############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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