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This page was generated on 2022-12-07 11:05:25 -0500 (Wed, 07 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4423
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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BUILD results for chromstaR on nebbiolo1


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? 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 319/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.25.0  (landing page)
Aaron Taudt
Snapshot Date: 2022-12-06 14:00:17 -0500 (Tue, 06 Dec 2022)
git_url: https://git.bioconductor.org/packages/chromstaR
git_branch: master
git_last_commit: 18c031d
git_last_commit_date: 2022-11-01 11:13:56 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: chromstaR
Version: 1.25.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2022-12-06 16:20:48 -0500 (Tue, 06 Dec 2022)
EndedAt: 2022-12-06 16:23:44 -0500 (Tue, 06 Dec 2022)
EllapsedTime: 175.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-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

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, aperm,
    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-3.17-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.02s
Making fixed-width bins for bin size 1000 ... 0.22s
Counting overlaps for binsize 1000 with offset 0 ... 1.13s
Counting overlaps for binsize 1000 with offset 500 ... 0.19s
Making bins with offsets ... 0.12s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 1.31s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.15s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.09s
Calculating states from maximum-posterior in each peak ... 0.06s
Re-estimating maximum posterior in peaks ... 0.06s
Making segmentation ... 0.08s
Writing to file /tmp/RtmpWis4A4/file7502a7c66a9c1_peaks_track-1.bed.gz ... 0.06s
Writing to file /tmp/RtmpWis4A4/file7502a648b39ea_counts_track-1.wig.gz ... 0.26s
Reading header from /home/biocbuild/bbs-3.17-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.23s
Counting overlaps for binsize 1000 with offset 500 ... 0.22s
Making bins with offsets ... 0.08s
Running Baum-Welch for offset = 0 ... 0.86s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 1.06s
Calculating states from posteriors ... 0.08s
Making segmentation ... 0.06s
Calculating states from maximum-posterior in each peak ... 0.04s
Re-estimating maximum posterior in peaks ... 0.04s
Making segmentation ... 0.07s
Writing to file /tmp/RtmpWis4A4/file7502a60d305f2_peaks_track-1.bed.gz ... 0.05s
Writing to file /tmp/RtmpWis4A4/file7502a5fdbe11b_counts_track-1.wig.gz ... 0.19s
Reading header from /home/biocbuild/bbs-3.17-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.04s
Counting overlaps for binsize 1000 with offset 0 ... 0.66s
Counting overlaps for binsize 1000 with offset 500 ... 0.64s
Making bins with offsets ... 0.07s
Running Baum-Welch for offset = 0 ... 0.77s
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.97s
Calculating states from posteriors ... 0.09s
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-3.17-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 ... 0.23s
Reading header from /home/biocbuild/bbs-3.17-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 ... 0.22s
Reading header from /home/biocbuild/bbs-3.17-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 ... 0.45s
Counting overlaps for binsize 1000 with offset 500 ... 0.45s
Reading header from /home/biocbuild/bbs-3.17-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.59s
Counting overlaps for binsize 1000 with offset 500 ... 0.58s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.09s
Obtaining states for offset = 500 ... 0.17s
Calculating states from posteriors ... 0.1s
Making segmentation ... 0.07s
Making bins with offsets ... 0.11s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.94s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.09s
Making segmentation ... 0.05s
Making bins with offsets ... 0.06s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.08s
Obtaining states for offset = 500 ... 0.13s
Calculating states from posteriors ... 0.08s
Making segmentation ... 0.05s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.9s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.08s
Making segmentation ... 0.04s
Getting coordinates ... 0s
Extracting read counts ... 0.13s
Getting combinatorial states ... 0.07s
Computing pre z-matrix ... 0s
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:  1.27s
Obtaining states for offset = 500 ... 0.46s
Collecting counts and posteriors over offsets ... 1.13s
Compiling coordinates, posteriors, states ... 0.1s
Adding combinations ... 0.02s
Making segmentation ... 0.15s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.06s
Obtaining peaks ... 0.08s
Time spent for chromosome = chr12: 6.2s
Merging chromosomes ... 0.1s
Getting coordinates ... 0s
Extracting read counts ... 0.12s
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 ... 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 ... 0.77s
Compiling coordinates, posteriors, states ... 0.09s
Adding combinations ... 0.02s
