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CHECK report for OUTRIDER on merida2

This page was generated on 2019-04-09 13:37:13 -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: /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_1.1.4.tar.gz
StartedAt: 2019-04-09 02:41:33 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:48:36 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 422.2 seconds
RetCode: 0
Status:  OK 
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/OUTRIDER.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.1.4’
* 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 <[email protected]> [aut, cre]
  Christian Mertes <[email protected]> [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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
aberrant        8.005  8.302   6.317
plotFunctions   8.280  2.942   5.565
findEncodingDim 8.397  1.062   7.445
OUTRIDER        4.205  1.686   3.724
* 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-3.9-bioc/meat/OUTRIDER.Rcheck/00check.log’
for details.

Installation output

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/3.6/Resources/library’
* installing *source* package ‘OUTRIDER’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
loss_n_gradient_functions.cpp:41:19: warning: unused variable 'c' [-Wunused-variable]
    double b, ll, c;
                  ^
loss_n_gradient_functions.cpp:68:15: warning: unused variable 'c' [-Wunused-variable]
    double b, c;
              ^
2 warnings generated.
clang++ -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 -fopenmp -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-darwin15/6.1.0 -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/3.6/Resources/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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: 6.50493037927917"
[1] "Tue Apr  9 02:47:27 2019: Iteration: 1 loss: 4.81271054321652"
[1] "Tue Apr  9 02:47:27 2019: Iteration: 2 loss: 4.72404955291122"
[1] "Tue Apr  9 02:47:28 2019: Iteration: 3 loss: 4.68678443830888"
[1] "Tue Apr  9 02:47:29 2019: Iteration: 4 loss: 4.66004324134607"
[1] "Tue Apr  9 02:47:29 2019: Iteration: 5 loss: 4.6404066666658"
[1] "Tue Apr  9 02:47:31 2019: Iteration: 6 loss: 4.63606577512442"
Time difference of 4.611521 secs
[1] "6 Final nb-AE loss: 4.63606577512442"
[1] "Initial PCA loss: 6.50493037927917"
[1] "Tue Apr  9 02:47:33 2019: Iteration: 1 loss: 4.81271054321652"
[1] "Tue Apr  9 02:47:34 2019: Iteration: 2 loss: 4.72404955291122"
[1] "Tue Apr  9 02:47:34 2019: Iteration: 3 loss: 4.68678443830888"
[1] "Tue Apr  9 02:47:35 2019: Iteration: 4 loss: 4.66004324134607"
[1] "Tue Apr  9 02:47:36 2019: Iteration: 5 loss: 4.6404066666658"
[1] "Tue Apr  9 02:47:36 2019: Iteration: 6 loss: 4.63606577512442"
Time difference of 3.980598 secs
[1] "6 Final nb-AE loss: 4.63606577512442"
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: 4.4719362093003"
[1] "Tue Apr  9 02:47:49 2019: Iteration: 1 loss: 4.14472302809584"
[1] "Tue Apr  9 02:47:49 2019: Iteration: 2 loss: 4.12725470310908"
[1] "Tue Apr  9 02:47:50 2019: Iteration: 3 loss: 4.10980899404035"
[1] "Tue Apr  9 02:47:50 2019: Iteration: 4 loss: 4.08657384699821"
[1] "Tue Apr  9 02:47:51 2019: Iteration: 5 loss: 4.04426663110023"
[1] "Tue Apr  9 02:47:51 2019: Iteration: 6 loss: 4.02271928410836"
[1] "Tue Apr  9 02:47:52 2019: Iteration: 7 loss: 4.00973994863496"
