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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.02s
Making fixed-width bins for bin size 1000 ... 0.14s
Counting overlaps for binsize 1000 with offset 0 ... 0.26s
Counting overlaps for binsize 1000 with offset 500 ... 0.19s
Making bins with offsets ... 0.61s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 0.85s
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 0.16s
Calculating states from posteriors ... 0.15s
Making segmentation ... 0.56s
Calculating states from maximum-posterior in each peak ... 0.08s
Re-estimating maximum posterior in peaks ... 0.05s
Making segmentation ... 0.12s
Writing to file /tmp/RtmpFmmvQR/filecc78265a8797_peaks_track-1.bed.gz ... 0.16s
Writing to file /tmp/RtmpFmmvQR/filecc7817bde2d_counts_track-1.wig.gz ... 0.18s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.04s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.22s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Making bins with offsets ... 0.09s
Running Baum-Welch for offset = 0 ... 0.5s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.17s
Calculating states from posteriors ... 0.14s
Making segmentation ... 0.07s
Calculating states from maximum-posterior in each peak ... 0.13s
Re-estimating maximum posterior in peaks ... 0.06s
Making segmentation ... 0.07s
Writing to file /tmp/RtmpFmmvQR/filecc7822f196d8_peaks_track-1.bed.gz ... 0.07s
Writing to file /tmp/RtmpFmmvQR/filecc7822e650d4_counts_track-1.wig.gz ... 0.2s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.06s
Counting overlaps for binsize 1000 with offset 0 ... 0.59s
Counting overlaps for binsize 1000 with offset 500 ... 0.57s
Making bins with offsets ... 0.07s
Running Baum-Welch for offset = 0 ... 0.58s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.17s
Calculating states from posteriors ... 0.15s
Making segmentation ... 0.07s
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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.21s
Counting overlaps for binsize 1000 with offset 500 ... 0.2s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.21s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.37s
Counting overlaps for binsize 1000 with offset 500 ... 0.37s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.49s
Counting overlaps for binsize 1000 with offset 500 ... 0.5s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.15s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.07s
Making bins with offsets ... 0.09s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.07s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.1s
Obtaining states for offset = 500 ... 0.15s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.57s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.12s
Making segmentation ... 0.07s
Getting coordinates ... 0s
Extracting read counts ... 0.22s
Getting combinatorial states ... 0.09s
Computing pre z-matrix ... 0s
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:  0.91s
Obtaining states for offset = 500 ... 0.38s
Collecting counts and posteriors over offsets ... 0.52s
Compiling coordinates, posteriors, states ... 0.11s
Adding combinations ... 0.03s
Making segmentation ... 0.23s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.13s
Time spent for chromosome = chr12: 3.98s
Merging chromosomes ... 0.16s
Getting coordinates ... 0s
Extracting read counts ... 0.18s
Getting combinatorial states ... 0.09s
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:  0.17s
Obtaining states for offset = 500 ... 0.11s
Collecting counts and posteriors over offsets ... 0.52s
Compiling coordinates, posteriors, states ... 0.1s
Adding combinations ... 0.03s
Making segmentation ... 0.18s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.1s
Time spent for chromosome = chr12: 2.85s
Merging chromosomes ... 0.14s
Writing to file /tmp/RtmpFmmvQR/filecc78723b27a2_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpFmmvQR/filecc78723b27a2_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/RtmpFmmvQR/filecc78723b27a2_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/RtmpFmmvQR/filecc789a73745_counts_H3K27me3-SHR-rep1.wig.gz ... 0.18s
Writing to file /tmp/RtmpFmmvQR/filecc789a73745_counts_H3K27me3-SHR-rep2.wig.gz ... 0.18s
Writing to file /tmp/RtmpFmmvQR/filecc789a73745_counts_H3K27me3-SHR-rep3.wig.gz ... 0.2s
Setting up parallel execution with 4 threads ... 0.36s
================
Binning the data
================
Obtaining chromosome length information from file /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0s
Making fixed-width bins for bin size 1000 ... 0.06s
Making fixed-width bins for bin size 500 ... 0.09s
Binning data ... 15.01s
Binning control ... 2.15s
========================
Calling univariate peaks
========================
Univariate peak calling ... 8.73s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.03s
Extracting read counts ... 0.33s
Getting combinatorial states ... 0.12s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.05s
Computing inverse of correlation matrix ... 0.01s
Setting up parallel multivariate with 4 threads ... 0.43s
Running multivariate ... 17.32s
Merging chromosomes ... 0.27s
Saving to file /tmp/RtmpFmmvQR/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.52s
Making plots ... 0.17s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.17s
Concatenating HMMs ... 0.63s
Making combinations ... 0.17s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.1s
Assigning combinatorial states ... 0.06s
Transferring counts and posteriors ... 0.08s
Making segmentation ... 0.2s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.11s
Redoing segmentation for each condition separately ... 0.11s
Saving to file /tmp/RtmpFmmvQR/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.38s
Plotting read count correlation ... 0.28s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpFmmvQR/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.04s
Writing to file /tmp/RtmpFmmvQR/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file /tmp/RtmpFmmvQR/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpFmmvQR/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/RtmpFmmvQR/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
==> Total time spent: 49s <==
Writing to file /tmp/RtmpFmmvQR/filecc7886287b5_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpFmmvQR/filecc7886287b5_peaks_H4K20me1-BN-rep2.bed.gz ... 0.01s
Writing to file /tmp/RtmpFmmvQR/filecc7886287b5_peaks_H4K20me1-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpFmmvQR/filecc787cbb805f_counts_H4K20me1-BN-rep1.wig.gz ... 0.2s
Writing to file /tmp/RtmpFmmvQR/filecc787cbb805f_counts_H4K20me1-BN-rep2.wig.gz ... 0.26s
Writing to file /tmp/RtmpFmmvQR/filecc787cbb805f_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s
Writing to file /tmp/RtmpFmmvQR/filecc7879e91cf2_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.41s
================
Binning the data
================
Obtaining chromosome length information from file /Library/Frameworks/R.framework/Versions/4.1/Resources/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 ... 0.08s
Binning data ... 14.93s
Binning control ... 1.29s
========================
Calling univariate peaks
========================
Univariate peak calling ... 9.21s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.03s
Extracting read counts ... 0.41s
Getting combinatorial states ... 0.14s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.02s
Setting up parallel multivariate with 4 threads ... 0.42s
Running multivariate ... 18.22s
Merging chromosomes ... 0.36s
Saving to file /tmp/RtmpFmmvQR/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.69s
Making plots ... 0.16s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.19s
Concatenating conditions ... 0.11s
Reassigning levels ... 0s
Assigning transition groups ... 0.57s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.08s
Making segmentation ... 0.32s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.1s
Redoing segmentation for each condition separately ... 0.05s
Saving to file /tmp/RtmpFmmvQR/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.54s
Plotting read count correlation ... 0.36s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpFmmvQR/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.08s
Writing to file /tmp/RtmpFmmvQR/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/RtmpFmmvQR/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.03s
Writing to file /tmp/RtmpFmmvQR/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/RtmpFmmvQR/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.02s
==> Total time spent: 50s <==
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