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CHECK report for OUTRIDER on merida1

This page was generated on 2019-04-16 12:11:04 -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: /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_1.0.4.tar.gz
StartedAt: 2019-04-16 01:44:50 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:51:14 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 383.9 seconds
RetCode: 0
Status:  OK 
CheckDir: OUTRIDER.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/OUTRIDER.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.4’
* 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 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
plotFunctions   8.190  3.489   4.736
findEncodingDim 6.171  1.727   5.369
OUTRIDER        4.292  1.770   2.977
* 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-3.8-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/3.5/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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, 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: 6.79519529641234"
[1] "Tue Apr 16 01:50:19 2019: Iteration: 1 loss: 5.02724808779847"
[1] "Tue Apr 16 01:50:19 2019: Iteration: 2 loss: 4.94980625250357"
[1] "Tue Apr 16 01:50:20 2019: Iteration: 3 loss: 4.90801200351714"
[1] "Tue Apr 16 01:50:20 2019: Iteration: 4 loss: 4.8934563671799"
[1] "Tue Apr 16 01:50:21 2019: Iteration: 5 loss: 4.88278737006242"
[1] "Tue Apr 16 01:50:21 2019: Iteration: 6 loss: 4.8778199338055"
Time difference of 2.663965 secs
[1] "6 Final nb-AE loss: 4.8778199338055"
[1] "Initial PCA loss: 6.79519529641234"
[1] "Tue Apr 16 01:50:23 2019: Iteration: 1 loss: 5.02724808779847"
[1] "Tue Apr 16 01:50:23 2019: Iteration: 2 loss: 4.94980625250357"
[1] "Tue Apr 16 01:50:24 2019: Iteration: 3 loss: 4.90801200351714"
[1] "Tue Apr 16 01:50:24 2019: Iteration: 4 loss: 4.8934563671799"
[1] "Tue Apr 16 01:50:25 2019: Iteration: 5 loss: 4.88278737006242"
[1] "Tue Apr 16 01:50:25 2019: Iteration: 6 loss: 4.8778199338055"
Time difference of 2.981153 secs
[1] "6 Final nb-AE loss: 4.8778199338055"
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: 4.51738471464968"
[1] "Tue Apr 16 01:50:36 2019: Iteration: 1 loss: 4.12696066620675"
[1] "Tue Apr 16 01:50:36 2019: Iteration: 2 loss: 4.11489707386273"
[1] "Tue Apr 16 01:50:37 2019: Iteration: 3 loss: 4.10663110997022"
[1] "Tue Apr 16 01:50:37 2019: Iteration: 4 loss: 4.09628747185159"
[1] "Tue Apr 16 01:50:37 2019: Iteration: 5 loss: 4.07162229118038"
[1] "Tue Apr 16 01:50:38 2019: Iteration: 6 loss: 4.04567750945746"
[1] "Tue Apr 16 01:50:38 2019: Iteration: 7 loss: 4.03712257400679"
[1] "Tue Apr 16 01:50:39 2019: Iteration: 8 loss: 4.01564771618424"
[1] "Tue Apr 16 01:50:39 2019: Iteration: 9 loss: 4.00873247865144"
[1] "Tue Apr 16 01:50:39 2019: Iteration: 10 loss: 4.00819657478305"
[1] "Tue Apr 16 01:50:40 2019: Iteration: 11 loss: 4.0078778395385"
[1] "Tue Apr 16 01:50:40 2019: Iteration: 12 loss: 4.00782598025904"
[1] "Tue Apr 16 01:50:41 2019: Iteration: 13 loss: 4.00781978796199"
Time difference of 5.215626 secs
[1] "13 Final nb-AE loss: 4.00781978796199"
[1] "Evaluation loss: 0.490949228823558"
[1] "Initial PCA loss: 4.48514121258334"
