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CHECK report for GenoGAM on celaya2

This page was generated on 2019-04-09 13:15:58 -0400 (Tue, 09 Apr 2019).

Package 639/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 2.1.9
Georg Stricker
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: master
Last Commit: 800ebfa
Last Changed Date: 2019-04-07 18:32:20 -0400 (Sun, 07 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK YES, new version is higher than in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK YES, new version is higher than in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: GenoGAM
Version: 2.1.9
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenoGAM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenoGAM_2.1.9.tar.gz
StartedAt: 2019-04-09 02:13:28 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:22:08 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 520.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenoGAM.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenoGAM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenoGAM_2.1.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenoGAM.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenoGAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenoGAM’ version ‘2.1.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'SummarizedExperiment', 'HDF5Array', 'rhdf5', 'S4Vectors', 'Matrix',
  'data.table'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenoGAM’ 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: ‘Biostrings’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Matrix’ ‘data.table’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘DelayedArray:::getAutoBlockLength’ ‘DelayedArray:::read_block’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GenoGAMFromHDF5: no visible binding for global variable ‘h5fits’
.GenoGAMFromHDF5: no visible binding for global variable ‘h5ses’
.callBroadPeaks_default: no visible binding for global variable ‘pval’
.callBroadPeaks_default: no visible binding for global variable
  ‘region’
.callBroadPeaks_default: no visible binding for global variable
  ‘estimate’
.callBroadPeaks_hdf5: no visible binding for global variable ‘pval’
.callBroadPeaks_hdf5: no visible binding for global variable ‘region’
.callBroadPeaks_hdf5: no visible binding for global variable ‘estimate’
.callBroadPeaks_split: no visible binding for global variable ‘pval’
.callBroadPeaks_split: no visible binding for global variable ‘region’
.callBroadPeaks_split: no visible binding for global variable
  ‘estimate’
.callBroadPeaks_split_hdf5: no visible binding for global variable
  ‘pval’
.callBroadPeaks_split_hdf5: no visible binding for global variable
  ‘region’
.callBroadPeaks_split_hdf5: no visible binding for global variable
  ‘estimate’
.setOptimalChunkSize: no visible global function definition for
  ‘count.fields’
.shorth_hdf5 : COMBINE : <anonymous>: no visible binding for global
  variable ‘tmp’
callPeaks: no visible binding for global variable ‘fdr’
computeRegionSignificance: no visible binding for global variable ‘p’
computeRegionSignificance: no visible binding for global variable
  ‘region’
plot_base: no visible global function definition for ‘par’
plot_base: no visible global function definition for ‘plot’
plot_base: no visible global function definition for ‘x11’
plot_base: no visible global function definition for ‘lines’
plot_base: no visible global function definition for ‘abline’
writeToBroadPeaks: no visible global function definition for
  ‘write.table’
writeToNarrowPeaks: no visible binding for global variable ‘chromosome’
writeToNarrowPeaks: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline chromosome count.fields estimate fdr h5fits h5ses lines p par
  plot pval region tmp write.table x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("utils", "count.fields", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'GenoGAM':
  ‘GenoGAM-class.Rd’ ‘GenoGAM.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getCountMatrix’ ‘is.HDF5’ ‘pvalue’
Undocumented S4 methods:
  generic 'dim' and siglist 'GenoGAMSetup'
  generic 'length' and siglist 'GenoGAMSetup'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
fitGenoGAM                 11.818  6.487   5.540
GenoGAMDataSet-class       12.294  0.805  13.143
GenoGAMDataSetList-metrics  6.717  1.329   7.053
readData                    6.424  0.812   7.238
GenoGAMDataSet-subsetting   6.334  0.070   6.405
* 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 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.

