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CHECK report for GenoGAM on tokay1

This page was generated on 2020-04-15 12:26:27 -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: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenoGAM.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenoGAM_2.4.0.tar.gz
StartedAt: 2020-04-15 03:25:47 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:56:29 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 1842.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenoGAM.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenoGAM.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenoGAM_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'GenoGAM' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYfVVmO/R.INSTALL20ec78525f48/GenoGAM/man/GenoGAMDataSet-class.Rd:139: file link 'GenoGAMSettings' in package 'GenoGAM' does not exist and so has been treated as a topic
  Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    extdata   3.0Mb
    libs      1.8Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/GenoGAM/libs/i386/GenoGAM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/GenoGAM/libs/x64/GenoGAM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GenoGAMDataSet-class       7.72   0.56    8.78
GenoGAMDataSetList-metrics 4.24   0.18   19.81
fitGenoGAM                 1.66   0.03   48.10
makeTestGenoGAMDataSetList 1.04   0.00   21.47
callPeaks                  0.95   0.00   13.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GenoGAMDataSet-class       8.61   0.17    8.78
GenoGAMDataSetList-metrics 6.50   0.02   24.09
readData                   5.12   0.03    5.16
fitGenoGAM                 2.23   0.03   53.53
makeTestGenoGAMDataSetList 1.52   0.02   20.28
callPeaks                  1.30   0.00   16.20
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck/00check.log'
for details.

Installation output

GenoGAM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GenoGAM_2.4.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.4.0.zip && rm GenoGAM_2.4.0.tar.gz GenoGAM_2.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3286k  100 3286k    0     0  50.0M      0 --:--:-- --:--:-- --:--:-- 53.4M

install for i386

* installing *source* package 'GenoGAM' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c matrixMult.cpp -o matrixMult.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/libs/i386
** 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
  converting help for package 'GenoGAM'
    finding HTML links ... done
    Coordinates-class                       html  
    GenoGAM-class                           html  
    GenoGAM                                 html  
    GenoGAMDataSet-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYfVVmO/R.INSTALL20ec78525f48/GenoGAM/man/GenoGAMDataSet-class.Rd:139: file link 'GenoGAMSettings' in package 'GenoGAM' does not exist and so has been treated as a topic
    GenoGAMDataSet-metrics                  html  
    GenoGAMDataSet-subsetting               html  
    GenoGAMDataSetList-class                html  
    GenoGAMDataSetList-metrics              html  
    GenoGAMDataSetList-subsetting           html  
    GenoGAMFamily-class                     html  
    GenoGAMList-class                       html  
    GenoGAMList-subsetting                  html  
    GenoGAMSettings-class                   html  
    asCoordinates                           html  
    callPeaks                               html  
    computeRegionSignificance               html  
    computeSignificance                     html  
    computeSizeFactors                      html  
    fitGenoGAM                              html  
    makeTestGenoGAM                         html  
    makeTestGenoGAMDataSet                  html  
    makeTestGenoGAMDataSetList              html  
    makeTestGenoGAMList                     html  
    plotGenoGAM                             html  
    readData                                html  
    writeToBEDFile                          html  
** 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'
** 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

install for x64

* installing *source* package 'GenoGAM' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c matrixMult.cpp -o matrixMult.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.buildbin-libdir/GenoGAM/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
* MD5 sums
packaged installation of 'GenoGAM' as GenoGAM_2.4.0.zip
* DONE (GenoGAM)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GenoGAM' successfully unpacked and MD5 sums checked