[1] "Tue Apr 16 01:50:42 2019: Iteration: 1 loss: 4.07251307641208"
[1] "Tue Apr 16 01:50:42 2019: Iteration: 2 loss: 4.06077567268319"
[1] "Tue Apr 16 01:50:43 2019: Iteration: 3 loss: 4.04606128755662"
[1] "Tue Apr 16 01:50:43 2019: Iteration: 4 loss: 4.02710193228173"
[1] "Tue Apr 16 01:50:44 2019: Iteration: 5 loss: 4.00864731774557"
[1] "Tue Apr 16 01:50:44 2019: Iteration: 6 loss: 3.99097311908767"
[1] "Tue Apr 16 01:50:45 2019: Iteration: 7 loss: 3.9737727719435"
[1] "Tue Apr 16 01:50:45 2019: Iteration: 8 loss: 3.9566129448841"
[1] "Tue Apr 16 01:50:46 2019: Iteration: 9 loss: 3.9258224799841"
[1] "Tue Apr 16 01:50:46 2019: Iteration: 10 loss: 3.92413538052278"
[1] "Tue Apr 16 01:50:46 2019: Iteration: 11 loss: 3.9238809533255"
[1] "Tue Apr 16 01:50:47 2019: Iteration: 12 loss: 3.92338945132556"
[1] "Tue Apr 16 01:50:47 2019: Iteration: 13 loss: 3.92196719219911"
[1] "Tue Apr 16 01:50:47 2019: Iteration: 14 loss: 3.91986590787131"
[1] "Tue Apr 16 01:50:48 2019: Iteration: 15 loss: 3.91328214726127"
Time difference of 6.315361 secs
[1] "15 Final nb-AE loss: 3.91328214726127"
[1] "Evaluation loss: 0.369786064294792"
[1] "Initial PCA loss: 4.43756216234584"
[1] "Tue Apr 16 01:50:49 2019: Iteration: 1 loss: 3.9809658174077"
[1] "Tue Apr 16 01:50:50 2019: Iteration: 2 loss: 3.95067199856787"
[1] "Tue Apr 16 01:50:50 2019: Iteration: 3 loss: 3.90987268880408"
[1] "Tue Apr 16 01:50:50 2019: Iteration: 4 loss: 3.86977225740511"
[1] "Tue Apr 16 01:50:51 2019: Iteration: 5 loss: 3.85678889549783"
[1] "Tue Apr 16 01:50:51 2019: Iteration: 6 loss: 3.84779635421761"
[1] "Tue Apr 16 01:50:52 2019: Iteration: 7 loss: 3.83801282538081"
[1] "Tue Apr 16 01:50:52 2019: Iteration: 8 loss: 3.8282508111774"
[1] "Tue Apr 16 01:50:52 2019: Iteration: 9 loss: 3.82118948440095"
[1] "Tue Apr 16 01:50:53 2019: Iteration: 10 loss: 3.81468129243501"
[1] "Tue Apr 16 01:50:53 2019: Iteration: 11 loss: 3.81114560655627"
[1] "Tue Apr 16 01:50:53 2019: Iteration: 12 loss: 3.81091619381618"
[1] "Tue Apr 16 01:50:54 2019: Iteration: 13 loss: 3.81090910322966"
Time difference of 5.092109 secs
[1] "13 Final nb-AE loss: 3.81090910322966"
[1] "Evaluation loss: 0.321486983131333"
[1] "Initial PCA loss: 6.46616282459584"
[1] "Tue Apr 16 01:51:01 2019: Iteration: 1 loss: 4.81518048146922"
[1] "Tue Apr 16 01:51:01 2019: Iteration: 2 loss: 4.78972706919211"
Time difference of 1.437918 secs
[1] "2 Final nb-AE loss: 4.78972706919211"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 108 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
147.692  80.982  63.923

Example timings

OUTRIDER.Rcheck/OUTRIDER-Ex.timings

nameusersystemelapsed
OUTRIDER4.2921.7702.977
OutriderDataSet-class0.7050.0300.742
aberrant2.8251.1291.858
computeGeneLength2.3700.2212.611
computeLatentSpace0.5150.0450.564
computePvalues0.8900.4931.046
computeZscores1.2630.8300.909
controlForConfounders0.7960.0690.885
counts0.3680.0050.379
estimateBestQ0.2490.0020.252
filterExpression1.0450.0141.063
findEncodingDim6.1711.7275.369
fit0.7160.0150.741
fpkm0.5490.0220.576
getter_setter_functions1.6190.0231.661
makeExampleOutriderDataSet0.7520.0050.762
normalizationFactors0.5290.0050.535
plotFunctions8.1903.4894.736
results1.7130.1241.704
sampleExclusionMask0.7260.6360.375
sizeFactors0.3830.0040.394