############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/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 Attaching package: 'BiocGenerics' 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-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.02s Making fixed-width bins for bin size 1000 ... 0.13s Counting overlaps for binsize 1000 with offset 0 ... 0.28s Counting overlaps for binsize 1000 with offset 500 ... 0.21s Making bins with offsets ... 0.32s Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff'). Running Baum-Welch for offset = 0 ... 2.59s Collecting counts and posteriors ... 0.16s Obtaining states for offset = 500 ... 0.2s Calculating states from posteriors ... 0.19s Making segmentation ... 0.09s Calculating states from maximum-posterior in each peak ... 0.11s Re-estimating maximum posterior in peaks ... 0.07s Making segmentation ... 0.13s Writing to file /tmp/Rtmp4gneft/file3ca67068ef122e_peaks_track-1.bed.gz ... 0.11s Writing to file /tmp/Rtmp4gneft/file3ca670592ed50c_counts_track-1.wig.gz ... 0.19s Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.04s Making fixed-width bins for bin size 1000 ... 0.06s Counting overlaps for binsize 1000 with offset 0 ... 0.24s Counting overlaps for binsize 1000 with offset 500 ... 0.25s Making bins with offsets ... 0.13s Running Baum-Welch for offset = 0 ... 0.55s Collecting counts and posteriors ... 0.13s Obtaining states for offset = 500 ... 0.2s Calculating states from posteriors ... 0.17s Making segmentation ... 0.07s Calculating states from maximum-posterior in each peak ... 0.07s Re-estimating maximum posterior in peaks ... 0.08s Making segmentation ... 0.09s Writing to file /tmp/Rtmp4gneft/file3ca6702b895e82_peaks_track-1.bed.gz ... 0.09s Writing to file /tmp/Rtmp4gneft/file3ca6704749143d_counts_track-1.wig.gz ... 0.18s Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s Making fixed-width bins for bin size 1000 ... 0.09s Counting overlaps for binsize 1000 with offset 0 ... 0.62s Counting overlaps for binsize 1000 with offset 500 ... 0.59s Making bins with offsets ... 0.11s Running Baum-Welch for offset = 0 ... 0.57s Collecting counts and posteriors ... 0.15s Obtaining states for offset = 500 ... 0.2s Calculating states from posteriors ... 0.18s 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 /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s 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 ... 0.22s Reading header from /home/biocbuild/bbs-3.14-bioc/R/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 ... 0.24s Counting overlaps for binsize 1000 with offset 500 ... 0.24s Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.01s Making fixed-width bins for bin size 1000 ... 0.08s Counting overlaps for binsize 1000 with offset 0 ... 0.42s Counting overlaps for binsize 1000 with offset 500 ... 0.4s Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.01s Making fixed-width bins for bin size 1000 ... 0.07s Counting overlaps for binsize 1000 with offset 0 ... 0.56s Counting overlaps for binsize 1000 with offset 500 ... 0.55s Making bins with offsets ... 0.14s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.13s Obtaining states for offset = 500 ... 1.93s Calculating states from posteriors ... 0.13s Making segmentation ... 0.08s Making bins with offsets ... 0.07s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.12s Obtaining states for offset = 500 ... 0.17s Calculating states from posteriors ... 0.15s Making segmentation ... 0.06s Making bins with offsets ... 0.08s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.19s Obtaining states for offset = 500 ... 0.2s Calculating states from posteriors ... 0.16s Making segmentation ... 0.09s Making bins with offsets ... 0.1s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.13s Obtaining states for offset = 500 ... 1.9s Calculating states from posteriors ... 0.13s Making segmentation ... 0.09s Getting coordinates ... 0s Extracting read counts ... 0.19s Getting combinatorial states ... 0.1s Computing pre z-matrix ... 0s Transfering values into z-matrix ... 0.05s 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: 1.44s Obtaining states for offset = 500 ... 0.54s Collecting counts and posteriors over offsets ... 1.58s Compiling coordinates, posteriors, states ... 0.13s Adding combinations ... 0.04s Making segmentation ... 0.2s Adding differential score ... 0.03s Getting maximum posterior in peaks ... 0.09s Obtaining peaks ... 0.12s Time spent for chromosome = chr12: 8.51s Merging chromosomes ... 0.16s Getting coordinates ... 0s Extracting read counts ... 0.19s Getting combinatorial states ... 0.14s 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: 0.21s Obtaining states for offset = 500 ... 0.15s Collecting counts and posteriors over offsets ... 1.1s Compiling coordinates, posteriors, states ... 0.13s Adding combinations ... 0.04s Making segmentation ... 0.15s Adding differential score ... 0.02s Getting maximum posterior in peaks ... 0.09s Obtaining peaks ... 0.08s Time spent for chromosome = chr12: 5.75s Merging chromosomes ... 