Georg Stricker
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/GenoGAM |
| Branch: master |
| Last Commit: df4ff0a |
| Last Changed Date: 2019-10-29 13:40:48 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:44:55 -0500 (Thu, 16 Jan 2020).
| Package 672/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenoGAM 2.5.0 Georg Stricker
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GenoGAM |
| Version: 2.5.0 |
| 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_2.5.0.tar.gz |
| StartedAt: 2020-01-16 04:48:22 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 04:59:06 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 644.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenoGAM.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### 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_2.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GenoGAM.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.5.0’
* 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 ‘/Users/biocbuild/bbs-3.11-bioc/meat/GenoGAM.Rcheck/00install.out’ for details.
* 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’
.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 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
fitGenoGAM 13.638 6.970 6.762
GenoGAMDataSet-class 16.730 0.557 17.473
GenoGAMDataSetList-metrics 10.111 1.794 9.961
GenoGAMDataSet-subsetting 10.338 0.107 10.506
readData 8.786 0.543 9.329
GenoGAMDataSet-metrics 7.641 0.074 7.940
makeTestGenoGAMDataSet 6.117 0.325 6.443
computeSizeFactors 6.209 0.148 6.357
* 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/GenoGAM.Rcheck/00check.log’
for details.
GenoGAM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenoGAM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘GenoGAM’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/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)
GenoGAM.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(GenoGAM)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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 [2020-01-16 04:56:37] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:42] GenoGAMDataSet created
INFO [2020-01-16 04:56:42] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:42] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:42] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:42] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:42] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:44] Reading in data
INFO [2020-01-16 04:56:44] Reading in wt_1
INFO [2020-01-16 04:56:46] Reading in wt_2
INFO [2020-01-16 04:56:47] Reading in mutant_1
INFO [2020-01-16 04:56:48] Reading in mutant_2
INFO [2020-01-16 04:56:48] Finished reading in data
INFO [2020-01-16 04:56:49] GenoGAMDataSet created
INFO [2020-01-16 04:56:49] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:50] Reading in data
INFO [2020-01-16 04:56:50] Reading in wt_1
INFO [2020-01-16 04:56:51] Reading in wt_2
INFO [2020-01-16 04:56:52] Reading in mutant_1
INFO [2020-01-16 04:56:52] Reading in mutant_2
INFO [2020-01-16 04:56:53] Finished reading in data
INFO [2020-01-16 04:56:53] GenoGAMDataSet created
INFO [2020-01-16 04:56:53] Creating GenoGAMDataSet
ERROR [2020-01-16 04:56:53] The data does not match the region specification in the bamParams settings.
INFO [2020-01-16 04:56:53] GenoGAMDataSet created
WARN [2020-01-16 04:56:53] Checks dismissed due to empty object or forgotten setting
INFO [2020-01-16 04:56:53] Creating GenoGAMDataSet
ERROR [2020-01-16 04:56:53] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2020-01-16 04:56:54] GenoGAMDataSet created
