############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r chromstaR -R && F:\biocbuild\bbs-3.15-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 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 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 F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.31s Making fixed-width bins for bin size 1000 ... 0.19s Counting overlaps for binsize 1000 with offset 0 ... 0.27s Counting overlaps for binsize 1000 with offset 500 ... 0.16s Making bins with offsets ... 0.73s 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 ... 0.1s Obtaining states for offset = 500 ... 0.11s Calculating states from posteriors ... 0.09s Making segmentation ... 0.08s !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. Calculating states from maximum-posterior in each peak ... 0.05s Re-estimating maximum posterior in peaks ... 0.03s Making segmentation ... 0.08s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d0e09f_peaks_track-1.bed.gz ... 0.04s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d0331e135_counts_track-1.wig.gz ... 0.17s Reading header from F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.06s Making fixed-width bins for bin size 1000 ... 0.05s Counting overlaps for binsize 1000 with offset 0 ... 0.17s Counting overlaps for binsize 1000 with offset 500 ... 0.22s Making bins with offsets ... 0.07s Running Baum-Welch for offset = 0 ... 0.45s Collecting counts and posteriors ... 0.69s Obtaining states for offset = 500 ... 0.11s Calculating states from posteriors ... 0.08s Making segmentation ... 0.04s !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. Calculating states from maximum-posterior in each peak ... 0.03s Re-estimating maximum posterior in peaks ... 0.05s Making segmentation ... 0.05s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d0132d16a3_peaks_track-1.bed.gz ... 0.03s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d014392822_counts_track-1.wig.gz ... 0.2s Reading header from F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.05s Making fixed-width bins for bin size 1000 ... 0.67s Counting overlaps for binsize 1000 with offset 0 ... 12.74s Counting overlaps for binsize 1000 with offset 500 ... 0.53s Making bins with offsets ... 0.06s Running Baum-Welch for offset = 0 ... 0.61s Collecting counts and posteriors ... 0.08s Obtaining states for offset = 500 ... 0.12s Calculating states from posteriors ... 0.08s Making segmentation ... 0.04s !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. 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") !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. Reading header from F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.03s Making fixed-width bins for bin size 1000 ... 0.05s Counting overlaps for binsize 1000 with offset 0 ... 1.97s Counting overlaps for binsize 1000 with offset 500 ... 0.22s Reading header from F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.05s Making fixed-width bins for bin size 1000 ... 0.03s Counting overlaps for binsize 1000 with offset 0 ... 2.47s Counting overlaps for binsize 1000 with offset 500 ... 0.18s Reading header from F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 3.84s Making fixed-width bins for bin size 1000 ... 0.03s Counting overlaps for binsize 1000 with offset 0 ... 4.55s Counting overlaps for binsize 1000 with offset 500 ... 0.35s Reading header from F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 2.11s Making fixed-width bins for bin size 1000 ... 0.05s Counting overlaps for binsize 1000 with offset 0 ... 4.86s Counting overlaps for binsize 1000 with offset 500 ... 0.63s Making bins with offsets ... 0.1s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.09s Obtaining states for offset = 500 ... 0.19s Calculating states from posteriors ... 0.1s 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 ... 0.14s Calculating states from posteriors ... 0.09s Making segmentation ... 0.07s Making bins with offsets ... 0.06s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.1s Obtaining states for offset = 500 ... 0.76s Calculating states from posteriors ... 0.09s Making segmentation ... 0.05s Making bins with offsets ... 0.11s ------------------------------------ Try 1 of 1 ------------------------------------- Collecting counts and posteriors ... 0.09s Obtaining states for offset = 500 ... 0.12s Calculating states from posteriors ... 0.08s Making segmentation ... 0.05s Getting coordinates ... 0s Extracting read counts ... 0.11s Getting combinatorial states ... 0.08s 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: 1.66s Obtaining states for offset = 500 ... 0.47s Collecting counts and posteriors over offsets ... 0.69s Compiling coordinates, posteriors, states ... 0.12s Adding combinations ... 0.02s Making segmentation ... 0.15s Adding differential score ... 0.02s Getting maximum posterior in peaks ... 0.05s Obtaining peaks ... 0.07s Time spent for chromosome = chr12: 5.11s Merging chromosomes ... 0.08s Getting coordinates ... 0s Extracting read counts ... 0.11s Getting combinatorial states ... 0.08s Computing pre z-matrix ... 0s 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: 0.17s Obtaining states for offset = 500 ... 0.11s Collecting counts and posteriors over offsets ... 0.63s Compiling coordinates, posteriors, states ... 0.09s Adding combinations ... 0.02s Making segmentation ... 0.11s Adding differential score ... 0.01s Getting maximum posterior in peaks ... 0.06s Obtaining peaks ... 0.05s Time spent for chromosome = chr12: 3.14s Merging chromosomes ... 0.08s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d01e127577_peaks_H3K27me3-SHR-rep1.bed.gz ... 0s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d01e127577_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d01e127577_peaks_H3K27me3-SHR-rep3.bed.gz ... 