Tests output

GenoGAM.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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 03:36:13] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:15] GenoGAMDataSet created
INFO [2020-04-15 03:36:15] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:15] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:15] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:15] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:15] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:16] Reading in data
INFO [2020-04-15 03:36:16] Reading in wt_1
INFO [2020-04-15 03:36:18] Reading in wt_2
INFO [2020-04-15 03:36:19] Reading in mutant_1
INFO [2020-04-15 03:36:19] Reading in mutant_2
INFO [2020-04-15 03:36:19] Finished reading in data
INFO [2020-04-15 03:36:20] GenoGAMDataSet created
INFO [2020-04-15 03:36:20] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:20] Reading in data
INFO [2020-04-15 03:36:20] Reading in wt_1
INFO [2020-04-15 03:36:21] Reading in wt_2
INFO [2020-04-15 03:36:21] Reading in mutant_1
INFO [2020-04-15 03:36:22] Reading in mutant_2
INFO [2020-04-15 03:36:22] Finished reading in data
INFO [2020-04-15 03:36:22] GenoGAMDataSet created
INFO [2020-04-15 03:36:22] Creating GenoGAMDataSet
ERROR [2020-04-15 03:36:22] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:36:22] GenoGAMDataSet created
WARN [2020-04-15 03:36:22] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:36:22] Creating GenoGAMDataSet
ERROR [2020-04-15 03:36:22] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2020-04-15 03:36:22] GenoGAMDataSet created
WARN [2020-04-15 03:36:22] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:36:22] Creating GenoGAMDataSet
INFO [2020-04-15 03:36:23] Reading in data
INFO [2020-04-15 03:36:23] Reading in wt_1
INFO [2020-04-15 03:36:24] Reading in wt_2
INFO [2020-04-15 03:36:24] Reading in mutant_1
INFO [2020-04-15 03:36:25] Reading in mutant_2
INFO [2020-04-15 03:36:26] Finished reading in data
ERROR [2020-04-15 03:36:26] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2020-04-15 03:36:26] GenoGAMDataSet created
ERROR [2020-04-15 03:36:26] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2020-04-15 03:37:31] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 03:37:31] Checks dismissed due to empty object or forgotten setting
ERROR [2020-04-15 03:37:31] 'by' variables could not be found in colData
INFO [2020-04-15 03:37:33] Reading in data
INFO [2020-04-15 03:37:33] Reading in wt_1
INFO [2020-04-15 03:37:33] Reading in wt_2
INFO [2020-04-15 03:37:34] Reading in mutant_1
INFO [2020-04-15 03:37:35] Reading in mutant_2
INFO [2020-04-15 03:37:35] Finished reading in data
INFO [2020-04-15 03:37:36] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:36] Reading in data
INFO [2020-04-15 03:37:36] Reading in wt_1
INFO [2020-04-15 03:37:37] Reading in wt_2
INFO [2020-04-15 03:37:37] Reading in mutant_1
INFO [2020-04-15 03:37:38] Reading in mutant_2
INFO [2020-04-15 03:37:38] Finished reading in data
INFO [2020-04-15 03:37:38] GenoGAMDataSet created
INFO [2020-04-15 03:37:40] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:41] GenoGAMDataSet created
INFO [2020-04-15 03:37:42] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:43] GenoGAMDataSet created
INFO [2020-04-15 03:37:45] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:46] GenoGAMDataSet created
INFO [2020-04-15 03:37:46] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:47] GenoGAMDataSet created
INFO [2020-04-15 03:37:47] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:48] Reading in data
INFO [2020-04-15 03:37:48] Reading in wt_1
INFO [2020-04-15 03:37:48] Reading in wt_2
INFO [2020-04-15 03:37:48] Reading in mutant_1
INFO [2020-04-15 03:37:49] Reading in mutant_2
INFO [2020-04-15 03:37:49] Finished reading in data
INFO [2020-04-15 03:37:50] GenoGAMDataSet created
INFO [2020-04-15 03:37:50] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:50] Reading in data
INFO [2020-04-15 03:37:50] Reading in wt_1
INFO [2020-04-15 03:37:50] Reading in wt_2
INFO [2020-04-15 03:37:51] Reading in mutant_1
INFO [2020-04-15 03:37:51] Reading in mutant_2
INFO [2020-04-15 03:37:51] Finished reading in data
INFO [2020-04-15 03:37:52] GenoGAMDataSet created
INFO [2020-04-15 03:37:52] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:53] Reading in data
INFO [2020-04-15 03:37:53] Reading in wt_1
INFO [2020-04-15 03:37:53] Reading in wt_2
INFO [2020-04-15 03:37:53] Reading in mutant_1
INFO [2020-04-15 03:37:54] Reading in mutant_2
INFO [2020-04-15 03:37:54] Finished reading in data
INFO [2020-04-15 03:37:55] GenoGAMDataSet created
INFO [2020-04-15 03:37:55] Creating GenoGAMDataSet
ERROR [2020-04-15 03:37:55] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:37:55] GenoGAMDataSet created
WARN [2020-04-15 03:37:55] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:37:55] Creating GenoGAMDataSet
ERROR [2020-04-15 03:37:55] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:37:55] GenoGAMDataSet created
WARN [2020-04-15 03:37:55] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:37:55] Creating GenoGAMDataSet
INFO [2020-04-15 03:37:56] Reading in data
INFO [2020-04-15 03:37:56] Reading in wt_1
INFO [2020-04-15 03:37:56] Reading in wt_2
INFO [2020-04-15 03:37:57] Reading in mutant_1
INFO [2020-04-15 03:37:57] Reading in mutant_2
INFO [2020-04-15 03:37:58] Finished reading in data
ERROR [2020-04-15 03:37:58] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2020-04-15 03:37:58] GenoGAMDataSet created
ERROR [2020-04-15 03:37:58] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2020-04-15 03:38:13] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 03:38:13] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:38:13] Creating GenoGAMDataSet
INFO [2020-04-15 03:38:14] Reading in data
INFO [2020-04-15 03:38:14] Reading in wt_1
INFO [2020-04-15 03:38:14] Reading in wt_2
INFO [2020-04-15 03:38:14] Reading in mutant_1
INFO [2020-04-15 03:38:14] Reading in mutant_2
INFO [2020-04-15 03:38:15] Finished reading in data
INFO [2020-04-15 03:38:15] GenoGAMDataSet created
ERROR [2020-04-15 03:38:15] 'by' variables could not be found in colData
WARN [2020-04-15 03:40:57] Some supplied parameters aren't valid and won't be used
WARN [2020-04-15 03:40:57] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 03:40:58] Creating GenoGAMDataSet
INFO [2020-04-15 03:40:58] GenoGAMDataSet created
INFO [2020-04-15 03:40:58] Creating GenoGAMDataSet
INFO [2020-04-15 03:40:59] GenoGAMDataSet created
ERROR [2020-04-15 03:44:53] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2020-04-15 03:44:53] Creating GenoGAMDataSet
INFO [2020-04-15 03:44:54] GenoGAMDataSet created
WARN [2020-04-15 03:44:56] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 03:45:16] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:16] GenoGAMDataSet created
INFO [2020-04-15 03:45:16] Computing size factors
INFO [2020-04-15 03:45:17] DONE
INFO [2020-04-15 03:45:17] Computing size factors
INFO [2020-04-15 03:45:17] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:18] GenoGAMDataSet created
INFO [2020-04-15 03:45:18] Computing size factors
ERROR [2020-04-15 03:45:18] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2020-04-15 03:45:18] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:19] GenoGAMDataSet created
== testthat results  ===========================================================
[ OK: 427 | SKIPPED: 0 | WARNINGS: 109 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  92.68    2.68  562.54