Making segmentation ... 0.11s
Adding differential score ... 0.01s
Getting maximum posterior in peaks ... 0.05s
Obtaining peaks ... 0.05s
Time spent for chromosome = chr12: 3.89s
Merging chromosomes ... 0.07s
Writing to file /tmp/RtmpWis4A4/file7502a68bb026c_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpWis4A4/file7502a68bb026c_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/RtmpWis4A4/file7502a68bb026c_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/RtmpWis4A4/file7502a3c763032_counts_H3K27me3-SHR-rep1.wig.gz ... 0.18s
Writing to file /tmp/RtmpWis4A4/file7502a3c763032_counts_H3K27me3-SHR-rep2.wig.gz ... 0.18s
Writing to file /tmp/RtmpWis4A4/file7502a3c763032_counts_H3K27me3-SHR-rep3.wig.gz ... 0.19s
Setting up parallel execution with 4 threads ... 0.25s
================
Binning the data
================
Obtaining chromosome length information from file /home/biocbuild/bbs-3.17-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.04s
Making fixed-width bins for bin size 500 ... 0.07s
Binning data ... 13.07s
Binning control ... 1.81s
========================
Calling univariate peaks
========================
Univariate peak calling ... 5.54s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.16s
Getting combinatorial states ... 0.06s
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 ... 0.22s
Running multivariate ... 13.75s
Merging chromosomes ... 0.16s
Saving to file /tmp/RtmpWis4A4/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.43s
Making plots ... 0.2s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.82s
Concatenating HMMs ... 0.08s
Making combinations ... 0.15s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.06s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.04s
Making segmentation ... 0.1s
Adding differential score ... 0.01s
Getting maximum posterior in peaks ... 0.06s
Redoing segmentation for each condition separately ... 0.06s
Saving to file /tmp/RtmpWis4A4/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.32s
Plotting read count correlation ... 0.29s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpWis4A4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.02s
Writing to file /tmp/RtmpWis4A4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file /tmp/RtmpWis4A4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpWis4A4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/RtmpWis4A4/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
==> Total time spent: 38s <==
Writing to file /tmp/RtmpWis4A4/file7502a68b01275_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpWis4A4/file7502a68b01275_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/RtmpWis4A4/file7502a68b01275_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpWis4A4/file7502a3a2785e_counts_H4K20me1-BN-rep1.wig.gz ... 0.18s
Writing to file /tmp/RtmpWis4A4/file7502a3a2785e_counts_H4K20me1-BN-rep2.wig.gz ... 0.18s
Writing to file /tmp/RtmpWis4A4/file7502a3a2785e_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s
Writing to file /tmp/RtmpWis4A4/file7502a6ee29f33_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.21s
================
Binning the data
================
Obtaining chromosome length information from file /home/biocbuild/bbs-3.17-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Making fixed-width bins for bin size 500 ... 0.06s
Binning data ... 11.12s
Binning control ... 0.66s
========================
Calling univariate peaks
========================
Univariate peak calling ... 5.7s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.17s
Getting combinatorial states ... 0.06s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.03s
Setting up parallel multivariate with 4 threads ... 0.23s
Running multivariate ... 14.71s
Merging chromosomes ... 0.16s
Saving to file /tmp/RtmpWis4A4/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.55s
Making plots ... 0.16s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.14s
Concatenating conditions ... 0.15s
Reassigning levels ... 0s
Assigning transition groups ... 0.04s
Assigning combinatorial states ... 0.03s
Transferring counts and posteriors ... 0.82s
Making segmentation ... 0.2s
Adding differential score ... 0.01s
Getting maximum posterior in peaks ... 0.07s
Redoing segmentation for each condition separately ... 0.03s
Saving to file /tmp/RtmpWis4A4/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.45s
Plotting read count correlation ... 0.29s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpWis4A4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s
Writing to file /tmp/RtmpWis4A4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/RtmpWis4A4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s
Writing to file /tmp/RtmpWis4A4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpWis4A4/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.02s
==> Total time spent: 37s <==
Quitting from lines 377-396 (chromstaR.Rnw) 
Error: processing vignette 'chromstaR.Rnw' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘chromstaR.Rnw’

SUMMARY: processing the following file failed:
  ‘chromstaR.Rnw’

Error: Vignette re-building failed.
Execution halted