0s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d03a03116e_counts_H3K27me3-SHR-rep1.wig.gz ... 0.18s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d03a03116e_counts_H3K27me3-SHR-rep2.wig.gz ... 0.19s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d03a03116e_counts_H3K27me3-SHR-rep3.wig.gz ... 0.2s Setting up parallel execution with 4 threads ... 0.31s ================ Binning the data ================ Obtaining chromosome length information from file F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0s Making fixed-width bins for bin size 1000 ... 0.03s Making fixed-width bins for bin size 500 ... 0.06s Binning data ... 20.88s Binning control ... 4.28s ======================== Calling univariate peaks ======================== Univariate peak calling ... 6.11s ========================== Calling multivariate peaks ========================== mode = differential --------------- mark = H4K20me1 --------------- Getting coordinates ... 0.01s Extracting read counts ... 0.17s Getting combinatorial states ... 0.07s 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 ... 0.35s Running multivariate ... 13.12s Merging chromosomes ... 0.13s Saving to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.37s Making plots ... 0.17s =========================== Combining multivariate HMMs =========================== Processing HMM 1 ... 0.09s Concatenating HMMs ... 0.08s Making combinations ... 0.16s Reassigning levels ... 0.01s Assigning transition groups ... 0.05s Assigning combinatorial states ... 0.01s Transferring counts and posteriors ... 0.05s Making segmentation ... 0.11s Adding differential score ... 0.01s Getting maximum posterior in peaks ... 0.07s Redoing segmentation for each condition separately ... 0.06s Saving to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.26s Plotting read count correlation ... 0.28s ======================= Exporting browser files ======================= Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.04s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0.02s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s ==> Total time spent: 48s <== Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d037b825c5_peaks_H4K20me1-BN-rep1.bed.gz ... 0s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d037b825c5_peaks_H4K20me1-BN-rep2.bed.gz ... 0s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d037b825c5_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d07c1448ac_counts_H4K20me1-BN-rep1.wig.gz ... 0.18s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d07c1448ac_counts_H4K20me1-BN-rep2.wig.gz ... 0.19s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d07c1448ac_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4\file31d06ef23f03_combinations.bed.gz ... 0s Setting up parallel execution with 4 threads ... 0.31s ================ Binning the data ================ Obtaining chromosome length information from file F:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0s Making fixed-width bins for bin size 1000 ... 0.05s Making fixed-width bins for bin size 500 ... 0.04s Binning data ... 14.06s Binning control ... 0.67s ======================== Calling univariate peaks ======================== Univariate peak calling ... 6.32s ========================== Calling multivariate peaks ========================== mode = combinatorial --------------- condition = SHR --------------- Getting coordinates ... 0.05s Extracting read counts ... 0.23s Getting combinatorial states ... 0.14s Computing pre z-matrix ... 0s Transfering values into z-matrix ... 0.04s Computing inverse of correlation matrix ... 0.01s Setting up parallel multivariate with 4 threads ... 0.31s Running multivariate ... 14.77s Merging chromosomes ... 1s Saving to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.51s Making plots ... 0.13s =========================== Combining multivariate HMMs =========================== Processing condition 1 ... 0.11s Concatenating conditions ... 0.09s Reassigning levels ... 0s Assigning transition groups ... 0.05s Assigning combinatorial states ... 0.03s Transferring counts and posteriors ... 0.03s Making segmentation ... 0.22s Adding differential score ... 0.01s Getting maximum posterior in peaks ... 0.07s Redoing segmentation for each condition separately ... 0.04s Saving to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.39s Plotting read count correlation ... 0.33s ======================= Exporting browser files ======================= Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.09s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.03s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.01s Writing to file F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpITsaK4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s ==> Total time spent: 41s <== !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. Ensembl site unresponsive, trying useast mirror Enrichment inside of annotations ... 1.29s Enrichment 15000bp before annotations 0.11s Enrichment 15000bp after annotations 0.11s Enrichment 10000bp before annotations 0.1s Enrichment 10000bp before annotations 0.14s !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. Overlaps with annotation ... 0.15s Getting surrounding indices ... 0.13s Getting read counts 0.03s Making the plot ... 0.16s !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. !!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)! pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user. Ensembl site unresponsive, trying asia mirror Quitting from lines 431-462 (chromstaR.Rnw) Error: processing vignette 'chromstaR.Rnw' failed with diagnostics: Gateway Timeout (HTTP 504). --- failed re-building 'chromstaR.Rnw' SUMMARY: processing the following file failed: 'chromstaR.Rnw' Error: Vignette re-building failed. Execution halted