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This page was generated on 2016-04-21 13:25:49 -0700 (Thu, 21 Apr 2016).
Package 291/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
derfinder 1.5.35 Leonardo Collado-Torres
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | ||||||
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
Package: derfinder |
Version: 1.5.35 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings derfinder_1.5.35.tar.gz |
StartedAt: 2016-04-21 01:29:56 -0700 (Thu, 21 Apr 2016) |
EndedAt: 2016-04-21 01:39:54 -0700 (Thu, 21 Apr 2016) |
EllapsedTime: 598.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: derfinder.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings derfinder_1.5.35.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck’ * using R version 3.3.0 beta (2016-04-06 r70435) * using platform: x86_64-apple-darwin13.4.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘derfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘derfinder’ version ‘1.5.35’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘derfinder’ can be installed ... [27s/28s] OK * 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 Unexported objects imported by ':::' calls: ‘GenomeInfoDb:::.guessSpeciesStyle’ ‘GenomeInfoDb:::.supportedSeqnameMappings’ 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [41s/42s] OK Examples with CPU or elapsed time > 5s user system elapsed railMatrix 10.77 1.729 13.141 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 97538 Segmentation fault: 11 ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 [267s/277s] ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 19: source_file(path, new.env(parent = env), chdir = TRUE) 20: force(code) 21: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE) end_context() }) 22: FUN(X[[i]], ...) 23: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE) 24: force(code) 25: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE)) 26: test_files(paths, reporter = reporter, env = env, ...) 27: test_dir(test_path, reporter = reporter, env = env, filter = filter, ...) 28: with_top_env(env, { test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)}) 29: run_tests(package, test_path, filter, reporter, ...) 30: test_check("derfinder") An irrecoverable exception occurred. R is aborting now ... * 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: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/00check.log’ for details.
test-all.Rout.fail:
R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (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. > ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE > > flag <- as.logical(Sys.getenv('R_DISABLE_TESTS')) > if(is.na(flag) | flag == FALSE) { + library('testthat') + test_check('derfinder') + } Loading required package: derfinder 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, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:base': colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: IRanges Loading required package: GenomeInfoDb 2016-04-21 01:35:27 collapseFullCoverage: Sorting fullCov 2016-04-21 01:35:27 collapseFullCoverage: Collapsing chromosomes information by sample 2016-04-21 01:35:27 sampleDepth: Calculating sample quantiles 2016-04-21 01:35:27 sampleDepth: Calculating sample adjustments 2016-04-21 01:35:28 calculateStats: calculating the F-statistics 2016-04-21 01:35:28 calculatePvalues: identifying data segments 2016-04-21 01:35:28 findRegions: segmenting information 2016-04-21 01:35:28 findRegions: identifying candidate regions 2016-04-21 01:35:28 findRegions: identifying region clusters 2016-04-21 01:35:28 calculatePvalues: calculating F-statistics for permutation 1 and seed 1 2016-04-21 01:35:28 findRegions: segmenting information 2016-04-21 01:35:28 findRegions: identifying candidate regions 2016-04-21 01:35:28 calculatePvalues: calculating F-statistics for permutation 2 and seed 2 2016-04-21 01:35:28 findRegions: segmenting information 2016-04-21 01:35:28 findRegions: identifying candidate regions 2016-04-21 01:35:29 calculatePvalues: calculating F-statistics for permutation 3 and seed 3 2016-04-21 01:35:29 findRegions: segmenting information 2016-04-21 01:35:29 findRegions: identifying candidate regions 2016-04-21 01:35:29 calculatePvalues: calculating F-statistics for permutation 4 and seed 4 2016-04-21 01:35:29 findRegions: segmenting information 2016-04-21 01:35:29 findRegions: identifying candidate regions 2016-04-21 01:35:29 calculatePvalues: calculating F-statistics for permutation 5 and seed 5 2016-04-21 01:35:29 findRegions: segmenting information 2016-04-21 01:35:29 findRegions: identifying candidate regions 2016-04-21 01:35:30 calculatePvalues: calculating F-statistics for permutation 6 and seed 6 2016-04-21 01:35:30 findRegions: segmenting information 2016-04-21 01:35:30 findRegions: identifying candidate regions 2016-04-21 01:35:30 calculatePvalues: calculating F-statistics for permutation 7 and seed 7 2016-04-21 01:35:30 findRegions: segmenting information 2016-04-21 01:35:30 findRegions: identifying candidate regions 2016-04-21 01:35:30 calculatePvalues: calculating F-statistics for permutation 8 and seed 8 2016-04-21 01:35:30 findRegions: segmenting information 2016-04-21 01:35:30 findRegions: identifying candidate regions 2016-04-21 01:35:30 calculatePvalues: calculating F-statistics for permutation 9 and seed 9 2016-04-21 01:35:30 findRegions: segmenting information 2016-04-21 01:35:30 findRegions: identifying candidate regions 2016-04-21 01:35:30 calculatePvalues: calculating F-statistics for permutation 10 and seed 10 2016-04-21 01:35:30 findRegions: segmenting information 2016-04-21 01:35:30 findRegions: identifying candidate regions 2016-04-21 01:35:30 calculatePvalues: calculating the p-values 1. Failure: calculatePvalues (@test_Fstats.R#79) ------------------------------- derfinder:::.calculateFWER(...) not equal to 3:2/3. 