WARN [2020-01-16 04:56:54] Checks dismissed due to empty object or forgotten setting
INFO [2020-01-16 04:56:54] Creating GenoGAMDataSet
INFO [2020-01-16 04:56:55] Reading in data
INFO [2020-01-16 04:56:55] Reading in wt_1
INFO [2020-01-16 04:56:55] Reading in wt_2
INFO [2020-01-16 04:56:56] Reading in mutant_1
INFO [2020-01-16 04:56:57] Reading in mutant_2
INFO [2020-01-16 04:56:57] Finished reading in data
ERROR [2020-01-16 04:56:58] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
INFO [2020-01-16 04:56:58] GenoGAMDataSet created
ERROR [2020-01-16 04:56:58] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
WARN [2020-01-16 04:57:03] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-01-16 04:57:03] Checks dismissed due to empty object or forgotten setting
ERROR [2020-01-16 04:57:03] 'by' variables could not be found in colData
INFO [2020-01-16 04:57:06] Reading in data
INFO [2020-01-16 04:57:06] Reading in wt_1
INFO [2020-01-16 04:57:07] Reading in wt_2
INFO [2020-01-16 04:57:07] Reading in mutant_1
INFO [2020-01-16 04:57:08] Reading in mutant_2
INFO [2020-01-16 04:57:09] Finished reading in data
INFO [2020-01-16 04:57:10] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:11] Reading in data
INFO [2020-01-16 04:57:11] Reading in wt_1
INFO [2020-01-16 04:57:11] Reading in wt_2
INFO [2020-01-16 04:57:12] Reading in mutant_1
INFO [2020-01-16 04:57:12] Reading in mutant_2
INFO [2020-01-16 04:57:13] Finished reading in data
INFO [2020-01-16 04:57:13] GenoGAMDataSet created
INFO [2020-01-16 04:57:16] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:17] GenoGAMDataSet created
INFO [2020-01-16 04:57:19] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:20] GenoGAMDataSet created
INFO [2020-01-16 04:57:23] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:24] GenoGAMDataSet created
INFO [2020-01-16 04:57:25] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:26] GenoGAMDataSet created
INFO [2020-01-16 04:57:26] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:27] Reading in data
INFO [2020-01-16 04:57:27] Reading in wt_1
INFO [2020-01-16 04:57:28] Reading in wt_2
INFO [2020-01-16 04:57:29] Reading in mutant_1
INFO [2020-01-16 04:57:29] Reading in mutant_2
INFO [2020-01-16 04:57:30] Finished reading in data
INFO [2020-01-16 04:57:32] GenoGAMDataSet created
INFO [2020-01-16 04:57:32] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:33] Reading in data
INFO [2020-01-16 04:57:33] Reading in wt_1
INFO [2020-01-16 04:57:34] Reading in wt_2
INFO [2020-01-16 04:57:35] Reading in mutant_1
INFO [2020-01-16 04:57:36] Reading in mutant_2
INFO [2020-01-16 04:57:36] Finished reading in data
INFO [2020-01-16 04:57:38] GenoGAMDataSet created
INFO [2020-01-16 04:57:38] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:38] Reading in data
INFO [2020-01-16 04:57:39] Reading in wt_1
INFO [2020-01-16 04:57:39] Reading in wt_2
INFO [2020-01-16 04:57:39] Reading in mutant_1
INFO [2020-01-16 04:57:40] Reading in mutant_2
INFO [2020-01-16 04:57:41] Finished reading in data
INFO [2020-01-16 04:57:42] GenoGAMDataSet created
INFO [2020-01-16 04:57:42] Creating GenoGAMDataSet
ERROR [2020-01-16 04:57:42] The data does not match the region specification in the bamParams settings.
INFO [2020-01-16 04:57:42] GenoGAMDataSet created
WARN [2020-01-16 04:57:42] Checks dismissed due to empty object or forgotten setting
INFO [2020-01-16 04:57:42] Creating GenoGAMDataSet
ERROR [2020-01-16 04:57:42] The data does not match the region specification in the bamParams settings.