GenoGAM.Rcheck/tests_x64/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-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 03:45:37] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:40] GenoGAMDataSet created
INFO [2020-04-15 03:45:40] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:40] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:40] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:40] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:40] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:41] Reading in data
INFO [2020-04-15 03:45:41] Reading in wt_1
INFO [2020-04-15 03:45:42] Reading in wt_2
INFO [2020-04-15 03:45:43] Reading in mutant_1
INFO [2020-04-15 03:45:43] Reading in mutant_2
INFO [2020-04-15 03:45:44] Finished reading in data
INFO [2020-04-15 03:45:44] GenoGAMDataSet created
INFO [2020-04-15 03:45:44] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:45] Reading in data
INFO [2020-04-15 03:45:45] Reading in wt_1
INFO [2020-04-15 03:45:46] Reading in wt_2
INFO [2020-04-15 03:45:46] Reading in mutant_1
INFO [2020-04-15 03:45:46] Reading in mutant_2
INFO [2020-04-15 03:45:47] Finished reading in data
INFO [2020-04-15 03:45:47] GenoGAMDataSet created
INFO [2020-04-15 03:45:47] Creating GenoGAMDataSet
ERROR [2020-04-15 03:45:47] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:45:47] GenoGAMDataSet created
WARN [2020-04-15 03:45:47] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:45:47] Creating GenoGAMDataSet
ERROR [2020-04-15 03:45:47] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2020-04-15 03:45:47] GenoGAMDataSet created
WARN [2020-04-15 03:45:47] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:45:47] Creating GenoGAMDataSet
INFO [2020-04-15 03:45:48] Reading in data
INFO [2020-04-15 03:45:48] Reading in wt_1
INFO [2020-04-15 03:45:49] Reading in wt_2
INFO [2020-04-15 03:45:49] Reading in mutant_1
INFO [2020-04-15 03:45:50] Reading in mutant_2
INFO [2020-04-15 03:45:50] Finished reading in data
ERROR [2020-04-15 03:45:50] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2020-04-15 03:45:50] GenoGAMDataSet created
ERROR [2020-04-15 03:45:50] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2020-04-15 03:47:03] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 03:47:03] Checks dismissed due to empty object or forgotten setting
ERROR [2020-04-15 03:47:03] 'by' variables could not be found in colData
INFO [2020-04-15 03:47:05] Reading in data
INFO [2020-04-15 03:47:05] Reading in wt_1
INFO [2020-04-15 03:47:06] Reading in wt_2
INFO [2020-04-15 03:47:06] Reading in mutant_1
INFO [2020-04-15 03:47:07] Reading in mutant_2
INFO [2020-04-15 03:47:07] Finished reading in data
INFO [2020-04-15 03:47:08] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:09] Reading in data
INFO [2020-04-15 03:47:09] Reading in wt_1
INFO [2020-04-15 03:47:09] Reading in wt_2
INFO [2020-04-15 03:47:10] Reading in mutant_1
INFO [2020-04-15 03:47:10] Reading in mutant_2
INFO [2020-04-15 03:47:11] Finished reading in data
INFO [2020-04-15 03:47:11] GenoGAMDataSet created
INFO [2020-04-15 03:47:14] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:15] GenoGAMDataSet created
INFO [2020-04-15 03:47:16] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:17] GenoGAMDataSet created
INFO [2020-04-15 03:47:19] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:20] GenoGAMDataSet created
INFO [2020-04-15 03:47:21] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:22] GenoGAMDataSet created
INFO [2020-04-15 03:47:22] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:23] Reading in data
INFO [2020-04-15 03:47:23] Reading in wt_1
INFO [2020-04-15 03:47:23] Reading in wt_2
INFO [2020-04-15 03:47:24] Reading in mutant_1
INFO [2020-04-15 03:47:24] Reading in mutant_2
