation loss: 0.285982828767323"
[1] "Initial PCA loss: 6.46616282459584"
[1] "Tue Apr  9 02:38:25 2019: Iteration: 1 loss: 4.8154263846794"
[1] "Tue Apr  9 02:38:27 2019: Iteration: 2 loss: 4.79016305976782"
Time difference of 4.459116 secs
[1] "2 Final nb-AE loss: 4.79016305976782"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 108 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
349.859   2.342 115.853

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER2.5520.5932.185
OutriderDataSet-class0.8820.0401.007
aberrant5.9533.2824.238
computeGeneLength1.5170.0192.069
computeLatentSpace0.3670.0000.367
computePvalues0.8310.5280.821
computeZscores0.5820.0360.591
controlForConfounders0.8380.0640.911
counts0.4510.0080.459
estimateBestQ0.3190.0000.319
filterExpression1.4290.0201.450
findEncodingDim10.011 0.015 9.610
fit0.8030.0080.812
fpkm0.7220.0040.730
getter_setter_functions1.9030.0081.912
makeExampleOutriderDataSet0.8580.0000.882
normalizationFactors0.6070.0000.607
plotFunctions6.6300.1004.871
results1.7670.0041.429
sampleExclusionMask0.3750.0000.374
sizeFactors0.5820.0030.587