Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:06:58 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for chromstaR on riesling1


To the developers/maintainers of the chromstaR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromstaR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 311/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.21.4  (landing page)
Aaron Taudt
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/chromstaR
git_branch: master
git_last_commit: 79057fd
git_last_commit_date: 2021-12-14 21:44:02 -0500 (Tue, 14 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: chromstaR
Version: 1.21.4
Command: chmod a+r chromstaR -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2022-01-21 16:30:40 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 16:35:05 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 265.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r chromstaR -R && D:\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 D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.24s
Making fixed-width bins for bin size 1000 ... 0.09s
Counting overlaps for binsize 1000 with offset 0 ... 0.17s
Counting overlaps for binsize 1000 with offset 500 ... 0.13s
Making bins with offsets ... 0.55s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 0.77s
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.11s
Calculating states from posteriors ... 0.08s
Making segmentation ... 0.05s
Calculating states from maximum-posterior in each peak ... 0.04s
Re-estimating maximum posterior in peaks ... 0.01s
Making segmentation ... 0.06s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c70cd325f_peaks_track-1.bed.gz ... 0.03s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c447576af_counts_track-1.wig.gz ... 0.17s
Reading header from D:/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 ... 0.03s
Counting overlaps for binsize 1000 with offset 0 ... 0.14s
Counting overlaps for binsize 1000 with offset 500 ... 0.16s
Making bins with offsets ... 0.06s
Running Baum-Welch for offset = 0 ... 0.41s
Collecting counts and posteriors ... 0.06s
Obtaining states for offset = 500 ... 0.09s
Calculating states from posteriors ... 0.06s
Making segmentation ... 0.03s
Calculating states from maximum-posterior in each peak ... 0.03s
Re-estimating maximum posterior in peaks ... 0.03s
Making segmentation ... 0.05s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c5ba94b41_peaks_track-1.bed.gz ... 0.03s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c7d163fc_counts_track-1.wig.gz ... 0.15s
Reading header from D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.03s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.66s
Counting overlaps for binsize 1000 with offset 500 ... 0.46s
Making bins with offsets ... 0.05s
Running Baum-Welch for offset = 0 ... 0.5s
Collecting counts and posteriors ... 0.06s
Obtaining states for offset = 500 ... 0.58s
Calculating states from posteriors ... 0.08s
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 D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.06s
Making fixed-width bins for bin size 1000 ... 0.03s
Counting overlaps for binsize 1000 with offset 0 ... 0.2s
Counting overlaps for binsize 1000 with offset 500 ... 0.14s
Reading header from D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.02s
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 ... 0.18s
Reading header from D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.08s
Making fixed-width bins for bin size 1000 ... 0.03s
Counting overlaps for binsize 1000 with offset 0 ... 0.4s
Counting overlaps for binsize 1000 with offset 500 ... 0.3s
Reading header from D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.1s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.58s
Counting overlaps for binsize 1000 with offset 500 ... 0.4s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.09s
Calculating states from posteriors ... 0.06s
Making segmentation ... 0.03s
Making bins with offsets ... 0.55s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.1s
Calculating states from posteriors ... 0.08s
Making segmentation ... 0.04s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.06s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.06s
Making segmentation ... 0.03s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.09s
Calculating states from posteriors ... 0.07s
Making segmentation ... 0.03s
Getting coordinates ... 0s
Extracting read counts ... 0.09s
Getting combinatorial states ... 0.05s
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:  0.92s
Obtaining states for offset = 500 ... 0.38s
Collecting counts and posteriors over offsets ... 0.5s
Compiling coordinates, posteriors, states ... 0.08s
Adding combinations ... 0.01s
Making segmentation ... 0.11s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.05s
Obtaining peaks ... 0.04s
Time spent for chromosome = chr12: 3.53s
Merging chromosomes ... 0.08s
Getting coordinates ... 0s
Extracting read counts ... 0.07s
Getting combinatorial states ... 0.05s
Computing pre z-matrix ... 0.02s
Transfering values into z-matrix ... 0.01s
Computing inverse of correlation matrix ... 0s
------------------
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 ... 0.09s
Collecting counts and posteriors over offsets ... 0.49s
Compiling coordinates, posteriors, states ... 0.08s
Adding combinations ... 0.01s
Making segmentation ... 0.1s
Adding differential score ... 0s
Getting maximum posterior in peaks ... 0.04s
Obtaining peaks ... 0.05s
Time spent for chromosome = chr12: 2.44s
Merging chromosomes ... 0.05s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c66e3492a_peaks_H3K27me3-SHR-rep1.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c66e3492a_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c66e3492a_peaks_H3K27me3-SHR-rep3.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c48816c0c_counts_H3K27me3-SHR-rep1.wig.gz ... 0.17s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c48816c0c_counts_H3K27me3-SHR-rep2.wig.gz ... 0.17s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c48816c0c_counts_H3K27me3-SHR-rep3.wig.gz ... 0.19s
Setting up parallel execution with 4 threads ... 0.18s
================
Binning the data
================
Obtaining chromosome length information from file D:/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 ... 0.05s
Binning data ... 8.51s
Binning control ... 1.11s
========================
Calling univariate peaks
========================