INFO [2020-04-15 03:47:25] Finished reading in data
INFO [2020-04-15 03:47:26] GenoGAMDataSet created
INFO [2020-04-15 03:47:26] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:27] Reading in data
INFO [2020-04-15 03:47:27] Reading in wt_1
INFO [2020-04-15 03:47:27] Reading in wt_2
INFO [2020-04-15 03:47:28] Reading in mutant_1
INFO [2020-04-15 03:47:28] Reading in mutant_2
INFO [2020-04-15 03:47:29] Finished reading in data
INFO [2020-04-15 03:47:30] GenoGAMDataSet created
INFO [2020-04-15 03:47:30] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:31] Reading in data
INFO [2020-04-15 03:47:31] Reading in wt_1
INFO [2020-04-15 03:47:32] Reading in wt_2
INFO [2020-04-15 03:47:32] Reading in mutant_1
INFO [2020-04-15 03:47:32] Reading in mutant_2
INFO [2020-04-15 03:47:33] Finished reading in data
INFO [2020-04-15 03:47:35] GenoGAMDataSet created
INFO [2020-04-15 03:47:35] Creating GenoGAMDataSet
ERROR [2020-04-15 03:47:35] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:47:35] GenoGAMDataSet created
WARN [2020-04-15 03:47:35] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:47:35] Creating GenoGAMDataSet
ERROR [2020-04-15 03:47:35] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 03:47:35] GenoGAMDataSet created
WARN [2020-04-15 03:47:35] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:47:35] Creating GenoGAMDataSet
INFO [2020-04-15 03:47:36] Reading in data
INFO [2020-04-15 03:47:36] Reading in wt_1
INFO [2020-04-15 03:47:37] Reading in wt_2
INFO [2020-04-15 03:47:37] Reading in mutant_1
INFO [2020-04-15 03:47:38] Reading in mutant_2
INFO [2020-04-15 03:47:39] Finished reading in data
ERROR [2020-04-15 03:47:40] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2020-04-15 03:47:40] GenoGAMDataSet created
ERROR [2020-04-15 03:47:40] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2020-04-15 03:48:00] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 03:48:00] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 03:48:00] Creating GenoGAMDataSet
INFO [2020-04-15 03:48:01] Reading in data
INFO [2020-04-15 03:48:01] Reading in wt_1
INFO [2020-04-15 03:48:01] Reading in wt_2
INFO [2020-04-15 03:48:02] Reading in mutant_1
INFO [2020-04-15 03:48:02] Reading in mutant_2
INFO [2020-04-15 03:48:03] Finished reading in data
INFO [2020-04-15 03:48:03] GenoGAMDataSet created
ERROR [2020-04-15 03:48:03] 'by' variables could not be found in colData
WARN [2020-04-15 03:51:13] Some supplied parameters aren't valid and won't be used
WARN [2020-04-15 03:51:13] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 03:51:13] Creating GenoGAMDataSet
INFO [2020-04-15 03:51:14] GenoGAMDataSet created
INFO [2020-04-15 03:51:14] Creating GenoGAMDataSet
INFO [2020-04-15 03:51:15] GenoGAMDataSet created
ERROR [2020-04-15 03:55:53] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2020-04-15 03:55:53] Creating GenoGAMDataSet
INFO [2020-04-15 03:55:54] GenoGAMDataSet created
WARN [2020-04-15 03:55:57] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 03:56:19] Creating GenoGAMDataSet
INFO [2020-04-15 03:56:20] GenoGAMDataSet created
INFO [2020-04-15 03:56:20] Computing size factors
INFO [2020-04-15 03:56:20] DONE
INFO [2020-04-15 03:56:21] Computing size factors
INFO [2020-04-15 03:56:21] Creating GenoGAMDataSet
INFO [2020-04-15 03:56:21] GenoGAMDataSet created
INFO [2020-04-15 03:56:21] Computing size factors
ERROR [2020-04-15 03:56:21] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2020-04-15 03:56:21] Creating GenoGAMDataSet
INFO [2020-04-15 03:56:22] GenoGAMDataSet created
== testthat results  ===========================================================
[ OK: 427 | SKIPPED: 0 | WARNINGS: 109 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 113.39    1.48  660.98