1/2 mismatches [2] 0.75 - 0.667 == 0.0833 extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens 2016-04-21 01:35:31 mergeResults: Saving options used 2016-04-21 01:35:31 Loading chromosome chr21 Neither 'cutoffFstatUsed' nor 'optionsStats' were supplied, so the FWER calculation step will be skipped. 2016-04-21 01:35:31 mergeResults: Saving fullNullSummary 2016-04-21 01:35:31 mergeResults: Re-calculating the p-values 2016-04-21 01:35:31 mergeResults: Saving fullRegions 2016-04-21 01:35:31 mergeResults: assigning genomic states 2016-04-21 01:35:32 annotateRegions: counting 2016-04-21 01:35:32 annotateRegions: annotating 2016-04-21 01:35:32 mergeResults: Saving fullAnnotatedRegions 2016-04-21 01:35:32 mergeResults: Saving fullFstats 2016-04-21 01:35:32 mergeResults: Saving fullTime 2016-04-21 01:35:32 collapseFullCoverage: Sorting fullCov 2016-04-21 01:35:32 collapseFullCoverage: Collapsing chromosomes information by sample 2016-04-21 01:35:32 sampleDepth: Calculating sample quantiles 2016-04-21 01:35:32 sampleDepth: Calculating sample adjustments extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens 2016-04-21 01:35:32 analyzeChr: Pre-processing the coverage data 2016-04-21 01:35:32 analyzeChr: Calculating statistics 2016-04-21 01:35:32 calculateStats: calculating the F-statistics 2016-04-21 01:35:32 analyzeChr: Calculating pvalues 2016-04-21 01:35:32 analyzeChr: Using the following manual cutoff for the F-statistics 1 2016-04-21 01:35:32 calculatePvalues: identifying data segments 2016-04-21 01:35:32 findRegions: segmenting information 2016-04-21 01:35:32 findRegions: identifying candidate regions 2016-04-21 01:35:32 findRegions: identifying region clusters 2016-04-21 01:35:33 calculatePvalues: calculating F-statistics for permutation 1 and seed 20140330 2016-04-21 01:35:33 findRegions: segmenting information 2016-04-21 01:35:33 findRegions: identifying candidate regions 2016-04-21 01:35:33 calculatePvalues: calculating the p-values 2016-04-21 01:35:33 analyzeChr: Annotating regions No annotationPackage supplied. Trying org.Hs.eg.db. Loading required package: org.Hs.eg.db Loading required package: AnnotationDbi 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")'. Getting TSS and TSE. Getting CSS and CSE. Getting exons. Annotating genes. extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens 2016-04-21 01:36:15 mergeResults: Saving options used 2016-04-21 01:36:15 Loading chromosome chr21 Neither 'cutoffFstatUsed' nor 'optionsStats' were supplied, so the FWER calculation step will be skipped. 2016-04-21 01:36:15 mergeResults: Saving fullNullSummary 2016-04-21 01:36:15 mergeResults: Re-calculating the p-values 2016-04-21 01:36:15 mergeResults: Saving fullRegions 2016-04-21 01:36:15 mergeResults: assigning genomic states 2016-04-21 01:36:15 annotateRegions: counting 2016-04-21 01:36:15 annotateRegions: annotating 2016-04-21 01:36:15 mergeResults: Saving fullAnnotatedRegions 2016-04-21 01:36:15 mergeResults: Saving fullFstats 2016-04-21 01:36:15 mergeResults: Saving fullTime Loading required package: GenomicFeatures extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens 2016-04-21 01:36:15 analyzeChr: Pre-processing the coverage data 2016-04-21 01:36:16 analyzeChr: Calculating statistics 2016-04-21 01:36:16 calculateStats: calculating the F-statistics 2016-04-21 01:36:16 analyzeChr: Calculating pvalues 2016-04-21 01:36:16 analyzeChr: Using the following manual cutoff for the F-statistics 1 2016-04-21 01:36:16 calculatePvalues: identifying data segments 2016-04-21 01:36:16 findRegions: segmenting information 2016-04-21 01:36:16 findRegions: identifying candidate regions 2016-04-21 01:36:16 findRegions: identifying region clusters 2016-04-21 01:36:16 calculatePvalues: calculating F-statistics for permutation 1 and seed 20160422 2016-04-21 01:36:16 findRegions: segmenting information 2016-04-21 01:36:16 findRegions: identifying candidate regions 2016-04-21 01:36:16 calculatePvalues: calculating the p-values 2016-04-21 01:36:16 analyzeChr: Annotating regions No annotationPackage supplied. Trying org.Hs.eg.db. Getting TSS and TSE. Getting CSS and CSE. Getting exons. Annotating genes. extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens 2016-04-21 01:36:52 analyzeChr: Pre-processing the coverage data 2016-04-21 01:36:52 analyzeChr: Calculating statistics 2016-04-21 01:36:52 calculateStats: calculating the F-statistics 2016-04-21 01:36:52 analyzeChr: Calculating pvalues 2016-04-21 01:36:52 analyzeChr: Using the following manual cutoff for the F-statistics 1 2016-04-21 01:36:52 calculatePvalues: identifying data segments 2016-04-21 01:36:52 findRegions: segmenting information 2016-04-21 01:36:52 findRegions: identifying candidate regions 2016-04-21 01:36:52 findRegions: identifying region clusters 2016-04-21 01:36:53 calculatePvalues: calculating F-statistics for permutation 1 and seed 20160422 2016-04-21 01:36:53 findRegions: segmenting information 2016-04-21 01:36:53 findRegions: identifying candidate regions 2016-04-21 01:36:53 calculatePvalues: calculating the p-values 2016-04-21 01:36:53 analyzeChr: Annotating regions No annotationPackage supplied. Trying org.Hs.eg.db. Getting TSS and TSE. Getting CSS and CSE. Getting exons. Annotating genes. 