Univariate peak calling ... 5.39s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.04s
Extracting read counts ... 0.15s
Getting combinatorial states ... 0.06s
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 ... 0.2s
Running multivariate ... 9.91s
Merging chromosomes ... 0.11s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.33s
Making plots ... 0.11s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.09s
Concatenating HMMs ... 0.1s
Making combinations ... 0.13s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.06s
Assigning combinatorial states ... 0.02s
Transferring counts and posteriors ... 0.03s
Making segmentation ... 0.09s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.05s
Redoing segmentation for each condition separately ... 0.54s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.24s
Plotting read count correlation ... 0.17s
=======================
Exporting browser files
=======================
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.03s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
==> Total time spent: 28s <==
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c14d71c03_peaks_H4K20me1-BN-rep1.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c14d71c03_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c14d71c03_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c64a94a13_counts_H4K20me1-BN-rep1.wig.gz ... 0.17s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c64a94a13_counts_H4K20me1-BN-rep2.wig.gz ... 0.18s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c64a94a13_counts_H4K20me1-SHR-rep1.wig.gz ... 0.15s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c10f559bc_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.17s
================
Binning the data
================
Obtaining chromosome length information from file D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.03s
Making fixed-width bins for bin size 500 ... 0.05s
Binning data ... 8.36s
Binning control ... 0.66s
========================
Calling univariate peaks
========================
Univariate peak calling ... 5.39s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.03s
Extracting read counts ... 0.78s
Getting combinatorial states ... 0.06s
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 ... 10.77s
Merging chromosomes ... 0.12s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.39s
Making plots ... 0.11s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.11s
Concatenating conditions ... 0.08s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.04s
Assigning combinatorial states ... 0.03s
Transferring counts and posteriors ... 0.03s
Making segmentation ... 0.19s
Adding differential score ... 0.01s
Getting maximum posterior in peaks ... 0.05s
Redoing segmentation for each condition separately ... 0.03s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.34s
Plotting read count correlation ... 0.19s
=======================
Exporting browser files
=======================
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s
==> Total time spent: 29s <==
Enrichment inside of annotations ... 0.97s
Enrichment 15000bp before annotations 0.08s
Enrichment 15000bp after annotations 0.07s
Enrichment 10000bp before annotations 0.06s
Enrichment 10000bp before annotations 0.08s
Overlaps with annotation ... 0.07s
Getting surrounding indices ... 0.13s
Getting read counts 0.03s
Making the plot ... 0.12s
Setting up parallel execution with 4 threads ... 0.17s
================
Binning the data
================
Obtaining chromosome length information from file D:/biocbuild/bbs-3.15-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0s
Making fixed-width bins for bin size 1000 ... 0.03s
Making fixed-width bins for bin size 500 ... 0.05s
Binning data ... 7.95s
Binning control ... 0.89s
========================
Calling univariate peaks
========================
Univariate peak calling ... 7.45s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H3K27me3
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.15s
Getting combinatorial states ... 0.07s
Computing pre z-matrix ... 0.01s
Transfering values into z-matrix ... 0.11s
Computing inverse of correlation matrix ... 0.02s
Setting up parallel multivariate with 4 threads ... 0.2s
Running multivariate ... 10.08s
Merging chromosomes ... 0.56s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/multivariate/multivariate_mode-differential_mark-H3K27me3_binsize1000_stepsize500.RData ... 0.45s
Making plots ... 0.1s
--------------
mark = H3K4me3
--------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.14s
Getting combinatorial states ... 0.08s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.01s
Computing inverse of correlation matrix ... 0.02s
Setting up parallel multivariate with 4 threads ... 0.2s
Running multivariate ... 10.02s
Merging chromosomes ... 0.11s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/multivariate/multivariate_mode-differential_mark-H3K4me3_binsize1000_stepsize500.RData ... 0.36s
Making plots ... 0.09s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.09s
Processing HMM 2 ... 0.1s
Concatenating HMMs ... 0.11s
Making combinations ... 0.74s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.05s
Assigning combinatorial states ... 0.02s
Transferring counts and posteriors ... 0.03s
Making segmentation ... 0.22s
Adding differential score ... 0.01s
Getting maximum posterior in peaks ... 0.09s
Redoing segmentation for each condition separately ... 0.05s
Saving to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.55s
Plotting read count correlation ... 0.19s
=======================
Exporting browser files
=======================
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.06s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.06s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K27me3-BN-rep1.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K27me3-BN-rep2.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K4me3-BN-rep1.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K4me3-BN-rep2.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.02s
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP/SHR-BN-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s
==> Total time spent: 42s <==
Writing to file D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp42ghEP\file42c665533df.bed.gz ... 0.02s
Ensembl site unresponsive, trying useast mirror
Quitting from lines 536-555 (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.
https://www.ensembl.org:443/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