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### Running command:
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### chmod a+r chromstaR -R && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data chromstaR
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* 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
