Back to Multiple platform build/check report for BioC 3.10
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GenoGAM on malbec1

This page was generated on 2020-04-15 12:11:12 -0400 (Wed, 15 Apr 2020).

Package 673/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 2.4.0
Georg Stricker
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: RELEASE_3_10
Last Commit: 6753a93
Last Changed Date: 2019-10-29 13:09:36 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 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: 2.4.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GenoGAM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GenoGAM_2.4.0.tar.gz
StartedAt: 2020-04-15 03:42:27 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:49:05 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 397.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenoGAM.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GenoGAM.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GenoGAM_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘2.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘S4Vectors::na.omit’ by ‘stats::na.omit’ when loading ‘GenoGAM’
See ‘/home/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata   3.0Mb
    libs      3.3Mb
* 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’
.pvals_hdf5_split: no visible binding for global variable ‘chrom’
.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 chrom 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       11.244  0.244  11.688
fitGenoGAM                  7.276  1.432   3.554
GenoGAMDataSet-subsetting   6.484  0.024   6.513
GenoGAMDataSetList-metrics  5.752  0.380   5.530
readData                    5.968  0.128   6.298
* 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: 3 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.

Installation output

GenoGAM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GenoGAM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘GenoGAM’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c matrixMult.cpp -o matrixMult.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o GenoGAM.so RcppExports.o matrixMult.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-GenoGAM/00new/GenoGAM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘S4Vectors::na.omit’ by ‘stats::na.omit’ when loading ‘GenoGAM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘S4Vectors::na.omit’ by ‘stats::na.omit’ when loading ‘GenoGAM’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘S4Vectors::na.omit’ by ‘stats::na.omit’ when loading ‘GenoGAM’
** testing if installed package keeps a record of temporary installation path
* DONE (GenoGAM)

Tests output

GenoGAM.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(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, 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, 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

