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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R 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
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 /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.02s
Making fixed-width bins for bin size 1000 ... 0.12s
Counting overlaps for binsize 1000 with offset 0 ... 0.28s
Counting overlaps for binsize 1000 with offset 500 ... 0.19s
Making bins with offsets ... 1.11s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 0.89s
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.71s
Calculating states from maximum-posterior in each peak ... 0.06s
Re-estimating maximum posterior in peaks ... 0.03s
Making segmentation ... 0.08s
Writing to file /tmp/Rtmpe02f8s/file137bcb3b0b0b6d_peaks_track-1.bed.gz ... 0.08s
Writing to file /tmp/Rtmpe02f8s/file137bcb43f2b658_counts_track-1.wig.gz ... 0.16s
Reading header from /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.03s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.23s
Counting overlaps for binsize 1000 with offset 500 ... 0.22s
Making bins with offsets ... 0.07s
Running Baum-Welch for offset = 0 ... 0.5s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.15s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.06s
Calculating states from maximum-posterior in each peak ... 0.06s
Re-estimating maximum posterior in peaks ... 0.05s
Making segmentation ... 0.05s
Writing to file /tmp/Rtmpe02f8s/file137bcb582f5ac8_peaks_track-1.bed.gz ... 0.06s
Writing to file /tmp/Rtmpe02f8s/file137bcb4c4bc78_counts_track-1.wig.gz ... 0.18s
Reading header from /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.65s
Counting overlaps for binsize 1000 with offset 500 ... 0.63s
Making bins with offsets ... 0.71s
Running Baum-Welch for offset = 0 ... 0.6s
Collecting counts and posteriors ... 0.09s
Obtaining states for offset = 500 ... 0.14s
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 /home/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 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.22s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Reading header from /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.23s
Counting overlaps for binsize 1000 with offset 500 ... 0.23s
Reading header from /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.43s
Counting overlaps for binsize 1000 with offset 500 ... 0.43s
Reading header from /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.62s
Counting overlaps for binsize 1000 with offset 500 ... 0.57s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.1s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.05s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.91s
Calculating states from posteriors ... 0.1s
Making segmentation ... 0.08s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 0.15s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.06s
Making bins with offsets ... 0.12s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.16s
Calculating states from posteriors ... 0.12s
Making segmentation ... 0.06s
Getting coordinates ... 0s
Extracting read counts ... 0.2s
Getting combinatorial states ... 0.88s
Computing pre z-matrix ... 0.01s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.05s
------------------
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:  1.87s
Obtaining states for offset = 500 ... 0.67s
Collecting counts and posteriors over offsets ... 1.21s
Compiling coordinates, posteriors, states ... 0.12s
Adding combinations ... 0.03s
Making segmentation ... 0.17s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.1s
Obtaining peaks ... 0.12s
Time spent for chromosome = chr12: 7.2s
Merging chromosomes ... 0.14s
Getting coordinates ... 0s
Extracting read counts ... 0.16s
Getting combinatorial states ... 0.08s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.01s
------------------
Chromosome = chr12
Starting multivariate HMM with 2 combinatorial states
Making bins with offsets ... 0.01s
Fitting Hidden Markov Model for offset = 0
Time spent in multivariate HMM:  0.19s
Obtaining states for offset = 500 ... 0.11s
Collecting counts and posteriors over offsets ... 0.76s
Compiling coordinates, posteriors, states ... 0.11s
Adding combinations ... 0.03s
Making segmentation ... 0.13s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.08s
Obtaining peaks ... 0.1s
Time spent for chromosome = chr12: 3.92s
Merging chromosomes ... 0.12s
Writing to file /tmp/Rtmpe02f8s/file137bcb74fddedc_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmpe02f8s/file137bcb74fddedc_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/Rtmpe02f8s/file137bcb74fddedc_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/Rtmpe02f8s/file137bcb34555a69_counts_H3K27me3-SHR-rep1.wig.gz ... 0.19s