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 2016-04-21 01:38:21 annotateRegions: counting 2016-04-21 01:38:21 annotateRegions: annotating 2016-04-21 01:38:22 loadCoverage: finding chromosome lengths 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:38:22 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:38:23 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:38:24 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:38:25 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:38:25 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:38:25 filterData: originally there were 48129895 rows, now there are 1434 rows. Meaning that 100 percent was filtered. 2016-04-21 01:38:25 loadCoverage: finding chromosome lengths 2016-04-21 01:38:25 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:38:25 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:38:25 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:38:25 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:38:25 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:38:26 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:38:27 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:38:28 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered. 2016-04-21 01:38:28 loadCoverage: finding chromosome lengths 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:38:28 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:38:29 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:38:30 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:38:31 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:38:31 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:38:31 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:38:31 filterData: originally there were 48129895 rows, now there are 1434 rows. Meaning that 100 percent was filtered. 2016-04-21 01:38:35 loadCoverage: finding chromosome lengths 2016-04-21 01:38:35 loadCoverage: loading BigWig file bw/ERR009101.bw 2016-04-21 01:38:35 loadCoverage: loading BigWig file bw/ERR009102.bw 2016-04-21 01:38:35 loadCoverage: loading BigWig file bw/ERR009105.bw 2016-04-21 01:38:35 loadCoverage: loading BigWig file bw/ERR009107.bw 2016-04-21 01:38:35 loadCoverage: loading BigWig file bw/ERR009108.bw 2016-04-21 01:38:35 loadCoverage: loading BigWig file bw/ERR009112.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009115.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009116.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009131.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009138.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009144.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009145.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009148.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009151.bw 2016-04-21 01:38:36 loadCoverage: loading BigWig file bw/ERR009152.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/ERR009153.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/ERR009159.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/ERR009161.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/ERR009163.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/ERR009164.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/ERR009167.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/SRR031812.bw 2016-04-21 01:38:37 loadCoverage: loading BigWig file bw/SRR031835.bw 2016-04-21 01:38:38 loadCoverage: loading BigWig file bw/SRR031904.bw 2016-04-21 01:38:38 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:38:38 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered. 2016-04-21 01:38:41 loadCoverage: finding chromosome lengths 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:38:41 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:38:42 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:38:43 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:38:44 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:38:45 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:38:46 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:38:47 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:38:48 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:38:49 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:38:50 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:38:51 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:38:51 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered. 2016-04-21 01:38:51 loadCoverage: finding chromosome lengths 2016-04-21 01:38:51 loadCoverage: loading BigWig file bw/ERR009101.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009101.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009101.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009102.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009102.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009102.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009105.