Warning message:
replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' 
> 
> test_check("GenoGAM")
INFO [2020-04-15 03:47:41] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:45] GenoGAMDataSet created
INFO [2020-04-15 03:47:45] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:45] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:45] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:45] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:45] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:46] Reading in data
INFO [2020-04-15 03:47:46] Reading in wt_1
INFO [2020-04-15 03:47:48] Reading in wt_2
INFO [2020-04-15 03:47:48] Reading in mutant_1
INFO [2020-04-15 03:47:49] Reading in mutant_2
INFO [2020-04-15 03:47:49] Finished reading in data
INFO [2020-04-15 03:47:50] GenoGAMDataSet created
INFO [2020-04-15 03:47:50] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:50] Reading in data
INFO [2020-04-15 03:47:50] Reading in wt_1
INFO [2020-04-15 03:47:51] Reading in wt_2
INFO [2020-04-15 03:47:51] Reading in mutant_1
INFO [2020-04-15 03:47:52] Reading in mutant_2
INFO [2020-04-15 03:47:52] Finished reading in data
INFO [2020-04-15 03:47:52] GenoGAMDataSet created
INFO [2020-04-15 03:47:52] Creating GenoGAMDataSet
ERROR [2020-04-15 03:47:52] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:47:52] GenoGAMDataSet created
WARN [2020-04-15 03:47:53] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:47:53] Creating GenoGAMDataSet
ERROR [2020-04-15 03:47:53] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2020-04-15 03:47:53] GenoGAMDataSet created
WARN [2020-04-15 03:47:53] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:47:53] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:53] Reading in data
INFO [2020-04-15 03:47:53] Reading in wt_1
INFO [2020-04-15 03:47:54] Reading in wt_2
INFO [2020-04-15 03:47:55] Reading in mutant_1
INFO [2020-04-15 03:47:55] Reading in mutant_2
INFO [2020-04-15 03:47:56] Finished reading in data
ERROR [2020-04-15 03:47:56] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2020-04-15 03:47:56] GenoGAMDataSet created
ERROR [2020-04-15 03:47:56] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2020-04-15 03:47:58] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 03:47:58] Checks dismissed due to empty object or forgotten setting
ERROR [2020-04-15 03:47:58] 'by' variables could not be found in colData
INFO [2020-04-15 03:48:00] Reading in data
INFO [2020-04-15 03:48:00] Reading in wt_1
INFO [2020-04-15 03:48:01] Reading in wt_2
INFO [2020-04-15 03:48:01] Reading in mutant_1
INFO [2020-04-15 03:48:02] Reading in mutant_2
INFO [2020-04-15 03:48:02] Finished reading in data
INFO [2020-04-15 03:48:03] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:04] Reading in data
INFO [2020-04-15 03:48:04] Reading in wt_1
INFO [2020-04-15 03:48:04] Reading in wt_2
INFO [2020-04-15 03:48:04] Reading in mutant_1
INFO [2020-04-15 03:48:05] Reading in mutant_2
INFO [2020-04-15 03:48:05] Finished reading in data
INFO [2020-04-15 03:48:05] GenoGAMDataSet created
INFO [2020-04-15 03:48:07] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:08] GenoGAMDataSet created
INFO [2020-04-15 03:48:09] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:10] GenoGAMDataSet created
INFO [2020-04-15 03:48:11] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:12] GenoGAMDataSet created
INFO [2020-04-15 03:48:12] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:13] GenoGAMDataSet created
INFO [2020-04-15 03:48:13] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:14] Reading in data
INFO [2020-04-15 03:48:14] Reading in wt_1
INFO [2020-04-15 03:48:14] Reading in wt_2
INFO [2020-04-15 03:48:15] Reading in mutant_1
INFO [2020-04-15 03:48:15] Reading in mutant_2
INFO [2020-04-15 03:48:15] Finished reading in data
INFO [2020-04-15 03:48:17] GenoGAMDataSet created
INFO [2020-04-15 03:48:17] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:17] Reading in data
INFO [2020-04-15 03:48:17] Reading in wt_1
INFO [2020-04-15 03:48:18] Reading in wt_2
INFO [2020-04-15 03:48:18] Reading in mutant_1
INFO [2020-04-15 03:48:18] Reading in mutant_2
INFO [2020-04-15 03:48:19] Finished reading in data
INFO [2020-04-15 03:48:20] GenoGAMDataSet created
INFO [2020-04-15 03:48:20] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:20] Reading in data
INFO [2020-04-15 03:48:20] Reading in wt_1
INFO [2020-04-15 03:48:21] Reading in wt_2
INFO [2020-04-15 03:48:21] Reading in mutant_1
INFO [2020-04-15 03:48:21] Reading in mutant_2
INFO [2020-04-15 03:48:22] Finished reading in data
INFO [2020-04-15 03:48:23] GenoGAMDataSet created
INFO [2020-04-15 03:48:23] Creating GenoGAMDataSet
ERROR [2020-04-15 03:48:23] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:48:23] GenoGAMDataSet created
WARN [2020-04-15 03:48:23] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:48:23] Creating GenoGAMDataSet
ERROR [2020-04-15 03:48:23] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:48:23] GenoGAMDataSet created
WARN [2020-04-15 03:48:23] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:48:23] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:24] Reading in data
INFO [2020-04-15 03:48:24] Reading in wt_1
INFO [2020-04-15 03:48:24] Reading in wt_2
INFO [2020-04-15 03:48:25] Reading in mutant_1
INFO [2020-04-15 03:48:25] Reading in mutant_2
INFO [2020-04-15 03:48:26] Finished reading in data
ERROR [2020-04-15 03:48:27] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2020-04-15 03:48:27] GenoGAMDataSet created
ERROR [2020-04-15 03:48:27] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2020-04-15 03:48:28] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 03:48:28] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:48:28] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:29] Reading in data
INFO [2020-04-15 03:48:29] Reading in wt_1
INFO [2020-04-15 03:48:30] Reading in wt_2
INFO [2020-04-15 03:48:30] Reading in mutant_1
INFO [2020-04-15 03:48:30] Reading in mutant_2
INFO [2020-04-15 03:48:31] Finished reading in data
INFO [2020-04-15 03:48:31] GenoGAMDataSet created
ERROR [2020-04-15 03:48:31] 'by' variables could not be found in colData
WARN [2020-04-15 03:48:46] Some supplied parameters aren't valid and won't be used
WARN [2020-04-15 03:48:46] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 03:48:46] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:47] GenoGAMDataSet created
INFO [2020-04-15 03:48:47] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:48] GenoGAMDataSet created
ERROR [2020-04-15 03:48:52] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2020-04-15 03:48:52] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:53] GenoGAMDataSet created
WARN [2020-04-15 03:48:55] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 03:48:56] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:57] GenoGAMDataSet created
INFO [2020-04-15 03:48:58] Computing size factors
INFO [2020-04-15 03:48:58] DONE
INFO [2020-04-15 03:48:58] Computing size factors
INFO [2020-04-15 03:48:58] Creating GenoGAMDataSet
INFO [2020-04-15 03:49:00] GenoGAMDataSet created
INFO [2020-04-15 03:49:00] Computing size factors
ERROR [2020-04-15 03:49:00] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2020-04-15 03:49:00] Creating GenoGAMDataSet
INFO [2020-04-15 03:49:01] GenoGAMDataSet created
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 427 | SKIPPED: 0 | WARNINGS: 109 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  99.78    8.36   96.30

Example timings

GenoGAM.Rcheck/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-class2.2080.3842.675
GenoGAMDataSet-class11.244 0.24411.688
GenoGAMDataSet-metrics4.9640.0084.978
GenoGAMDataSet-subsetting6.4840.0246.513
GenoGAMDataSetList-metrics5.7520.3805.530
GenoGAMList-class0.4120.0000.411
GenoGAMSettings-class0.0480.0000.049
callPeaks1.3160.1880.731
computeRegionSignificance0.8080.0400.645
computeSignificance0.1840.0160.210
computeSizeFactors2.9320.0282.965
fitGenoGAM7.2761.4323.554
makeTestGenoGAM0.1240.0040.132
makeTestGenoGAMDataSet3.8560.0964.003
makeTestGenoGAMDataSetList1.2840.4040.915
makeTestGenoGAMList0.3640.0200.384
readData5.9680.1286.298