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CHECK report for GenoGAM on merida1

This page was generated on 2019-04-16 11:59:29 -0400 (Tue, 16 Apr 2019).

Package 617/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 2.0.3
Georg Stricker
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: RELEASE_3_8
Last Commit: bb9cd4a
Last Changed Date: 2019-03-19 18:01:09 -0400 (Tue, 19 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GenoGAM
Version: 2.0.3
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_2.0.3.tar.gz
StartedAt: 2019-04-16 00:11:16 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:18:09 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 412.8 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_2.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GenoGAM.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 ‘GenoGAM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenoGAM’ version ‘2.0.3’
* 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
GenoGAMDataSet-class       11.275  0.382  11.984
fitGenoGAM                  8.304  3.351   3.994
readData                    6.459  0.355   6.969
GenoGAMDataSetList-metrics  4.750  0.730   4.819
GenoGAMDataSet-subsetting   5.381  0.032   5.524
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘GenoGAM’ ...
** 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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/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/3.5/Resources/library/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
* DONE (GenoGAM)

Tests output

GenoGAM.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(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, 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

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

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 [2019-04-16 00:16:49] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:51] GenoGAMDataSet created
INFO [2019-04-16 00:16:51] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:51] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:51] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:51] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:51] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:52] Reading in data
INFO [2019-04-16 00:16:52] Reading in wt_1
INFO [2019-04-16 00:16:54] Reading in wt_2
INFO [2019-04-16 00:16:54] Reading in mutant_1
INFO [2019-04-16 00:16:55] Reading in mutant_2
INFO [2019-04-16 00:16:56] Finished reading in data
INFO [2019-04-16 00:16:56] GenoGAMDataSet created
INFO [2019-04-16 00:16:56] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:57] Reading in data
INFO [2019-04-16 00:16:57] Reading in wt_1
INFO [2019-04-16 00:16:57] Reading in wt_2
INFO [2019-04-16 00:16:57] Reading in mutant_1
INFO [2019-04-16 00:16:58] Reading in mutant_2
INFO [2019-04-16 00:16:58] Finished reading in data
INFO [2019-04-16 00:16:58] GenoGAMDataSet created
INFO [2019-04-16 00:16:58] Creating GenoGAMDataSet
ERROR [2019-04-16 00:16:58] The data does not match the region specification in the bamParams settings.
INFO [2019-04-16 00:16:58] GenoGAMDataSet created
WARN [2019-04-16 00:16:58] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-16 00:16:58] Creating GenoGAMDataSet
ERROR [2019-04-16 00:16:58] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2019-04-16 00:16:58] GenoGAMDataSet created
WARN [2019-04-16 00:16:58] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-16 00:16:59] Creating GenoGAMDataSet
INFO [2019-04-16 00:16:59] Reading in data
INFO [2019-04-16 00:16:59] Reading in wt_1
INFO [2019-04-16 00:17:00] Reading in wt_2
INFO [2019-04-16 00:17:00] Reading in mutant_1
INFO [2019-04-16 00:17:01] Reading in mutant_2
INFO [2019-04-16 00:17:01] Finished reading in data
ERROR [2019-04-16 00:17:01] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2019-04-16 00:17:01] GenoGAMDataSet created
ERROR [2019-04-16 00:17:01] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2019-04-16 00:17:04] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2019-04-16 00:17:04] Checks dismissed due to empty object or forgotten setting
ERROR [2019-04-16 00:17:04] 'by' variables could not be found in colData
INFO [2019-04-16 00:17:06] Reading in data
INFO [2019-04-16 00:17:06] Reading in wt_1
INFO [2019-04-16 00:17:06] Reading in wt_2
INFO [2019-04-16 00:17:07] Reading in mutant_1
INFO [2019-04-16 00:17:07] Reading in mutant_2
INFO [2019-04-16 00:17:08] Finished reading in data
INFO [2019-04-16 00:17:08] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:09] Reading in data
INFO [2019-04-16 00:17:09] Reading in wt_1
INFO [2019-04-16 00:17:09] Reading in wt_2
INFO [2019-04-16 00:17:10] Reading in mutant_1
INFO [2019-04-16 00:17:10] Reading in mutant_2
INFO [2019-04-16 00:17:10] Finished reading in data
INFO [2019-04-16 00:17:11] GenoGAMDataSet created
INFO [2019-04-16 00:17:12] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:13] GenoGAMDataSet created
INFO [2019-04-16 00:17:14] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:15] GenoGAMDataSet created