Writing to file /tmp/Rtmpe02f8s/file137bcb34555a69_counts_H3K27me3-SHR-rep2.wig.gz ... 0.18s
Writing to file /tmp/Rtmpe02f8s/file137bcb34555a69_counts_H3K27me3-SHR-rep3.wig.gz ... 0.19s
Setting up parallel execution with 4 threads ... 0.3s
================
Binning the data
================
Obtaining chromosome length information from file /home/biocbuild/bbs-3.13-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Making fixed-width bins for bin size 500 ... 0.07s
Binning data ... 10.69s
Binning control ... 1.45s
========================
Calling univariate peaks
========================
Univariate peak calling ... 5.72s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.04s
Extracting read counts ... 0.19s
Getting combinatorial states ... 0.1s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.02s
Computing inverse of correlation matrix ... 0.01s
Setting up parallel multivariate with 4 threads ... 0.28s
Running multivariate ... 13.02s
Merging chromosomes ... 0.2s
Saving to file /tmp/Rtmpe02f8s/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.43s
Making plots ... 0.15s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.11s
Concatenating HMMs ... 0.09s
Making combinations ... 0.14s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.07s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.06s
Making segmentation ... 0.13s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.83s
Redoing segmentation for each condition separately ... 0.08s
Saving to file /tmp/Rtmpe02f8s/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.32s
Plotting read count correlation ... 0.19s
=======================
Exporting browser files
=======================
Writing to file /tmp/Rtmpe02f8s/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.02s
Writing to file /tmp/Rtmpe02f8s/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file /tmp/Rtmpe02f8s/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/Rtmpe02f8s/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/Rtmpe02f8s/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
==> Total time spent: 35s <==
Writing to file /tmp/Rtmpe02f8s/file137bcb76703e87_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/Rtmpe02f8s/file137bcb76703e87_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/Rtmpe02f8s/file137bcb76703e87_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file /tmp/Rtmpe02f8s/file137bcb2807bfd1_counts_H4K20me1-BN-rep1.wig.gz ... 0.18s
Writing to file /tmp/Rtmpe02f8s/file137bcb2807bfd1_counts_H4K20me1-BN-rep2.wig.gz ... 0.19s
Writing to file /tmp/Rtmpe02f8s/file137bcb2807bfd1_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s
Writing to file /tmp/Rtmpe02f8s/file137bcb3ef43eac_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.2s
================
Binning the data
================
Obtaining chromosome length information from file /home/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 ... 0.04s
Making fixed-width bins for bin size 500 ... 0.06s
Binning data ... 9.66s
Binning control ... 0.93s
========================
Calling univariate peaks
========================
Univariate peak calling ... 6.59s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.28s
Getting combinatorial states ... 0.11s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.01s
Setting up parallel multivariate with 4 threads ... 0.25s
Running multivariate ... 13.99s
Merging chromosomes ... 0.27s
Saving to file /tmp/Rtmpe02f8s/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.55s
Making plots ... 0.11s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.15s
Concatenating conditions ... 0.08s
Reassigning levels ... 0s
Assigning transition groups ... 0.05s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.08s
Making segmentation ... 0.2s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.83s
Redoing segmentation for each condition separately ... 0.05s
Saving to file /tmp/Rtmpe02f8s/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.47s
Plotting read count correlation ... 0.21s
=======================
Exporting browser files
=======================
Writing to file /tmp/Rtmpe02f8s/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s
Writing to file /tmp/Rtmpe02f8s/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/Rtmpe02f8s/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s
Writing to file /tmp/Rtmpe02f8s/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/Rtmpe02f8s/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.02s
==> Total time spent: 36s <==
Ensembl site unresponsive, trying www mirror
Quitting from lines 377-397 (chromstaR.Rnw) 
Error: processing vignette 'chromstaR.Rnw' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building ‘chromstaR.Rnw’

SUMMARY: processing the following file failed:
  ‘chromstaR.Rnw’

Error: Vignette re-building failed.
Execution halted