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This page was generated on 2021-09-22 15:04:48 -0400 (Wed, 22 Sep 2021).

BUILD results for chromstaR on nebbiolo1

To the developers/maintainers of the chromstaR package:
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raw results

Package 307/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.18.0  (landing page)
Aaron Taudt
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/chromstaR
git_branch: RELEASE_3_13
git_last_commit: 8f44dd4
git_last_commit_date: 2021-05-19 12:21:16 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: chromstaR
Version: 1.18.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2021-09-21 06:56:51 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 06:59:28 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 156.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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 ... 0.11s
Counting overlaps for binsize 1000 with offset 0 ... 0.27s
Counting overlaps for binsize 1000 with offset 500 ... 0.18s
Making bins with offsets ... 0.65s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 0.83s
Collecting counts and posteriors ... 0.1s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.12s
Making segmentation ... 0.62s
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 /tmp/RtmpTM5Usk/file22bdc3691c07d7_peaks_track-1.bed.gz ... 0.07s
Writing to file /tmp/RtmpTM5Usk/file22bdc3605f0f33_counts_track-1.wig.gz ... 0.15s
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 ... 0.2s
Counting overlaps for binsize 1000 with offset 500 ... 0.2s
Making bins with offsets ... 0.06s
Running Baum-Welch for offset = 0 ... 0.43s
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.12s
Calculating states from posteriors ... 0.1s
Making segmentation ... 0.05s
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/RtmpTM5Usk/file22bdc36c82cfac_peaks_track-1.bed.gz ... 0.07s
Writing to file /tmp/RtmpTM5Usk/file22bdc34610e624_counts_track-1.wig.gz ... 0.19s
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 ... 0.59s
Making bins with offsets ... 0.81s
Running Baum-Welch for offset = 0 ... 0.57s
Collecting counts and posteriors ... 0.09s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.06s
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 ... 0.21s
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 ... 0.24s
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 ... 0.41s
Counting overlaps for binsize 1000 with offset 500 ... 0.4s
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 ... 0.63s
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 ... 0.14s
Calculating states from posteriors ... 0.11s
Making segmentation ... 0.05s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.1s
Obtaining states for offset = 500 ... 0.7s
Calculating states from posteriors ... 0.1s
Making segmentation ... 0.07s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.1s
Making segmentation ... 0.05s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.1s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.1s
Making segmentation ... 0.06s
Getting coordinates ... 0s
Extracting read counts ... 0.16s
Getting combinatorial states ... 0.71s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.04s
------------------
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:  0.85s
Obtaining states for offset = 500 ... 0.32s
Collecting counts and posteriors over offsets ... 0.66s
Compiling coordinates, posteriors, states ... 0.1s
Adding combinations ... 0.03s
Making segmentation ... 0.13s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.06s
Obtaining peaks ... 0.09s
Time spent for chromosome = chr12: 4.37s
Merging chromosomes ... 0.11s
Getting coordinates ... 0s
Extracting read counts ... 0.13s
Getting combinatorial states ... 0.07s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.02s
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:  0.15s
Obtaining states for offset = 500 ... 0.11s
Collecting counts and posteriors over offsets ... 0.75s
Compiling coordinates, posteriors, states ... 0.1s
Adding combinations ... 0.03s
Making segmentation ... 0.11s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.06s
Obtaining peaks ... 0.07s
Time spent for chromosome = chr12: 3.6s
Merging chromosomes ... 0.1s
Writing to file /tmp/RtmpTM5Usk/file22bdc3fe97035_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpTM5Usk/file22bdc3fe97035_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/RtmpTM5Usk/file22bdc3fe97035_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/RtmpTM5Usk/file22bdc39c22a41_counts_H3K27me3-SHR-rep1.wig.gz ... 0.18s
Writing to file /tmp/RtmpTM5Usk/file22bdc39c22a41_counts_H3K27me3-SHR-rep2.wig.gz ... 0.17s
Writing to file /tmp/RtmpTM5Usk/file22bdc39c22a41_counts_H3K27me3-SHR-rep3.wig.gz ... 0.17s
Setting up parallel execution with 4 threads ... 0.21s
================
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 ... 0s
Making fixed-width bins for bin size 1000 ... 0.04s
Making fixed-width bins for bin size 500 ... 0.06s
Binning data ... 11.38s
Binning control ... 1.53s
========================
Calling univariate peaks
========================
Univariate peak calling ... 5.88s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.2s
Getting combinatorial states ... 0.09s
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 ... 0.2s
Running multivariate ... 15.17s
Merging chromosomes ... 0.2s
Saving to file /tmp/RtmpTM5Usk/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.43s
Making plots ... 0.13s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.1s
Concatenating HMMs ... 0.09s
Making combinations ... 0.14s
Reassigning levels ... 0s
Assigning transition groups ... 0.07s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.06s
Making segmentation ... 0.13s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.88s
Redoing segmentation for each condition separately ... 0.08s
Saving to file /tmp/RtmpTM5Usk/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.29s
Plotting read count correlation ... 0.2s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpTM5Usk/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.02s
Writing to file /tmp/RtmpTM5Usk/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file /tmp/RtmpTM5Usk/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpTM5Usk/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/RtmpTM5Usk/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
==> Total time spent: 38s <==
Writing to file /tmp/RtmpTM5Usk/file22bdc3492c5b70_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpTM5Usk/file22bdc3492c5b70_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/RtmpTM5Usk/file22bdc3492c5b70_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpTM5Usk/file22bdc35c2d3a68_counts_H4K20me1-BN-rep1.wig.gz ... 0.18s
Writing to file /tmp/RtmpTM5Usk/file22bdc35c2d3a68_counts_H4K20me1-BN-rep2.wig.gz ... 0.19s
Writing to file /tmp/RtmpTM5Usk/file22bdc35c2d3a68_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s
Writing to file /tmp/RtmpTM5Usk/file22bdc36a8f257a_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-3.13-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 ... 11.41s
Binning control ... 0.87s
========================
Calling univariate peaks
========================
Univariate peak calling ... 6.62s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.05s
Extracting read counts ... 0.25s
Getting combinatorial states ... 0.09s
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 ... 0.29s
Running multivariate ... 15.23s
Merging chromosomes ... 0.22s
Saving to file /tmp/RtmpTM5Usk/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.58s
Making plots ... 0.12s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.14s
Concatenating conditions ... 0.08s
Reassigning levels ... 0s
Assigning transition groups ... 0.05s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.09s
Making segmentation ... 0.24s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.11s
Redoing segmentation for each condition separately ... 0.05s
Saving to file /tmp/RtmpTM5Usk/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.44s
Plotting read count correlation ... 0.22s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpTM5Usk/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s
Writing to file /tmp/RtmpTM5Usk/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/RtmpTM5Usk/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s
Writing to file /tmp/RtmpTM5Usk/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpTM5Usk/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s
==> Total time spent: 38s <==
Ensembl site unresponsive, trying useast 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