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009105.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009105.bw 2016-04-21 01:38:52 loadCoverage: loading BigWig file bw/ERR009107.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009107.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009107.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009108.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009108.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009108.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009112.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009112.bw 2016-04-21 01:38:53 loadCoverage: loading BigWig file bw/ERR009112.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009115.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009115.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009115.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009116.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009116.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009116.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009131.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009131.bw 2016-04-21 01:38:54 loadCoverage: loading BigWig file bw/ERR009131.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009138.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009138.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009138.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009144.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009144.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009144.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009145.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009145.bw 2016-04-21 01:38:55 loadCoverage: loading BigWig file bw/ERR009145.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009148.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009148.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009148.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009151.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009151.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009151.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009152.bw 2016-04-21 01:38:56 loadCoverage: loading BigWig file bw/ERR009152.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009152.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009153.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009153.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009153.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009159.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009159.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009159.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009161.bw 2016-04-21 01:38:57 loadCoverage: loading BigWig file bw/ERR009161.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009161.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009163.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009163.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009163.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009164.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009164.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009164.bw 2016-04-21 01:38:58 loadCoverage: loading BigWig file bw/ERR009167.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/ERR009167.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/ERR009167.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031812.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031812.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031812.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031835.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031835.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031835.bw 2016-04-21 01:38:59 loadCoverage: loading BigWig file bw/SRR031904.bw 2016-04-21 01:39:00 loadCoverage: loading BigWig file bw/SRR031904.bw 2016-04-21 01:39:00 loadCoverage: loading BigWig file bw/SRR031904.bw 2016-04-21 01:39:00 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:39:00 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered. 2016-04-21 01:39:00 fullCoverage: processing chromosome 21 2016-04-21 01:39:00 loadCoverage: finding chromosome lengths 2016-04-21 01:39:00 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam 2016-04-21 01:39:00 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009102_accepted_hits.bam 2016-04-21 01:39:00 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009105_accepted_hits.bam 2016-04-21 01:39:00 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009107_accepted_hits.bam 2016-04-21 01:39:00 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009108_accepted_hits.bam 2016-04-21 01:39:00 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009112_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009115_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009116_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009131_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009138_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009144_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009145_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009148_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009151_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009152_accepted_hits.bam 2016-04-21 