Example timings

GenoGAM.Rcheck/examples_i386/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-class1.040.021.06
GenoGAMDataSet-class7.720.568.78
GenoGAMDataSet-metrics2.870.002.87
GenoGAMDataSet-subsetting4.080.014.10
GenoGAMDataSetList-metrics 4.24 0.1819.81
GenoGAMList-class0.250.000.25
GenoGAMSettings-class0.010.010.03
callPeaks 0.95 0.0013.36
computeRegionSignificance0.440.000.44
computeSignificance0.130.000.12
computeSizeFactors2.450.002.45
fitGenoGAM 1.66 0.0348.10
makeTestGenoGAM0.060.000.06
makeTestGenoGAMDataSet2.30.02.3
makeTestGenoGAMDataSetList 1.04 0.0021.47
makeTestGenoGAMList0.300.000.29
readData3.80.24.0

GenoGAM.Rcheck/examples_x64/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-class1.290.001.30
GenoGAMDataSet-class8.610.178.78
GenoGAMDataSet-metrics3.330.003.33
GenoGAMDataSet-subsetting4.790.024.82
GenoGAMDataSetList-metrics 6.50 0.0224.09
GenoGAMList-class0.420.000.42
GenoGAMSettings-class0.050.000.05
callPeaks 1.3 0.016.2
computeRegionSignificance0.530.000.53
computeSignificance0.260.000.27
computeSizeFactors3.770.003.76
fitGenoGAM 2.23 0.0353.53
makeTestGenoGAM0.110.000.11
makeTestGenoGAMDataSet4.190.014.22
makeTestGenoGAMDataSetList 1.52 0.0220.28
makeTestGenoGAMList0.360.000.36
readData5.120.035.16