[1] "Tue Apr  9 02:47:53 2019: Iteration: 8 loss: 4.00867681785484"
[1] "Tue Apr  9 02:47:53 2019: Iteration: 9 loss: 4.00860618099004"
[1] "Tue Apr  9 02:47:54 2019: Iteration: 10 loss: 4.0086039839524"
Time difference of 5.830482 secs
[1] "10 Final nb-AE loss: 4.0086039839524"
[1] "Evaluation loss: 0.629939296212684"
[1] "Initial PCA loss: 4.44686607976973"
[1] "Tue Apr  9 02:47:56 2019: Iteration: 1 loss: 4.07968786529379"
[1] "Tue Apr  9 02:47:56 2019: Iteration: 2 loss: 4.0634794818966"
[1] "Tue Apr  9 02:47:57 2019: Iteration: 3 loss: 4.04897929700731"
[1] "Tue Apr  9 02:47:58 2019: Iteration: 4 loss: 4.03144262626311"
[1] "Tue Apr  9 02:47:58 2019: Iteration: 5 loss: 4.01731618842644"
[1] "Tue Apr  9 02:47:59 2019: Iteration: 6 loss: 4.00209339470541"
[1] "Tue Apr  9 02:47:59 2019: Iteration: 7 loss: 3.99366987840398"
[1] "Tue Apr  9 02:48:00 2019: Iteration: 8 loss: 3.99260267968552"
[1] "Tue Apr  9 02:48:00 2019: Iteration: 9 loss: 3.99123297826263"
[1] "Tue Apr  9 02:48:01 2019: Iteration: 10 loss: 3.98806199532992"
[1] "Tue Apr  9 02:48:02 2019: Iteration: 11 loss: 3.98027602707699"
[1] "Tue Apr  9 02:48:02 2019: Iteration: 12 loss: 3.95975916100963"
[1] "Tue Apr  9 02:48:03 2019: Iteration: 13 loss: 3.95229289693649"
[1] "Tue Apr  9 02:48:03 2019: Iteration: 14 loss: 3.95226883010706"
[1] "Tue Apr  9 02:48:04 2019: Iteration: 15 loss: 3.95226484803289"
Time difference of 8.790493 secs
[1] "15 Final nb-AE loss: 3.95226484803289"
[1] "Evaluation loss: 0.625704502268891"
[1] "Initial PCA loss: 4.42321198832525"
[1] "Tue Apr  9 02:48:06 2019: Iteration: 1 loss: 3.99345539351436"
[1] "Tue Apr  9 02:48:06 2019: Iteration: 2 loss: 3.9737128015804"
[1] "Tue Apr  9 02:48:07 2019: Iteration: 3 loss: 3.95860504732685"
[1] "Tue Apr  9 02:48:08 2019: Iteration: 4 loss: 3.94028523943564"
[1] "Tue Apr  9 02:48:08 2019: Iteration: 5 loss: 3.92017613062575"
[1] "Tue Apr  9 02:48:09 2019: Iteration: 6 loss: 3.90294271242154"
[1] "Tue Apr  9 02:48:09 2019: Iteration: 7 loss: 3.8952286838654"
[1] "Tue Apr  9 02:48:10 2019: Iteration: 8 loss: 3.88130782433682"
[1] "Tue Apr  9 02:48:10 2019: Iteration: 9 loss: 3.86071488931001"
[1] "Tue Apr  9 02:48:11 2019: Iteration: 10 loss: 3.85941426620578"
[1] "Tue Apr  9 02:48:12 2019: Iteration: 11 loss: 3.85940660944549"
Time difference of 6.411012 secs
[1] "11 Final nb-AE loss: 3.85940660944549"
[1] "Evaluation loss: 0.632413763637222"
[1] "Initial PCA loss: 6.46616282459584"
[1] "Tue Apr  9 02:48:21 2019: Iteration: 1 loss: 4.81518048146922"
[1] "Tue Apr  9 02:48:22 2019: Iteration: 2 loss: 4.78972706919211"
Time difference of 1.832711 secs
[1] "2 Final nb-AE loss: 4.78972706919211"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 108 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
171.960  84.327  78.966

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER4.2051.6863.724
OutriderDataSet-class1.0240.0821.146
aberrant8.0058.3026.317
computeGeneLength1.7430.1701.936
computeLatentSpace0.6310.0030.645
computePvalues1.1540.5591.240
computeZscores1.4450.6001.062
controlForConfounders1.0040.0691.090
counts0.5010.0040.510
estimateBestQ0.3630.0030.369
filterExpression1.5400.0171.579
findEncodingDim8.3971.0627.445
fit0.9590.0150.986
fpkm0.7760.0040.787
getter_setter_functions2.5070.0102.552
makeExampleOutriderDataSet0.8000.0030.813
normalizationFactors0.5260.0040.534
plotFunctions8.2802.9425.565
results2.3070.0802.315
sampleExclusionMask0.8690.4550.436
sizeFactors0.5920.0030.608