Installation output

GenoGAM.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenoGAM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GenoGAM’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -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  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -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  -fPIC  -Wall -g -O2  -c matrixMult.cpp -o matrixMult.o
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 GenoGAM.so RcppExports.o matrixMult.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-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/00LOCK-GenoGAM/00new/GenoGAM/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 (GenoGAM)

Tests output

GenoGAM.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-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(GenoGAM)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

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: HDF5Array
Loading required package: rhdf5
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

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

> 
> test_check("GenoGAM")
INFO [2019-04-09 02:20:19] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:20] GenoGAMDataSet created
INFO [2019-04-09 02:20:20] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:20] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:20] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:21] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:21] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:22] Reading in data
INFO [2019-04-09 02:20:22] Reading in wt_1
INFO [2019-04-09 02:20:25] Reading in wt_2
INFO [2019-04-09 02:20:25] Reading in mutant_1
INFO [2019-04-09 02:20:25] Reading in mutant_2
INFO [2019-04-09 02:20:26] Finished reading in data
INFO [2019-04-09 02:20:26] GenoGAMDataSet created
INFO [2019-04-09 02:20:26] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:27] Reading in data
INFO [2019-04-09 02:20:27] Reading in wt_1
INFO [2019-04-09 02:20:28] Reading in wt_2
INFO [2019-04-09 02:20:28] Reading in mutant_1
INFO [2019-04-09 02:20:28] Reading in mutant_2
INFO [2019-04-09 02:20:29] Finished reading in data
INFO [2019-04-09 02:20:29] GenoGAMDataSet created
INFO [2019-04-09 02:20:29] Creating GenoGAMDataSet
ERROR [2019-04-09 02:20:29] The data does not match the region specification in the bamParams settings.
INFO [2019-04-09 02:20:29] GenoGAMDataSet created
WARN [2019-04-09 02:20:29] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-09 02:20:29] Creating GenoGAMDataSet
ERROR [2019-04-09 02:20:29] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2019-04-09 02:20:29] GenoGAMDataSet created
WARN [2019-04-09 02:20:29] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-09 02:20:29] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:30] Reading in data
INFO [2019-04-09 02:20:30] Reading in wt_1
INFO [2019-04-09 02:20:31] Reading in wt_2
INFO [2019-04-09 02:20:31] Reading in mutant_1
INFO [2019-04-09 02:20:32] Reading in mutant_2
INFO [2019-04-09 02:20:32] Finished reading in data
ERROR [2019-04-09 02:20:33] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2019-04-09 02:20:33] GenoGAMDataSet created
ERROR [2019-04-09 02:20:33] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2019-04-09 02:20:37] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2019-04-09 02:20:37] Checks dismissed due to empty object or forgotten setting
ERROR [2019-04-09 02:20:37] 'by' variables could not be found in colData
INFO [2019-04-09 02:20:39] Reading in data
INFO [2019-04-09 02:20:39] Reading in wt_1
INFO [2019-04-09 02:20:40] Reading in wt_2
INFO [2019-04-09 02:20:41] Reading in mutant_1
INFO [2019-04-09 02:20:41] Reading in mutant_2
INFO [2019-04-09 02:20:42] Finished reading in data
INFO [2019-04-09 02:20:42] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:43] Reading in data
INFO [2019-04-09 02:20:43] Reading in wt_1
INFO [2019-04-09 02:20:43] Reading in wt_2
INFO [2019-04-09 02:20:44] Reading in mutant_1
INFO [2019-04-09 02:20:44] Reading in mutant_2
INFO [2019-04-09 02:20:45] Finished reading in data
INFO [2019-04-09 02:20:45] GenoGAMDataSet created
INFO [2019-04-09 02:20:47] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:48] GenoGAMDataSet created
INFO [2019-04-09 02:20:48] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:49] GenoGAMDataSet created
INFO [2019-04-09 02:20:52] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:53] GenoGAMDataSet created
INFO [2019-04-09 02:20:53] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:54] GenoGAMDataSet created
INFO [2019-04-09 02:20:54] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:54] Reading in data
