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This page was generated on 2021-09-24 15:06:42 -0400 (Fri, 24 Sep 2021).

CHECK results for GenoGAM on machv2

To the developers/maintainers of the GenoGAM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenoGAM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 734/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 2.10.0  (landing page)
Georg Stricker
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/GenoGAM
git_branch: RELEASE_3_13
git_last_commit: 3b86b0c
git_last_commit_date: 2021-05-19 12:19:19 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GenoGAM
Version: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2021-09-23 19:11:47 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 19:20:06 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 499.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenoGAM.Rcheck
Warnings: 3

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_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GenoGAM.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘GenoGAM’
  Warning: replacing previous import ‘S4Vectors::na.omit’ by ‘stats::na.omit’ when loading ‘GenoGAM’
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/GenoGAM.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   3.0Mb
* 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 ‘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 pval region tmp write.table x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "abline", "lines", "par")
  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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
GenoGAMDataSet-class       15.988  0.351  16.382
fitGenoGAM                  8.676  2.823   4.755
GenoGAMDataSet-subsetting   9.451  0.075   9.534
GenoGAMDataSetList-metrics  7.657  1.083   7.101
readData                    7.506  0.271   7.797
computeSizeFactors          7.159  0.106   7.270
GenoGAMDataSet-metrics      5.792  0.047   5.845
makeTestGenoGAMDataSet      5.485  0.155   5.648
* 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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/library’
* installing *source* package ‘GenoGAM’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrixMult.cpp -o matrixMult.o
clang++ -mmacosx-version-min=10.13 -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-darwin18/8.2.0 -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/4.1/Resources/library/00LOCK-GenoGAM/00new/GenoGAM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘GenoGAM’
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 ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘GenoGAM’
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 ‘HDF5Array::h5ls’ by ‘rhdf5::h5ls’ when loading ‘GenoGAM’
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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

