############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-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 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