INFO [2019-04-16 00:17:16] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:17] GenoGAMDataSet created
INFO [2019-04-16 00:17:17] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:18] GenoGAMDataSet created
INFO [2019-04-16 00:17:18] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:19] Reading in data
INFO [2019-04-16 00:17:19] Reading in wt_1
INFO [2019-04-16 00:17:19] Reading in wt_2
INFO [2019-04-16 00:17:19] Reading in mutant_1
INFO [2019-04-16 00:17:20] Reading in mutant_2
INFO [2019-04-16 00:17:20] Finished reading in data
INFO [2019-04-16 00:17:21] GenoGAMDataSet created
INFO [2019-04-16 00:17:21] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:22] Reading in data
INFO [2019-04-16 00:17:22] Reading in wt_1
INFO [2019-04-16 00:17:22] Reading in wt_2
INFO [2019-04-16 00:17:23] Reading in mutant_1
INFO [2019-04-16 00:17:23] Reading in mutant_2
INFO [2019-04-16 00:17:23] Finished reading in data
INFO [2019-04-16 00:17:24] GenoGAMDataSet created
INFO [2019-04-16 00:17:24] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:25] Reading in data
INFO [2019-04-16 00:17:25] Reading in wt_1
INFO [2019-04-16 00:17:25] Reading in wt_2
INFO [2019-04-16 00:17:25] Reading in mutant_1
INFO [2019-04-16 00:17:26] Reading in mutant_2
INFO [2019-04-16 00:17:26] Finished reading in data
INFO [2019-04-16 00:17:27] GenoGAMDataSet created
INFO [2019-04-16 00:17:27] Creating GenoGAMDataSet
ERROR [2019-04-16 00:17:27] The data does not match the region specification in the bamParams settings.
INFO [2019-04-16 00:17:27] GenoGAMDataSet created
WARN [2019-04-16 00:17:27] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-16 00:17:27] Creating GenoGAMDataSet
ERROR [2019-04-16 00:17:27] The data does not match the region specification in the bamParams settings.
INFO [2019-04-16 00:17:27] GenoGAMDataSet created
WARN [2019-04-16 00:17:27] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-16 00:17:27] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:27] Reading in data
INFO [2019-04-16 00:17:27] Reading in wt_1
INFO [2019-04-16 00:17:28] Reading in wt_2
INFO [2019-04-16 00:17:28] Reading in mutant_1
INFO [2019-04-16 00:17:29] Reading in mutant_2
INFO [2019-04-16 00:17:29] Finished reading in data
ERROR [2019-04-16 00:17:30] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2019-04-16 00:17:30] GenoGAMDataSet created
ERROR [2019-04-16 00:17:30] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2019-04-16 00:17:31] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2019-04-16 00:17:31] Checks dismissed due to empty object or forgotten setting
INFO [2019-04-16 00:17:31] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:32] Reading in data
INFO [2019-04-16 00:17:32] Reading in wt_1
INFO [2019-04-16 00:17:33] Reading in wt_2
INFO [2019-04-16 00:17:33] Reading in mutant_1
INFO [2019-04-16 00:17:33] Reading in mutant_2
INFO [2019-04-16 00:17:34] Finished reading in data
INFO [2019-04-16 00:17:34] GenoGAMDataSet created
ERROR [2019-04-16 00:17:34] 'by' variables could not be found in colData
WARN [2019-04-16 00:17:48] Some supplied parameters aren't valid and won't be used
WARN [2019-04-16 00:17:48] Some supplied parameters aren't valid and won't be used
INFO [2019-04-16 00:17:48] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:49] GenoGAMDataSet created
INFO [2019-04-16 00:17:49] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:50] GenoGAMDataSet created
ERROR [2019-04-16 00:17:55] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2019-04-16 00:17:55] Creating GenoGAMDataSet
INFO [2019-04-16 00:17:56] GenoGAMDataSet created
WARN [2019-04-16 00:17:59] Some supplied parameters aren't valid and won't be used
INFO [2019-04-16 00:18:00] Creating GenoGAMDataSet
INFO [2019-04-16 00:18:01] GenoGAMDataSet created
INFO [2019-04-16 00:18:01] Computing size factors
INFO [2019-04-16 00:18:02] DONE
INFO [2019-04-16 00:18:02] Computing size factors
INFO [2019-04-16 00:18:02] Creating GenoGAMDataSet
INFO [2019-04-16 00:18:02] GenoGAMDataSet created
INFO [2019-04-16 00:18:02] Computing size factors
ERROR [2019-04-16 00:18:02] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2019-04-16 00:18:02] Creating GenoGAMDataSet
INFO [2019-04-16 00:18:03] GenoGAMDataSet created
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 536 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 93.036  15.507  91.248

Example timings

GenoGAM.Rcheck/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-class1.0760.0251.118
GenoGAMDataSet-class11.275 0.38211.984
GenoGAMDataSet-metrics4.2640.0244.437
GenoGAMDataSet-subsetting5.3810.0325.524
GenoGAMDataSetList-metrics4.7500.7304.819
GenoGAMList-class0.1550.0040.160
GenoGAMSettings-class0.0330.0020.036
callPeaks1.0090.6290.930
computeRegionSignificance2.2740.5030.586
computeSignificance0.3040.1790.168
computeSizeFactors2.8440.1072.986
fitGenoGAM8.3043.3513.994
makeTestGenoGAM0.2260.3090.094
makeTestGenoGAMDataSet3.5200.2213.848
makeTestGenoGAMDataSetList1.1640.5820.920
makeTestGenoGAMList0.2300.0310.260
readData6.4590.3556.969