0.15s Writing to file /tmp/Rtmp4gneft/file3ca670698e04a7_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s Writing to file /tmp/Rtmp4gneft/file3ca670698e04a7_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s Writing to file /tmp/Rtmp4gneft/file3ca670698e04a7_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s Writing to file /tmp/Rtmp4gneft/file3ca670363e2c6_counts_H3K27me3-SHR-rep1.wig.gz ... 0.2s Writing to file /tmp/Rtmp4gneft/file3ca670363e2c6_counts_H3K27me3-SHR-rep2.wig.gz ... 0.2s Writing to file /tmp/Rtmp4gneft/file3ca670363e2c6_counts_H3K27me3-SHR-rep3.wig.gz ... 0.2s Setting up parallel execution with 4 threads ... 0.28s ================ Binning the data ================ Obtaining chromosome length information from file /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-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 ... 13.52s Binning control ... 1.42s ======================== Calling univariate peaks ======================== Univariate peak calling ... 7.17s ========================== Calling multivariate peaks ========================== mode = differential --------------- mark = H4K20me1 --------------- Getting coordinates ... 0.02s Extracting read counts ... 0.24s Getting combinatorial states ... 0.08s 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 ... 0.22s Running multivariate ... 16.93s Merging chromosomes ... 0.2s Saving to file /tmp/Rtmp4gneft/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.4s Making plots ... 0.21s =========================== Combining multivariate HMMs =========================== Processing HMM 1 ... 0.1s Concatenating HMMs ... 0.11s Making combinations ... 0.16s Reassigning levels ... 0.01s Assigning transition groups ... 0.09s Assigning combinatorial states ... 0.06s Transferring counts and posteriors ... 0.09s Making segmentation ... 0.16s Adding differential score ... 0.03s Getting maximum posterior in peaks ... 0.1s Redoing segmentation for each condition separately ... 1.17s Saving to file /tmp/Rtmp4gneft/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.32s Plotting read count correlation ... 0.23s ======================= Exporting browser files ======================= Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.02s Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0.01s ==> Total time spent: 44s <== Writing to file /tmp/Rtmp4gneft/file3ca670148f25ee_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s Writing to file /tmp/Rtmp4gneft/file3ca670148f25ee_peaks_H4K20me1-BN-rep2.bed.gz ... 0s Writing to file /tmp/Rtmp4gneft/file3ca670148f25ee_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s Writing to file /tmp/Rtmp4gneft/file3ca6705953cfb8_counts_H4K20me1-BN-rep1.wig.gz ... 0.18s Writing to file /tmp/Rtmp4gneft/file3ca6705953cfb8_counts_H4K20me1-BN-rep2.wig.gz ... 0.18s Writing to file /tmp/Rtmp4gneft/file3ca6705953cfb8_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s Writing to file /tmp/Rtmp4gneft/file3ca67072e40d7b_combinations.bed.gz ... 0s Setting up parallel execution with 4 threads ... 0.23s ================ Binning the data ================ Obtaining chromosome length information from file /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s Making fixed-width bins for bin size 1000 ... 0.05s Making fixed-width bins for bin size 500 ... 0.06s Binning data ... 11.14s Binning control ... 0.94s ======================== Calling univariate peaks ======================== Univariate peak calling ... 8.66s ========================== Calling multivariate peaks ========================== mode = combinatorial --------------- condition = SHR --------------- Getting coordinates ... 0.03s Extracting read counts ... 0.27s Getting combinatorial states ... 0.1s 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 ... 0.28s Running multivariate ... 15.13s Merging chromosomes ... 0.25s Saving to file /tmp/Rtmp4gneft/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.54s Making plots ... 0.11s =========================== Combining multivariate HMMs =========================== Processing condition 1 ... 0.14s Concatenating conditions ... 0.09s Reassigning levels ... 0s Assigning transition groups ... 0.05s Assigning combinatorial states ... 0.04s Transferring counts and posteriors ... 0.08s Making segmentation ... 0.24s Adding differential score ... 0.02s Getting maximum posterior in peaks ... 1.1s Redoing segmentation for each condition separately ... 0.05s Saving to file /tmp/Rtmp4gneft/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.44s Plotting read count correlation ... 0.23s ======================= Exporting browser files ======================= Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.01s Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s ==> Total time spent: 41s <== Enrichment inside of annotations ... 1.25s Enrichment 15000bp before annotations 0.11s Enrichment 15000bp after annotations 0.09s Enrichment 10000bp before annotations 0.09s Enrichment 10000bp before annotations 0.08s Overlaps with annotation ... 0.13s Getting surrounding indices ... 0.21s Getting read counts 0.05s Making the plot ... 0.14s Ensembl site unresponsive, trying useast mirror Quitting from lines 431-462 (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