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 messages:
1: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM' 
2: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' 
> 
> test_check("GenoGAM")
INFO [2021-09-23 19:17:54] Creating GenoGAMDataSet
INFO [2021-09-23 19:17:58] GenoGAMDataSet created
INFO [2021-09-23 19:17:58] Creating GenoGAMDataSet
INFO [2021-09-23 19:17:58] Creating GenoGAMDataSet
INFO [2021-09-23 19:17:58] Creating GenoGAMDataSet
INFO [2021-09-23 19:17:58] Creating GenoGAMDataSet
INFO [2021-09-23 19:17:58] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:00] Reading in data
INFO [2021-09-23 19:18:00] Reading in wt_1
INFO [2021-09-23 19:18:01] Reading in wt_2
INFO [2021-09-23 19:18:02] Reading in mutant_1
INFO [2021-09-23 19:18:02] Reading in mutant_2
INFO [2021-09-23 19:18:03] Finished reading in data
INFO [2021-09-23 19:18:03] GenoGAMDataSet created
INFO [2021-09-23 19:18:03] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:05] Reading in data
INFO [2021-09-23 19:18:05] Reading in wt_1
INFO [2021-09-23 19:18:05] Reading in wt_2
INFO [2021-09-23 19:18:06] Reading in mutant_1
INFO [2021-09-23 19:18:06] Reading in mutant_2
INFO [2021-09-23 19:18:07] Finished reading in data
INFO [2021-09-23 19:18:07] GenoGAMDataSet created
INFO [2021-09-23 19:18:07] Creating GenoGAMDataSet
ERROR [2021-09-23 19:18:08] The data does not match the region specification in the bamParams settings.
INFO [2021-09-23 19:18:08] GenoGAMDataSet created
WARN [2021-09-23 19:18:08] Checks dismissed due to empty object or forgotten setting
INFO [2021-09-23 19:18:08] Creating GenoGAMDataSet
ERROR [2021-09-23 19:18:08] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2021-09-23 19:18:08] GenoGAMDataSet created
WARN [2021-09-23 19:18:08] Checks dismissed due to empty object or forgotten setting
INFO [2021-09-23 19:18:08] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:09] Reading in data
INFO [2021-09-23 19:18:09] Reading in wt_1
INFO [2021-09-23 19:18:09] Reading in wt_2
INFO [2021-09-23 19:18:10] Reading in mutant_1
INFO [2021-09-23 19:18:11] Reading in mutant_2
INFO [2021-09-23 19:18:11] Finished reading in data
ERROR [2021-09-23 19:18:12] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2021-09-23 19:18:12] GenoGAMDataSet created
ERROR [2021-09-23 19:18:12] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2021-09-23 19:18:17] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2021-09-23 19:18:17] Checks dismissed due to empty object or forgotten setting
ERROR [2021-09-23 19:18:17] 'by' variables could not be found in colData
INFO [2021-09-23 19:18:20] Reading in data
INFO [2021-09-23 19:18:20] Reading in wt_1
INFO [2021-09-23 19:18:20] Reading in wt_2
INFO [2021-09-23 19:18:21] Reading in mutant_1
INFO [2021-09-23 19:18:22] Reading in mutant_2
INFO [2021-09-23 19:18:22] Finished reading in data
INFO [2021-09-23 19:18:23] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:25] Reading in data
INFO [2021-09-23 19:18:25] Reading in wt_1
INFO [2021-09-23 19:18:25] Reading in wt_2
INFO [2021-09-23 19:18:26] Reading in mutant_1
INFO [2021-09-23 19:18:26] Reading in mutant_2
INFO [2021-09-23 19:18:27] Finished reading in data
INFO [2021-09-23 19:18:27] GenoGAMDataSet created
INFO [2021-09-23 19:18:30] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:32] GenoGAMDataSet created
INFO [2021-09-23 19:18:33] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:35] GenoGAMDataSet created
INFO [2021-09-23 19:18:37] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:39] GenoGAMDataSet created
INFO [2021-09-23 19:18:39] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:41] GenoGAMDataSet created
INFO [2021-09-23 19:18:41] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:42] Reading in data
INFO [2021-09-23 19:18:42] Reading in wt_1
INFO [2021-09-23 19:18:43] Reading in wt_2
INFO [2021-09-23 19:18:43] Reading in mutant_1
INFO [2021-09-23 19:18:44] Reading in mutant_2
INFO [2021-09-23 19:18:45] Finished reading in data
INFO [2021-09-23 19:18:46] GenoGAMDataSet created
INFO [2021-09-23 19:18:46] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:48] Reading in data
INFO [2021-09-23 19:18:48] Reading in wt_1
INFO [2021-09-23 19:18:48] Reading in wt_2
INFO [2021-09-23 19:18:49] Reading in mutant_1
INFO [2021-09-23 19:18:49] Reading in mutant_2
