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) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:43:26 -0400 (Wed, 15 Apr 2020).
| Package 673/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenoGAM 2.4.0 Georg Stricker
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: GenoGAM |
| Version: 2.4.0 |
| 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_2.4.0.tar.gz |
| StartedAt: 2020-04-15 02:35:06 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:42:26 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 440.1 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_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.4.0’
* 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 ‘/Users/biocbuild/bbs-3.10-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 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 13.016 0.369 13.687
fitGenoGAM 8.842 4.167 4.223
GenoGAMDataSetList-metrics 6.494 0.821 6.429
GenoGAMDataSet-subsetting 7.038 0.114 7.223
readData 5.689 0.275 6.048
GenoGAMDataSet-metrics 5.339 0.029 5.487
* 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-3.10-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/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 [2020-04-15 02:40:43] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:46] GenoGAMDataSet created
INFO [2020-04-15 02:40:46] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:46] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:46] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:47] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:47] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:47] Reading in data
INFO [2020-04-15 02:40:47] Reading in wt_1
INFO [2020-04-15 02:40:49] Reading in wt_2
INFO [2020-04-15 02:40:50] Reading in mutant_1
INFO [2020-04-15 02:40:50] Reading in mutant_2
INFO [2020-04-15 02:40:51] Finished reading in data
INFO [2020-04-15 02:40:51] GenoGAMDataSet created
INFO [2020-04-15 02:40:51] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:52] Reading in data
INFO [2020-04-15 02:40:52] Reading in wt_1
INFO [2020-04-15 02:40:52] Reading in wt_2
INFO [2020-04-15 02:40:53] Reading in mutant_1
INFO [2020-04-15 02:40:53] Reading in mutant_2
INFO [2020-04-15 02:40:54] Finished reading in data
INFO [2020-04-15 02:40:54] GenoGAMDataSet created
INFO [2020-04-15 02:40:54] Creating GenoGAMDataSet
ERROR [2020-04-15 02:40:54] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 02:40:54] GenoGAMDataSet created
WARN [2020-04-15 02:40:54] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 02:40:54] Creating GenoGAMDataSet
ERROR [2020-04-15 02:40:54] No chromosomes to read in. Check either the specified settings or the header of BAM file
INFO [2020-04-15 02:40:54] GenoGAMDataSet created
WARN [2020-04-15 02:40:54] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 02:40:54] Creating GenoGAMDataSet
INFO [2020-04-15 02:40:55] Reading in data
INFO [2020-04-15 02:40:55] Reading in wt_1
INFO [2020-04-15 02:40:56] Reading in wt_2
INFO [2020-04-15 02:40:56] Reading in mutant_1
INFO [2020-04-15 02:40:57] Reading in mutant_2
INFO [2020-04-15 02:40:57] Finished reading in data
ERROR [2020-04-15 02:40:57] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
INFO [2020-04-15 02:40:58] GenoGAMDataSet created
ERROR [2020-04-15 02:40:58] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
WARN [2020-04-15 02:41:01] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 02:41:01] Checks dismissed due to empty object or forgotten setting
ERROR [2020-04-15 02:41:01] 'by' variables could not be found in colData
INFO [2020-04-15 02:41:03] Reading in data
INFO [2020-04-15 02:41:03] Reading in wt_1
INFO [2020-04-15 02:41:03] Reading in wt_2
INFO [2020-04-15 02:41:04] Reading in mutant_1
INFO [2020-04-15 02:41:04] Reading in mutant_2
INFO [2020-04-15 02:41:05] Finished reading in data
INFO [2020-04-15 02:41:06] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:06] Reading in data
INFO [2020-04-15 02:41:06] Reading in wt_1
INFO [2020-04-15 02:41:07] Reading in wt_2
INFO [2020-04-15 02:41:07] Reading in mutant_1
INFO [2020-04-15 02:41:07] Reading in mutant_2
INFO [2020-04-15 02:41:08] Finished reading in data
INFO [2020-04-15 02:41:08] GenoGAMDataSet created
INFO [2020-04-15 02:41:11] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:12] GenoGAMDataSet created
INFO [2020-04-15 02:41:13] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:14] GenoGAMDataSet created
INFO [2020-04-15 02:41:15] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:16] GenoGAMDataSet created
INFO [2020-04-15 02:41:17] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:18] GenoGAMDataSet created
INFO [2020-04-15 02:41:18] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:19] Reading in data
INFO [2020-04-15 02:41:19] Reading in wt_1
INFO [2020-04-15 02:41:19] Reading in wt_2
INFO [2020-04-15 02:41:19] Reading in mutant_1
INFO [2020-04-15 02:41:20] Reading in mutant_2
INFO [2020-04-15 02:41:20] Finished reading in data
INFO [2020-04-15 02:41:21] GenoGAMDataSet created
INFO [2020-04-15 02:41:21] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:22] Reading in data
INFO [2020-04-15 02:41:22] Reading in wt_1
INFO [2020-04-15 02:41:22] Reading in wt_2
INFO [2020-04-15 02:41:23] Reading in mutant_1
INFO [2020-04-15 02:41:23] Reading in mutant_2
INFO [2020-04-15 02:41:23] Finished reading in data
INFO [2020-04-15 02:41:24] GenoGAMDataSet created
INFO [2020-04-15 02:41:24] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:25] Reading in data
INFO [2020-04-15 02:41:25] Reading in wt_1
INFO [2020-04-15 02:41:25] Reading in wt_2
INFO [2020-04-15 02:41:26] Reading in mutant_1
INFO [2020-04-15 02:41:26] Reading in mutant_2
INFO [2020-04-15 02:41:26] Finished reading in data
INFO [2020-04-15 02:41:27] GenoGAMDataSet created
INFO [2020-04-15 02:41:28] Creating GenoGAMDataSet
ERROR [2020-04-15 02:41:28] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 02:41:28] GenoGAMDataSet created
WARN [2020-04-15 02:41:28] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 02:41:28] Creating GenoGAMDataSet
ERROR [2020-04-15 02:41:28] The data does not match the region specification in the bamParams settings.
