Back to the "Multiple platform build/check report" A  B  C [D] E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.3: CHECK report for derfinder on morelia

This page was generated on 2016-04-21 13:25:49 -0700 (Thu, 21 Apr 2016).

Package 291/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.5.35
Leonardo Collado-Torres
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinder
Last Changed Rev: 116593 / Revision: 116626
Last Changed Date: 2016-04-20 08:54:52 -0700 (Wed, 20 Apr 2016)
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 

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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:

nameusersystemelapsed
advancedArg0.0070.0000.009
analyzeChr1.0000.0171.073
annotateRegions0.6690.0090.685
calculatePvalues1.0990.0081.127
calculateStats0.2510.0040.255
coerceGR0.1130.0130.126
collapseFullCoverage0.0140.0030.018
coverageToExon2.9810.4203.434
createBw0.2140.0020.218
createBwSample0.0830.0020.086
extendedMapSeqlevels0.1340.0070.140
filterData0.2430.0110.254
findRegions0.4120.0200.434
fullCoverage0.4070.0130.423
getRegionCoverage0.3820.0090.423
loadCoverage0.2440.0150.282
makeGenomicState4.5970.0374.722
makeModels0.0500.0010.051
mergeResults0.5200.0130.536
preprocessCoverage0.2410.0030.245
railMatrix10.770 1.72913.141
rawFiles0.0070.0000.007
regionMatrix0.4840.0100.504
sampleDepth0.0290.0010.030