INFO [2019-04-09 02:20:55] Reading in wt_1
INFO [2019-04-09 02:20:55] Reading in wt_2
INFO [2019-04-09 02:20:55] Reading in mutant_1
INFO [2019-04-09 02:20:56] Reading in mutant_2
INFO [2019-04-09 02:20:56] Finished reading in data
INFO [2019-04-09 02:20:57] GenoGAMDataSet created
INFO [2019-04-09 02:20:57] Creating GenoGAMDataSet
INFO [2019-04-09 02:20:58] Reading in data
INFO [2019-04-09 02:20:58] Reading in wt_1
INFO [2019-04-09 02:20:58] Reading in wt_2
INFO [2019-04-09 02:20:59] Reading in mutant_1
INFO [2019-04-09 02:20:59] Reading in mutant_2
INFO [2019-04-09 02:20:59] Finished reading in data
INFO [2019-04-09 02:21:00] GenoGAMDataSet created
INFO [2019-04-09 02:21:01] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:01] Reading in data
INFO [2019-04-09 02:21:01] Reading in wt_1
INFO [2019-04-09 02:21:02] Reading in wt_2
INFO [2019-04-09 02:21:02] Reading in mutant_1
INFO [2019-04-09 02:21:03] Reading in mutant_2
INFO [2019-04-09 02:21:03] Finished reading in data
INFO [2019-04-09 02:21:04] GenoGAMDataSet created
INFO [2019-04-09 02:21:04] Creating GenoGAMDataSet
ERROR [2019-04-09 02:21:04] The data does not match the region specification in the bamParams settings.
INFO [2019-04-09 02:21:04] GenoGAMDataSet created
WARN [2019-04-09 02:21:04] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-09 02:21:04] Creating GenoGAMDataSet
ERROR [2019-04-09 02:21:04] The data does not match the region specification in the bamParams settings.
INFO [2019-04-09 02:21:04] GenoGAMDataSet created
WARN [2019-04-09 02:21:04] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-09 02:21:04] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:05] Reading in data
INFO [2019-04-09 02:21:05] Reading in wt_1
INFO [2019-04-09 02:21:06] Reading in wt_2
INFO [2019-04-09 02:21:06] Reading in mutant_1
INFO [2019-04-09 02:21:07] Reading in mutant_2
INFO [2019-04-09 02:21:07] Finished reading in data
ERROR [2019-04-09 02:21:08] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2019-04-09 02:21:08] GenoGAMDataSet created
ERROR [2019-04-09 02:21:09] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2019-04-09 02:21:10] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2019-04-09 02:21:10] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-09 02:21:10] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:11] Reading in data
INFO [2019-04-09 02:21:11] Reading in wt_1
INFO [2019-04-09 02:21:12] Reading in wt_2
INFO [2019-04-09 02:21:13] Reading in mutant_1
INFO [2019-04-09 02:21:13] Reading in mutant_2
INFO [2019-04-09 02:21:13] Finished reading in data
INFO [2019-04-09 02:21:14] GenoGAMDataSet created
ERROR [2019-04-09 02:21:14] 'by' variables could not be found in colData
WARN [2019-04-09 02:21:33] Some supplied parameters aren't valid and won't be used
WARN [2019-04-09 02:21:34] Some supplied parameters aren't valid and won't be used
INFO [2019-04-09 02:21:34] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:35] GenoGAMDataSet created
INFO [2019-04-09 02:21:35] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:36] GenoGAMDataSet created
ERROR [2019-04-09 02:21:44] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2019-04-09 02:21:45] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:46] GenoGAMDataSet created
WARN [2019-04-09 02:21:49] Some supplied parameters aren't valid and won't be used
INFO [2019-04-09 02:21:53] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:54] GenoGAMDataSet created
INFO [2019-04-09 02:21:55] Computing size factors
INFO [2019-04-09 02:21:56] DONE
INFO [2019-04-09 02:21:56] Computing size factors
INFO [2019-04-09 02:21:56] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:57] GenoGAMDataSet created
INFO [2019-04-09 02:21:57] Computing size factors
ERROR [2019-04-09 02:21:57] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2019-04-09 02:21:57] Creating GenoGAMDataSet
INFO [2019-04-09 02:21:58] GenoGAMDataSet created
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 536 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
121.375  28.440 119.759

Example timings

GenoGAM.Rcheck/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-class0.5590.0660.628
GenoGAMDataSet-class12.294 0.80513.143
GenoGAMDataSet-metrics4.4690.0574.556
GenoGAMDataSet-subsetting6.3340.0706.405
GenoGAMDataSetList-metrics6.7171.3297.053
GenoGAMList-class0.3350.0510.386
GenoGAMSettings-class0.0630.0110.073
callPeaks0.9460.7950.896
computeRegionSignificance2.3940.7300.913
computeSignificance0.3580.2020.253
computeSizeFactors4.3360.3864.758
fitGenoGAM11.818 6.487 5.540
makeTestGenoGAM0.1730.0950.123
makeTestGenoGAMDataSet4.2160.5004.716
makeTestGenoGAMDataSetList1.4890.9941.210
makeTestGenoGAMList0.2780.0520.330
readData6.4240.8127.238