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This page was generated on 2021-05-06 12:35:05 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the GenoGAM package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 709/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenoGAM 2.8.0 (landing page) Georg Stricker
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: GenoGAM |
Version: 2.8.0 |
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_2.8.0.tar.gz |
StartedAt: 2021-05-06 02:04:55 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 02:12:16 -0400 (Thu, 06 May 2021) |
EllapsedTime: 440.4 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_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GenoGAM.Rcheck’ * using R version 4.0.5 (2021-03-31) * 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 ‘2.8.0’ * 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-3.12-bioc/meat/GenoGAM.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: R 1.7Mb 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 11.472 0.254 11.753 fitGenoGAM 8.548 2.886 4.190 readData 7.043 0.608 7.125 GenoGAMDataSetList-metrics 6.297 0.805 6.045 GenoGAMDataSet-subsetting 6.684 0.061 6.755 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.12-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++ -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable] SEXP data = Parent::get__(); ^ 1 warning generated. 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c matrixMult.cpp -o matrixMult.o In file included from matrixMult.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable] SEXP data = Parent::get__(); ^ 1 warning generated. 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/4.0/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 version 4.0.5 (2021-03-31) -- "Shake and Throw" 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 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")'. 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 Loading required package: rhdf5 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 [2021-05-06 02:10:36] Creating GenoGAMDataSet INFO [2021-05-06 02:10:39] GenoGAMDataSet created INFO [2021-05-06 02:10:39] Creating GenoGAMDataSet INFO [2021-05-06 02:10:39] Creating GenoGAMDataSet INFO [2021-05-06 02:10:39] Creating GenoGAMDataSet INFO [2021-05-06 02:10:39] Creating GenoGAMDataSet INFO [2021-05-06 02:10:39] Creating GenoGAMDataSet INFO [2021-05-06 02:10:40] Reading in data INFO [2021-05-06 02:10:40] Reading in wt_1 INFO [2021-05-06 02:10:42] Reading in wt_2 INFO [2021-05-06 02:10:43] Reading in mutant_1 INFO [2021-05-06 02:10:43] Reading in mutant_2 INFO [2021-05-06 02:10:43] Finished reading in data INFO [2021-05-06 02:10:43] GenoGAMDataSet created INFO [2021-05-06 02:10:44] Creating GenoGAMDataSet INFO [2021-05-06 02:10:44] Reading in data INFO [2021-05-06 02:10:44] Reading in wt_1 INFO [2021-05-06 02:10:45] Reading in wt_2 INFO [2021-05-06 02:10:45] Reading in mutant_1 INFO [2021-05-06 02:10:46] Reading in mutant_2 INFO [2021-05-06 02:10:46] Finished reading in data INFO [2021-05-06 02:10:46] GenoGAMDataSet created INFO [2021-05-06 02:10:46] Creating GenoGAMDataSet ERROR [2021-05-06 02:10:46] The data does not match the region specification in the bamParams settings. INFO [2021-05-06 02:10:46] GenoGAMDataSet created WARN [2021-05-06 02:10:46] Checks dismissed due to empty object or forgotten setting INFO [2021-05-06 02:10:46] Creating GenoGAMDataSet ERROR [2021-05-06 02:10:46] No chromosomes to read in. Check either the specified settings or the header of BAM file INFO [2021-05-06 02:10:46] GenoGAMDataSet created WARN [2021-05-06 02:10:46] Checks dismissed due to empty object or forgotten setting INFO [2021-05-06 02:10:46] Creating GenoGAMDataSet INFO [2021-05-06 02:10:47] Reading in data INFO [2021-05-06 02:10:47] Reading in wt_1 INFO [2021-05-06 02:10:48] Reading in wt_2 INFO [2021-05-06 02:10:48] Reading in mutant_1 INFO [2021-05-06 02:10:49] Reading in mutant_2 INFO [2021-05-06 02:10:49] Finished reading in data ERROR [2021-05-06 02:10:49] Checks failed. Following settings display errors: formula "'by' variables in design don't match colData" INFO [2021-05-06 02:10:49] GenoGAMDataSet created ERROR [2021-05-06 02:10:49] Checks failed. Following settings display errors: formula "'by' variables in design don't match colData" WARN [2021-05-06 02:10:53] Settings checking deactivated. Modeling on these tiles might yield wrong results. WARN [2021-05-06 02:10:53] Checks dismissed due to empty object or forgotten setting ERROR [2021-05-06 02:10:53] 'by' variables could not be found in colData INFO [2021-05-06 02:10:55] Reading in data INFO [2021-05-06 02:10:55] Reading in wt_1 INFO [2021-05-06 02:10:55] Reading in wt_2 INFO [2021-05-06 02:10:56] Reading in mutant_1 INFO [2021-05-06 02:10:57] Reading in mutant_2 INFO [2021-05-06 02:10:57] Finished reading in data INFO [2021-05-06 02:10:58] Creating GenoGAMDataSet INFO [2021-05-06 02:10:59] Reading in data INFO [2021-05-06 02:10:59] Reading in wt_1 INFO [2021-05-06 02:10:59] Reading in wt_2 INFO [2021-05-06 02:11:00] Reading in mutant_1 INFO [2021-05-06 02:11:00] Reading in mutant_2 INFO [2021-05-06 02:11:00] Finished reading in data INFO [2021-05-06 02:11:01] GenoGAMDataSet created INFO [2021-05-06 02:11:02] Creating GenoGAMDataSet INFO [2021-05-06 02:11:03] GenoGAMDataSet created INFO [2021-05-06 02:11:04] Creating GenoGAMDataSet INFO [2021-05-06 02:11:05] GenoGAMDataSet created INFO [2021-05-06 02:11:07] Creating GenoGAMDataSet INFO [2021-05-06 02:11:08] GenoGAMDataSet created INFO [2021-05-06 02:11:08] Creating GenoGAMDataSet INFO [2021-05-06 02:11:09] GenoGAMDataSet created INFO [2021-05-06 02:11:09] Creating GenoGAMDataSet INFO [2021-05-06 02:11:10] Reading in data INFO [2021-05-06 02:11:10] Reading in wt_1 INFO [2021-05-06 02:11:10] Reading in wt_2 INFO [2021-05-06 02:11:11] Reading in mutant_1 INFO [2021-05-06 02:11:11] Reading in mutant_2 INFO [2021-05-06 02:11:11] Finished reading in data INFO [2021-05-06 02:11:12] GenoGAMDataSet created INFO [2021-05-06 02:11:13] Creating GenoGAMDataSet INFO [2021-05-06 02:11:13] Reading in data INFO [2021-05-06 02:11:13] Reading in wt_1 INFO [2021-05-06 02:11:14] Reading in wt_2 INFO [2021-05-06 02:11:14] Reading in mutant_1 INFO [2021-05-06 02:11:15] Reading in mutant_2 INFO [2021-05-06 02:11:15] Finished reading in data INFO [2021-05-06 02:11:16] GenoGAMDataSet created INFO [2021-05-06 02:11:16] Creating GenoGAMDataSet INFO [2021-05-06 02:11:17] Reading in data INFO [2021-05-06 02:11:17] Reading in wt_1 INFO [2021-05-06 02:11:17] Reading in wt_2 INFO [2021-05-06 02:11:18] Reading in mutant_1 INFO [2021-05-06 02:11:18] Reading in mutant_2 INFO [2021-05-06 02:11:19] Finished reading in data INFO [2021-05-06 02:11:20] GenoGAMDataSet created INFO [2021-05-06 02:11:20] Creating GenoGAMDataSet ERROR [2021-05-06 02:11:20] The data does not match the region specification in the bamParams settings. INFO [2021-05-06 02:11:20] GenoGAMDataSet created WARN [2021-05-06 02:11:20] Checks dismissed due to empty object or forgotten setting INFO [2021-05-06 02:11:20] Creating GenoGAMDataSet ERROR [2021-05-06 02:11:20] The data does not match the region specification in the bamParams settings. INFO [2021-05-06 02:11:20] GenoGAMDataSet