01:39:01 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009153_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009159_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009161_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009163_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009164_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/ERR009167_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031812_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031835_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031867_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031868_accepted_hits.bam 2016-04-21 01:39:02 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031900_accepted_hits.bam 2016-04-21 01:39:03 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031904_accepted_hits.bam 2016-04-21 01:39:03 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031914_accepted_hits.bam 2016-04-21 01:39:03 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031936_accepted_hits.bam 2016-04-21 01:39:03 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031958_accepted_hits.bam 2016-04-21 01:39:03 loadCoverage: loading BAM file /Users/biocbuild/bbs-3.3-bioc/meat/derfinder.Rcheck/derfinder/extdata/genomeData/SRR031960_accepted_hits.bam 2016-04-21 01:39:03 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:39:03 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered. extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens 2016-04-21 01:39:03 fullCoverage: processing chromosome chr21 2016-04-21 01:39:03 loadCoverage: finding chromosome lengths 2016-04-21 01:39:03 loadCoverage: loading BigWig file bw/ERR009101.bw 2016-04-21 01:39:03 loadCoverage: loading BigWig file bw/ERR009102.bw 2016-04-21 01:39:03 loadCoverage: loading BigWig file bw/ERR009105.bw 2016-04-21 01:39:03 loadCoverage: loading BigWig file bw/ERR009107.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009108.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009112.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009115.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009116.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009131.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009138.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009144.bw 2016-04-21 01:39:04 loadCoverage: loading BigWig file bw/ERR009145.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009148.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009151.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009152.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009153.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009159.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009161.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009163.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009164.bw 2016-04-21 01:39:05 loadCoverage: loading BigWig file bw/ERR009167.bw 2016-04-21 01:39:06 loadCoverage: loading BigWig file bw/SRR031812.bw 2016-04-21 01:39:06 loadCoverage: loading BigWig file bw/SRR031835.bw 2016-04-21 01:39:06 loadCoverage: loading BigWig file bw/SRR031904.bw 2016-04-21 01:39:06 loadCoverage: applying the cutoff to the merged data 2016-04-21 01:39:06 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered. Loading required package: Biostrings Loading required package: XVector 2016-04-21 01:39:09 filterData: originally there were 48129895 rows, now there are 1434 rows. Meaning that 100 percent was filtered. 2016-04-21 01:39:09 getRegionCoverage: processing chr21 2016-04-21 01:39:09 getRegionCoverage: done processing chr21 class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA 2016-04-21 01:39:19 coverageToExon: processing chromosome chr21 class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA class: SerialParam bpisup: TRUE; bpworkers: 1; bptasks: 0; bpjobname: BPJOB bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE bptimeout: 2592000; bpprogressbar: FALSE bplogdir: NA 2016-04-21 01:39:42 filterData: originally there were 1434 rows, now there are 33 rows. Meaning that 97.7 percent was filtered. 2016-04-21 01:39:43 filterData: originally there were 1434 rows, now there are 33 rows. Meaning that 97.7 percent was filtered. 2016-04-21 01:39:43 findRegions: identifying potential segments 2016-04-21 01:39:43 findRegions: segmenting information 2016-04-21 01:39:43 .getSegmentsRle: segmenting with cutoff(s) 19.7936614060235 2016-04-21 01:39:43 findRegions: identifying candidate regions 2016-04-21 01:39:43 findRegions: identifying region clusters 2016-04-21 01:39:43 findRegions: identifying potential segments 2016-04-21 01:39:43 findRegions: segmenting information 2016-04-21 01:39:43 .getSegmentsRle: segmenting with cutoff(s) 1 2016-04-21 01:39:43 findRegions: identifying candidate regions 2016-04-21 01:39:43 findRegions: identifying region clusters 2016-04-21 01:39:43 findRegions: identifying potential segments 2016-04-21 01:39:43 findRegions: segmenting information 2016-04-21 01:39:43 .getSegmentsRle: segmenting with cutoff(s) 1 2016-04-21 01:39:43 findRegions: identifying candidate regions Loading required package: foreach Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 getSegments: segmenting getSegments: splitting 2016-04-21 01:39:46 findRegions: smoothing 2016-04-21 01:39:46 findRegions: identifying potential segments 2016-04-21 01:39:46 findRegions: segmenting information 2016-04-21 01:39:46 .getSegmentsRle: segmenting with cutoff(s) 16.3681899295041 2016-04-21 01:39:46 findRegions: identifying candidate regions 2016-04-21 01:39:46 findRegions: identifying region clusters 2016-04-21 01:39:46 findRegions: smoothing 2016-04-21 01:39:46 findRegions: identifying potential segments 2016-04-21 01:39:46 findRegions: segmenting information 2016-04-21 01:39:46 .getSegmentsRle: segmenting with cutoff(s) 19.7936614060235 2016-04-21 01:39:46 findRegions: identifying candidate regions 2016-04-21 01:39:46 findRegions: identifying region clusters 2016-04-21 01:39:46 findRegions: smoothing *** caught segfault *** address 0x7fd4fb9259e0, cause 'memory not mapped' Traceback: 1: (function (y, x, cluster, weights, smoothFun, ...) { hostPackage <- environmentName(environment(smoothFun)) requireNamespace(hostPackage) smoothed <- .runFunFormal(smoothFun, y = y, x = x, cluster = cluster, weights = weights, ...) if (any(!smoothed$smoothed)) { smoothed$fitted[!smoothed$smoothed] <- y[!smoothed$smoothed] } res <- Rle(smoothed$fitted) return(res)})(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]], dots[[4L]][[1L]], smoothFun = function (y, x = NULL, cluster, weights = NULL, minNum = 7, bpSpan = 1000, minInSpan = 0, verbose = TRUE) { if (is.null(dim(y))) y <- matrix(y, ncol = 1) if (!is.null(weights) && is.null(dim(weights))) weights <- matrix(weights, ncol = 1) if (is.null(x)) x <- seq(along = y) if (is.null(weights)) weights <- matrix(1, nrow = nrow(y), ncol = ncol(y)) Indexes <- split(seq(along = cluster), cluster) clusterL <- sapply(Indexes, length) smoothed <- rep(TRUE, nrow(y)) for (i in seq(along = Indexes)) { if (verbose) if (i%%10000 == 0) cat(".") Index <- Indexes[[i]] if (clusterL[i] >= minNum & sum(rowSums(is.na(y[Index, , drop = FALSE])) == 0) >= minNum) { nn <- minInSpan/length(Index) for (j in 1:ncol(y)) { sdata <- data.frame(pos = x[Index], y = y[Index, j], weights = weights[Index, j]) fit <- locfit(y ˜ lp(pos, nn = nn, h = bpSpan), data = sdata, weights = weights, family = "gaussian", maxk = 10000) pp <- preplot(fit, where = "data", band = "local", newdata = data.frame(pos = x[Index])) y[Index, j] <- pp$trans(pp$fit) } } else { y[Index, ] <- NA smoothed[Index] <- FALSE } } return(list(fitted = y, smoothed = smoothed, smoother = "locfit")) }, verbose = TRUE, minNum = 1435) 2: .mapply(.FUN, dots, .MoreArgs) 3: FUN(...) 4: withCallingHandlers(expr, warning = handle_warning, error = handle_error) 5: doWithOneRestart(return(expr), restart) 6: withOneRestart(expr, restarts[[1L]]) 7: withRestarts({ withCallingHandlers(expr, warning = handle_warning, error = handle_error)}, abort = handle_abort) 8: .try(FUN(...)) 9: FUN(X[[i]], ...) 10: lapply(X, FUN, ...) 11: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM) 12: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd, .MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM) 13: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks, weightChunks, MoreArgs = list(smoothFun = smoothFunction, ...), BPPARAM = BPPARAM) 14: bpmapply(.smoothFstatsFun, fstatsChunks, posChunks, clusterChunks, weightChunks, MoreArgs = list(smoothFun = smoothFunction, ...), BPPARAM = BPPARAM) 15: .smootherFstats(fstats = fstats, position = position, weights = weights, smoothFunction = smoothFunction, ...) 16: findRegions(prep$position, genomeFstats, "chr21", verbose = TRUE, smooth = TRUE, minNum = 1435) 17: eval(expr, envir, enclos) 18: eval(exprs, env) 19: source_file(path, new.env(parent = env), chdir = TRUE) 20: force(code) 21: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE) end_context() }) 22: FUN(X[[i]], ...) 23: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE) 24: force(code) 25: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE)) 26: test_files(paths, reporter = reporter, env = env, ...) 27: test_dir(test_path, reporter = reporter, env = env, filter = filter, ...) 28: with_top_env(env, { test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)}) 29: run_tests(package, test_path, filter, reporter, ...) 30: test_check("derfinder") An irrecoverable exception occurred. R is aborting now ...
derfinder.Rcheck/00install.out:
* installing *source* package ‘derfinder’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (derfinder)
derfinder.Rcheck/derfinder-Ex.timings:
name | user | system | elapsed | |
advancedArg | 0.007 | 0.000 | 0.009 | |
analyzeChr | 1.000 | 0.017 | 1.073 | |
annotateRegions | 0.669 | 0.009 | 0.685 | |
calculatePvalues | 1.099 | 0.008 | 1.127 | |
calculateStats | 0.251 | 0.004 | 0.255 | |
coerceGR | 0.113 | 0.013 | 0.126 | |
collapseFullCoverage | 0.014 | 0.003 | 0.018 | |
coverageToExon | 2.981 | 0.420 | 3.434 | |
createBw | 0.214 | 0.002 | 0.218 | |
createBwSample | 0.083 | 0.002 | 0.086 | |
extendedMapSeqlevels | 0.134 | 0.007 | 0.140 | |
filterData | 0.243 | 0.011 | 0.254 | |
findRegions | 0.412 | 0.020 | 0.434 | |
fullCoverage | 0.407 | 0.013 | 0.423 | |
getRegionCoverage | 0.382 | 0.009 | 0.423 | |
loadCoverage | 0.244 | 0.015 | 0.282 | |
makeGenomicState | 4.597 | 0.037 | 4.722 | |
makeModels | 0.050 | 0.001 | 0.051 | |
mergeResults | 0.520 | 0.013 | 0.536 | |
preprocessCoverage | 0.241 | 0.003 | 0.245 | |
railMatrix | 10.770 | 1.729 | 13.141 | |
rawFiles | 0.007 | 0.000 | 0.007 | |
regionMatrix | 0.484 | 0.010 | 0.504 | |
sampleDepth | 0.029 | 0.001 | 0.030 | |