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###
### Running command:
###
###   chmod a+r chromstaR -R && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data chromstaR
###
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* checking for file 'chromstaR/DESCRIPTION' ... OK
* preparing 'chromstaR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'chromstaR.Rnw' using knitr
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which.max,
    which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: chromstaRData

Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.

Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.5s
Making fixed-width bins for bin size 1000 ... 0.22s
Counting overlaps for binsize 1000 with offset 0 ... 1.27s
Counting overlaps for binsize 1000 with offset 500 ... 0.31s
Making bins with offsets ... 0.11s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 1.23s
Collecting counts and posteriors ... 0.67s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.14s
Making segmentation ... 0.08s
Calculating states from maximum-posterior in each peak ... 0.13s
Re-estimating maximum posterior in peaks ... 0.08s
Making segmentation ... 0.15s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c59f167e2_peaks_track-1.bed.gz ... 0.11s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c1739a6b_counts_track-1.wig.gz ... 0.29s
Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.15s
Making fixed-width bins for bin size 1000 ... 0.1s
Counting overlaps for binsize 1000 with offset 0 ... 1.23s
Counting overlaps for binsize 1000 with offset 500 ... 0.37s
Making bins with offsets ... 0.11s
Running Baum-Welch for offset = 0 ... 0.67s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.19s
Calculating states from posteriors ... 0.14s
Making segmentation ... 0.04s
Calculating states from maximum-posterior in each peak ... 0.12s
Re-estimating maximum posterior in peaks ... 0.1s
Making segmentation ... 0.12s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c6718752a_peaks_track-1.bed.gz ... 0.09s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c3dac36d8_counts_track-1.wig.gz ... 0.32s
Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.76s
Making fixed-width bins for bin size 1000 ... 0.08s
Counting overlaps for binsize 1000 with offset 0 ... 5.81s
Counting overlaps for binsize 1000 with offset 500 ... 0.95s
Making bins with offsets ... 0.08s
Running Baum-Welch for offset = 0 ... 0.78s
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.12s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.05s
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figure/univariate_braod_H4K20me1_2")
Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.69s
Making fixed-width bins for bin size 1000 ... 0.08s
Counting overlaps for binsize 1000 with offset 0 ... 1.28s
Counting overlaps for binsize 1000 with offset 500 ... 0.37s
Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.56s
Making fixed-width bins for bin size 1000 ... 0.09s
Counting overlaps for binsize 1000 with offset 0 ... 1.69s
Counting overlaps for binsize 1000 with offset 500 ... 0.39s
Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.73s
Making fixed-width bins for bin size 1000 ... 0.11s
Counting overlaps for binsize 1000 with offset 0 ... 3.4s
Counting overlaps for binsize 1000 with offset 500 ... 0.69s
Reading header from C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.47s
Making fixed-width bins for bin size 1000 ... 0.08s
Counting overlaps for binsize 1000 with offset 0 ... 2.66s
Counting overlaps for binsize 1000 with offset 500 ... 0.88s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.83s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.14s
Making segmentation ... 0.06s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.05s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.09s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.06s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.09s
Obtaining states for offset = 500 ... 0.72s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.06s
Getting coordinates ... 0s
Extracting read counts ... 0.16s
Getting combinatorial states ... 0.09s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.03s
------------------
Chromosome = chr12
Starting multivariate HMM with 16 combinatorial states
Making bins with offsets ... 0s
Fitting Hidden Markov Model for offset = 0
Time spent in multivariate HMM:  1s
Obtaining states for offset = 500 ... 0.49s
Collecting counts and posteriors over offsets ... 0.61s
Compiling coordinates, posteriors, states ... 0.13s
Adding combinations ... 0.03s
Making segmentation ... 0.18s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.11s
Time spent for chromosome = chr12: 4.56s
Merging chromosomes ... 0.13s
Getting coordinates ... 0s
Extracting read counts ... 0.16s
Getting combinatorial states ... 0.09s
Computing pre z-matrix ... 0.02s
Transfering values into z-matrix ... 0.01s
Computing inverse of correlation matrix ... 0.02s
------------------
Chromosome = chr12
Starting multivariate HMM with 2 combinatorial states
Making bins with offsets ... 0s
Fitting Hidden Markov Model for offset = 0
Time spent in multivariate HMM:  0.21s
Obtaining states for offset = 500 ... 0.11s
Collecting counts and posteriors over offsets ... 0.64s