INFO [2020-04-15 02:41:28] GenoGAMDataSet created
WARN [2020-04-15 02:41:28] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 02:41:28] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:29] Reading in data
INFO [2020-04-15 02:41:29] Reading in wt_1
INFO [2020-04-15 02:41:29] Reading in wt_2
INFO [2020-04-15 02:41:30] Reading in mutant_1
INFO [2020-04-15 02:41:30] Reading in mutant_2
INFO [2020-04-15 02:41:31] Finished reading in data
ERROR [2020-04-15 02:41:32] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
INFO [2020-04-15 02:41:32] GenoGAMDataSet created
ERROR [2020-04-15 02:41:32] Checks failed. Following settings display errors:
formula
"'by' variables in design don't match colData"
WARN [2020-04-15 02:41:33] Settings checking deactivated. Modeling on these tiles might yield wrong results.
WARN [2020-04-15 02:41:33] Checks dismissed due to empty object or forgotten setting
INFO [2020-04-15 02:41:34] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:35] Reading in data
INFO [2020-04-15 02:41:35] Reading in wt_1
INFO [2020-04-15 02:41:35] Reading in wt_2
INFO [2020-04-15 02:41:36] Reading in mutant_1
INFO [2020-04-15 02:41:36] Reading in mutant_2
INFO [2020-04-15 02:41:36] Finished reading in data
INFO [2020-04-15 02:41:37] GenoGAMDataSet created
ERROR [2020-04-15 02:41:37] 'by' variables could not be found in colData
WARN [2020-04-15 02:41:55] Some supplied parameters aren't valid and won't be used
WARN [2020-04-15 02:41:55] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 02:41:56] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:57] GenoGAMDataSet created
INFO [2020-04-15 02:41:57] Creating GenoGAMDataSet
INFO [2020-04-15 02:41:58] GenoGAMDataSet created
ERROR [2020-04-15 02:42:02] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize().
INFO [2020-04-15 02:42:02] Creating GenoGAMDataSet
INFO [2020-04-15 02:42:03] GenoGAMDataSet created
WARN [2020-04-15 02:42:05] Some supplied parameters aren't valid and won't be used
INFO [2020-04-15 02:42:07] Creating GenoGAMDataSet
INFO [2020-04-15 02:42:08] GenoGAMDataSet created
INFO [2020-04-15 02:42:09] Computing size factors
INFO [2020-04-15 02:42:09] DONE
INFO [2020-04-15 02:42:10] Computing size factors
INFO [2020-04-15 02:42:10] Creating GenoGAMDataSet
INFO [2020-04-15 02:42:10] GenoGAMDataSet created
INFO [2020-04-15 02:42:11] Computing size factors
ERROR [2020-04-15 02:42:11] GenoGAMDataSet doesn't have column names. No size factors computed.
INFO [2020-04-15 02:42:11] Creating GenoGAMDataSet
INFO [2020-04-15 02:42:12] GenoGAMDataSet created
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 427 | SKIPPED: 0 | WARNINGS: 109 | FAILED: 0 ]
>
> proc.time()
user system elapsed
108.574 13.462 104.539
GenoGAM.Rcheck/GenoGAM-Ex.timings
| name | user | system | elapsed | |
| GenoGAM-class | 1.924 | 0.023 | 1.957 | |
| GenoGAMDataSet-class | 13.016 | 0.369 | 13.687 | |
| GenoGAMDataSet-metrics | 5.339 | 0.029 | 5.487 | |
| GenoGAMDataSet-subsetting | 7.038 | 0.114 | 7.223 | |
| GenoGAMDataSetList-metrics | 6.494 | 0.821 | 6.429 | |
| GenoGAMList-class | 0.304 | 0.005 | 0.316 | |
| GenoGAMSettings-class | 0.029 | 0.002 | 0.030 | |
| callPeaks | 0.715 | 0.432 | 0.676 | |
| computeRegionSignificance | 1.778 | 2.162 | 0.955 | |
| computeSignificance | 0.362 | 0.247 | 0.280 | |
| computeSizeFactors | 4.218 | 0.105 | 4.373 | |
| fitGenoGAM | 8.842 | 4.167 | 4.223 | |
| makeTestGenoGAM | 0.142 | 0.109 | 0.111 | |
| makeTestGenoGAMDataSet | 3.692 | 0.165 | 3.902 | |
| makeTestGenoGAMDataSetList | 1.687 | 0.966 | 1.282 | |
| makeTestGenoGAMList | 0.307 | 0.034 | 0.343 | |
| readData | 5.689 | 0.275 | 6.048 | |