INFO [2020-01-16 04:57:42] GenoGAMDataSet created
WARN [2020-01-16 04:57:42] Checks dismissed due to empty object or forgotten setting
INFO [2020-01-16 04:57:42] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:43] Reading in data
INFO [2020-01-16 04:57:43] Reading in wt_1
INFO [2020-01-16 04:57:44] Reading in wt_2
INFO [2020-01-16 04:57:45] Reading in mutant_1
INFO [2020-01-16 04:57:45] Reading in mutant_2
INFO [2020-01-16 04:57:46] Finished reading in data
ERROR [2020-01-16 04:57:48] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
INFO [2020-01-16 04:57:48] GenoGAMDataSet created
ERROR [2020-01-16 04:57:48] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
WARN [2020-01-16 04:57:50] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-01-16 04:57:50] Checks dismissed due to empty object or forgotten setting
INFO [2020-01-16 04:57:50] Creating GenoGAMDataSet
INFO [2020-01-16 04:57:52] Reading in data
INFO [2020-01-16 04:57:52] Reading in wt_1
INFO [2020-01-16 04:57:53] Reading in wt_2
INFO [2020-01-16 04:57:54] Reading in mutant_1
INFO [2020-01-16 04:57:55] Reading in mutant_2
INFO [2020-01-16 04:57:55] Finished reading in data
INFO [2020-01-16 04:57:56] GenoGAMDataSet created
ERROR [2020-01-16 04:57:56] 'by' variables could not be found in colData
WARN [2020-01-16 04:58:28] Some supplied parameters aren't valid and won't be used
WARN [2020-01-16 04:58:28] Some supplied parameters aren't valid and won't be used
INFO [2020-01-16 04:58:29] Creating GenoGAMDataSet
INFO [2020-01-16 04:58:30] GenoGAMDataSet created
INFO [2020-01-16 04:58:31] Creating GenoGAMDataSet
INFO [2020-01-16 04:58:32] GenoGAMDataSet created
ERROR [2020-01-16 04:58:39] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2020-01-16 04:58:39] Creating GenoGAMDataSet
INFO [2020-01-16 04:58:41] GenoGAMDataSet created
WARN [2020-01-16 04:58:46] Some supplied parameters aren't valid and won't be used
INFO [2020-01-16 04:58:50] Creating GenoGAMDataSet
INFO [2020-01-16 04:58:52] GenoGAMDataSet created
INFO [2020-01-16 04:58:52] Computing size factors
INFO [2020-01-16 04:58:53] DONE
INFO [2020-01-16 04:58:54] Computing size factors
INFO [2020-01-16 04:58:54] Creating GenoGAMDataSet
INFO [2020-01-16 04:58:55] GenoGAMDataSet created
INFO [2020-01-16 04:58:55] Computing size factors
ERROR [2020-01-16 04:58:55] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2020-01-16 04:58:55] Creating GenoGAMDataSet
INFO [2020-01-16 04:58:57] GenoGAMDataSet created
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 427 | SKIPPED: 0 | WARNINGS: 109 | FAILED: 0 ]
>
> proc.time()
user system elapsed
167.801 29.346 164.609
GenoGAM.Rcheck/GenoGAM-Ex.timings
| name | user | system | elapsed | |
| GenoGAM-class | 2.495 | 0.087 | 2.584 | |
| GenoGAMDataSet-class | 16.730 | 0.557 | 17.473 | |
| GenoGAMDataSet-metrics | 7.641 | 0.074 | 7.940 | |
| GenoGAMDataSet-subsetting | 10.338 | 0.107 | 10.506 | |
| GenoGAMDataSetList-metrics | 10.111 | 1.794 | 9.961 | |
| GenoGAMList-class | 0.534 | 0.024 | 0.557 | |
| GenoGAMSettings-class | 0.040 | 0.004 | 0.044 | |
| callPeaks | 1.241 | 0.934 | 1.296 | |
| computeRegionSignificance | 2.403 | 1.473 | 1.515 | |
| computeSignificance | 0.462 | 0.059 | 0.522 | |
| computeSizeFactors | 6.209 | 0.148 | 6.357 | |
| fitGenoGAM | 13.638 | 6.970 | 6.762 | |
| makeTestGenoGAM | 0.178 | 0.037 | 0.214 | |
| makeTestGenoGAMDataSet | 6.117 | 0.325 | 6.443 | |
| makeTestGenoGAMDataSetList | 2.669 | 1.577 | 2.107 | |
| makeTestGenoGAMList | 0.626 | 0.113 | 0.740 | |
| readData | 8.786 | 0.543 | 9.329 | |