Compiling coordinates, posteriors, states ... 0.11s
Adding combinations ... 0.02s
Making segmentation ... 0.14s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.08s
Obtaining peaks ... 0.07s
Time spent for chromosome = chr12: 3.23s
Merging chromosomes ... 0.13s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c55e921f3_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c55e921f3_peaks_H3K27me3-SHR-rep2.bed.gz ... 0s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c55e921f3_peaks_H3K27me3-SHR-rep3.bed.gz ... 0s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c76ef3304_counts_H3K27me3-SHR-rep1.wig.gz ... 0.23s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c76ef3304_counts_H3K27me3-SHR-rep2.wig.gz ... 0.24s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c76ef3304_counts_H3K27me3-SHR-rep3.wig.gz ... 0.26s
Setting up parallel execution with 4 threads ... 0.42s
================
Binning the data
================
Obtaining chromosome length information from file C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.02s
Making fixed-width bins for bin size 1000 ... 0.08s
Making fixed-width bins for bin size 500 ... 0.14s
Binning data ... 15.53s
Binning control ... 3.45s
========================
Calling univariate peaks
========================
Univariate peak calling ... 6.52s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.05s
Extracting read counts ... 0.34s
Getting combinatorial states ... 0.14s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.04s
Setting up parallel multivariate with 4 threads ... 0.37s
Running multivariate ... 14.34s
Merging chromosomes ... 0.29s
Saving to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.52s
Making plots ... 0.17s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.12s
Concatenating HMMs ... 0.11s
Making combinations ... 0.22s
Reassigning levels ... 0s
Assigning transition groups ... 0.06s
Assigning combinatorial states ... 0.05s
Transferring counts and posteriors ... 0.09s
Making segmentation ... 0.15s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.11s
Redoing segmentation for each condition separately ... 0.07s
Saving to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.33s
Plotting read count correlation ... 0.41s
=======================
Exporting browser files
=======================
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.06s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.72s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
==> Total time spent: 46s <==
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c50283b35_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c50283b35_peaks_H4K20me1-BN-rep2.bed.gz ... 0.02s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c50283b35_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c74ab4e16_counts_H4K20me1-BN-rep1.wig.gz ... 0.25s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c74ab4e16_counts_H4K20me1-BN-rep2.wig.gz ... 0.24s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c74ab4e16_counts_H4K20me1-SHR-rep1.wig.gz ... 0.23s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG\file1a5c22305bc1_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.39s
================
Binning the data
================
Obtaining chromosome length information from file C:/Users/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.07s
Making fixed-width bins for bin size 500 ... 0.1s
Binning data ... 12.55s
Binning control ... 1.16s
========================
Calling univariate peaks
========================
Univariate peak calling ... 8.61s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.05s
Extracting read counts ... 0.37s
Getting combinatorial states ... 0.14s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.06s
Computing inverse of correlation matrix ... 0.02s
Setting up parallel multivariate with 4 threads ... 0.36s
Running multivariate ... 13.62s
Merging chromosomes ... 0.38s
Saving to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.72s
Making plots ... 0.14s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.14s
Concatenating conditions ... 0.75s
Reassigning levels ... 0.02s
Assigning transition groups ... 0.05s
Assigning combinatorial states ... 0.03s
Transferring counts and posteriors ... 0.06s
Making segmentation ... 0.23s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.08s
Redoing segmentation for each condition separately ... 0.05s
Saving to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.4s
Plotting read count correlation ... 0.22s
=======================
Exporting browser files
=======================
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.06s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.03s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.05s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.01s
Writing to file C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQ3iKQG/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.02s
==> Total time spent: 42s <==
Quitting from lines 377-397 (chromstaR.Rnw) 
Error: processing vignette 'chromstaR.Rnw' failed with diagnostics:
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://may2012.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
--- failed re-building 'chromstaR.Rnw'

SUMMARY: processing the following file failed:
  'chromstaR.Rnw'

Error: Vignette re-building failed.
Execution halted