created WARN [2021-05-06 02:11:20] Checks dismissed due to empty object or forgotten setting INFO [2021-05-06 02:11:20] Creating GenoGAMDataSet INFO [2021-05-06 02:11:21] Reading in data INFO [2021-05-06 02:11:21] Reading in wt_1 INFO [2021-05-06 02:11:21] Reading in wt_2 INFO [2021-05-06 02:11:22] Reading in mutant_1 INFO [2021-05-06 02:11:22] Reading in mutant_2 INFO [2021-05-06 02:11:23] Finished reading in data ERROR [2021-05-06 02:11:24] Checks failed. Following settings display errors: formula "'by' variables in design don't match colData" INFO [2021-05-06 02:11:24] GenoGAMDataSet created ERROR [2021-05-06 02:11:24] Checks failed. Following settings display errors: formula "'by' variables in design don't match colData" WARN [2021-05-06 02:11:25] Settings checking deactivated. Modeling on these tiles might yield wrong results. WARN [2021-05-06 02:11:25] Checks dismissed due to empty object or forgotten setting INFO [2021-05-06 02:11:26] Creating GenoGAMDataSet INFO [2021-05-06 02:11:26] Reading in data INFO [2021-05-06 02:11:26] Reading in wt_1 INFO [2021-05-06 02:11:27] Reading in wt_2 INFO [2021-05-06 02:11:27] Reading in mutant_1 INFO [2021-05-06 02:11:28] Reading in mutant_2 INFO [2021-05-06 02:11:28] Finished reading in data INFO [2021-05-06 02:11:28] GenoGAMDataSet created ERROR [2021-05-06 02:11:28] 'by' variables could not be found in colData WARN [2021-05-06 02:11:48] Some supplied parameters aren't valid and won't be used WARN [2021-05-06 02:11:48] Some supplied parameters aren't valid and won't be used INFO [2021-05-06 02:11:49] Creating GenoGAMDataSet INFO [2021-05-06 02:11:50] GenoGAMDataSet created INFO [2021-05-06 02:11:50] Creating GenoGAMDataSet INFO [2021-05-06 02:11:51] GenoGAMDataSet created ERROR [2021-05-06 02:11:55] The overhang size covers the entire tile. Change parameter to a lower meaningful value. See getOverhangSize(). INFO [2021-05-06 02:11:56] Creating GenoGAMDataSet INFO [2021-05-06 02:11:57] GenoGAMDataSet created WARN [2021-05-06 02:11:59] Some supplied parameters aren't valid and won't be used INFO [2021-05-06 02:12:02] Creating GenoGAMDataSet INFO [2021-05-06 02:12:03] GenoGAMDataSet created INFO [2021-05-06 02:12:03] Computing size factors INFO [2021-05-06 02:12:04] DONE INFO [2021-05-06 02:12:04] Computing size factors INFO [2021-05-06 02:12:05] Creating GenoGAMDataSet INFO [2021-05-06 02:12:06] GenoGAMDataSet created INFO [2021-05-06 02:12:06] Computing size factors ERROR [2021-05-06 02:12:06] GenoGAMDataSet doesn't have column names. No size factors computed. INFO [2021-05-06 02:12:06] Creating GenoGAMDataSet INFO [2021-05-06 02:12:07] GenoGAMDataSet created [ FAIL 0 | WARN 109 | SKIP 0 | PASS 427 ] > > proc.time() user system elapsed 113.330 14.502 107.004
GenoGAM.Rcheck/GenoGAM-Ex.timings
name | user | system | elapsed | |
GenoGAM-class | 2.457 | 0.029 | 2.490 | |
GenoGAMDataSet-class | 11.472 | 0.254 | 11.753 | |
GenoGAMDataSet-metrics | 4.427 | 0.026 | 4.456 | |
GenoGAMDataSet-subsetting | 6.684 | 0.061 | 6.755 | |
GenoGAMDataSetList-metrics | 6.297 | 0.805 | 6.045 | |
GenoGAMList-class | 0.325 | 0.010 | 0.336 | |
GenoGAMSettings-class | 0.033 | 0.003 | 0.036 | |
callPeaks | 0.671 | 0.384 | 0.671 | |
computeRegionSignificance | 0.598 | 0.061 | 0.659 | |
computeSignificance | 0.214 | 0.023 | 0.237 | |
computeSizeFactors | 4.657 | 0.067 | 4.729 | |
fitGenoGAM | 8.548 | 2.886 | 4.190 | |
makeTestGenoGAM | 0.103 | 0.010 | 0.113 | |
makeTestGenoGAMDataSet | 3.407 | 0.114 | 3.525 | |
makeTestGenoGAMDataSetList | 1.210 | 0.495 | 1.122 | |
makeTestGenoGAMList | 0.411 | 0.135 | 0.552 | |
readData | 7.043 | 0.608 | 7.125 | |