INFO [2021-09-23 19:18:50] Finished reading in data
INFO [2021-09-23 19:18:51] GenoGAMDataSet created
INFO [2021-09-23 19:18:51] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:52] Reading in data
INFO [2021-09-23 19:18:52] Reading in wt_1
INFO [2021-09-23 19:18:53] Reading in wt_2
INFO [2021-09-23 19:18:54] Reading in mutant_1
INFO [2021-09-23 19:18:55] Reading in mutant_2
INFO [2021-09-23 19:18:55] Finished reading in data
INFO [2021-09-23 19:18:57] GenoGAMDataSet created
INFO [2021-09-23 19:18:57] Creating GenoGAMDataSet
ERROR [2021-09-23 19:18:57] The data does not match the region specification in the bamParams settings.
INFO [2021-09-23 19:18:57] GenoGAMDataSet created
WARN [2021-09-23 19:18:57] Checks dismissed due to empty object or forgotten setting
INFO [2021-09-23 19:18:57] Creating GenoGAMDataSet
ERROR [2021-09-23 19:18:57] The data does not match the region specification in the bamParams settings.
INFO [2021-09-23 19:18:57] GenoGAMDataSet created
WARN [2021-09-23 19:18:57] Checks dismissed due to empty object or forgotten setting
INFO [2021-09-23 19:18:57] Creating GenoGAMDataSet
INFO [2021-09-23 19:18:58] Reading in data
INFO [2021-09-23 19:18:58] Reading in wt_1
INFO [2021-09-23 19:18:59] Reading in wt_2
INFO [2021-09-23 19:19:00] Reading in mutant_1
INFO [2021-09-23 19:19:00] Reading in mutant_2
INFO [2021-09-23 19:19:01] Finished reading in data
ERROR [2021-09-23 19:19:02] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
INFO [2021-09-23 19:19:02] GenoGAMDataSet created
ERROR [2021-09-23 19:19:02] Checks failed. Following settings display errors:
                                       formula 
"'by' variables in design don't match colData" 
WARN [2021-09-23 19:19:04] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2021-09-23 19:19:04] Checks dismissed due to empty object or forgotten setting
INFO [2021-09-23 19:19:04] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:06] Reading in data
INFO [2021-09-23 19:19:06] Reading in wt_1
INFO [2021-09-23 19:19:07] Reading in wt_2
INFO [2021-09-23 19:19:07] Reading in mutant_1
INFO [2021-09-23 19:19:08] Reading in mutant_2
INFO [2021-09-23 19:19:08] Finished reading in data
INFO [2021-09-23 19:19:08] GenoGAMDataSet created
ERROR [2021-09-23 19:19:08] 'by' variables could not be found in colData
WARN [2021-09-23 19:19:34] Some supplied parameters aren't valid and won't be used
WARN [2021-09-23 19:19:34] Some supplied parameters aren't valid and won't be used
INFO [2021-09-23 19:19:35] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:36] GenoGAMDataSet created
INFO [2021-09-23 19:19:36] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:38] GenoGAMDataSet created
ERROR [2021-09-23 19:19:42] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2021-09-23 19:19:42] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:44] GenoGAMDataSet created
WARN [2021-09-23 19:19:46] Some supplied parameters aren't valid and won't be used
INFO [2021-09-23 19:19:49] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:51] GenoGAMDataSet created
INFO [2021-09-23 19:19:51] Computing size factors
INFO [2021-09-23 19:19:53] DONE
INFO [2021-09-23 19:19:53] Computing size factors
INFO [2021-09-23 19:19:53] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:54] GenoGAMDataSet created
INFO [2021-09-23 19:19:55] Computing size factors
ERROR [2021-09-23 19:19:55] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2021-09-23 19:19:55] Creating GenoGAMDataSet
INFO [2021-09-23 19:19:56] GenoGAMDataSet created
[ FAIL 0 | WARN 109 | SKIP 0 | PASS 427 ]
> 
> proc.time()
   user  system elapsed 
146.671  17.548 139.218 

Example timings

GenoGAM.Rcheck/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-class1.9240.0481.981
GenoGAMDataSet-class15.988 0.35116.382
GenoGAMDataSet-metrics5.7920.0475.845
GenoGAMDataSet-subsetting9.4510.0759.534
GenoGAMDataSetList-metrics7.6571.0837.101
GenoGAMList-class0.3870.0120.399
GenoGAMSettings-class0.0610.0050.066
callPeaks0.8760.5020.911
computeRegionSignificance0.8870.0960.988
computeSignificance0.2490.0190.269
computeSizeFactors7.1590.1067.270
fitGenoGAM8.6762.8234.755
makeTestGenoGAM0.1730.0170.191
makeTestGenoGAMDataSet5.4850.1555.648
makeTestGenoGAMDataSetList2.2320.8671.503
makeTestGenoGAMList0.3720.0270.399
readData7.5060.2717.797