############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R 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 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