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This page was generated on 2021-09-24 15:06:36 -0400 (Fri, 24 Sep 2021).

BUILD results for chromstaR on machv2

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
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raw results

Package 307/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.18.0  (landing page)
Aaron Taudt
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2021-09-23 11:14:36 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 11:18:08 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 212.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.02s
Making fixed-width bins for bin size 1000 ... 0.12s
Counting overlaps for binsize 1000 with offset 0 ... 0.29s
Counting overlaps for binsize 1000 with offset 500 ... 0.19s
Making bins with offsets ... 0.2s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 1.47s
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 0.18s
Calculating states from posteriors ... 0.18s
Making segmentation ... 0.1s
Calculating states from maximum-posterior in each peak ... 0.08s
Re-estimating maximum posterior in peaks ... 0.04s
Making segmentation ... 0.12s
Writing to file /tmp/RtmpoyrwC3/file222a60ce5ef2_peaks_track-1.bed.gz ... 0.09s
Writing to file /tmp/RtmpoyrwC3/file222acbb9385_counts_track-1.wig.gz ... 0.17s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.03s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.21s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Making bins with offsets ... 0.09s
Running Baum-Welch for offset = 0 ... 0.53s
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.19s
Calculating states from posteriors ... 0.16s
Making segmentation ... 0.09s
Calculating states from maximum-posterior in each peak ... 0.08s
Re-estimating maximum posterior in peaks ... 0.07s
Making segmentation ... 0.07s
Writing to file /tmp/RtmpoyrwC3/file222a22d426e9_peaks_track-1.bed.gz ... 0.09s
Writing to file /tmp/RtmpoyrwC3/file222a16469cdc_counts_track-1.wig.gz ... 0.23s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0s
Making fixed-width bins for bin size 1000 ... 0.07s
Counting overlaps for binsize 1000 with offset 0 ... 0.65s
Counting overlaps for binsize 1000 with offset 500 ... 0.62s
Making bins with offsets ... 0.59s
Running Baum-Welch for offset = 0 ... 0.58s
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.15s
Calculating states from posteriors ... 0.15s
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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.21s
Counting overlaps for binsize 1000 with offset 500 ... 0.2s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.06s
Counting overlaps for binsize 1000 with offset 0 ... 0.22s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.39s
Counting overlaps for binsize 1000 with offset 500 ... 0.38s
Reading header from /Library/Frameworks/R.framework/Versions/4.1/Resources/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 ... 0.52s
Counting overlaps for binsize 1000 with offset 500 ... 0.51s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.16s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.58s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.16s
Making segmentation ... 0.08s
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 ... 0.12s
Making segmentation ... 0.08s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.11s
Obtaining states for offset = 500 ... 0.63s
Calculating states from posteriors ... 0.12s
Making segmentation ... 0.07s
Getting coordinates ... 0s
Extracting read counts ... 0.18s
Getting combinatorial states ... 0.09s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.04s
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:  0.9s
Obtaining states for offset = 500 ... 0.37s
Collecting counts and posteriors over offsets ... 0.52s
Compiling coordinates, posteriors, states ... 0.11s
Adding combinations ... 0.03s
Making segmentation ... 0.24s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.14s
Time spent for chromosome = chr12: 3.99s
Merging chromosomes ... 0.15s
Getting coordinates ... 0s
Extracting read counts ... 0.18s
Getting combinatorial states ... 0.09s
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 ... 0.14s
Collecting counts and posteriors over offsets ... 0.51s
Compiling coordinates, posteriors, states ... 0.1s
Adding combinations ... 0.04s
Making segmentation ... 0.18s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.09s
Time spent for chromosome = chr12: 2.89s
Merging chromosomes ... 0.15s
Writing to file /tmp/RtmpoyrwC3/file222a3057acd5_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpoyrwC3/file222a3057acd5_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/RtmpoyrwC3/file222a3057acd5_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/RtmpoyrwC3/file222a4c13ecbe_counts_H3K27me3-SHR-rep1.wig.gz ... 0.17s
Writing to file /tmp/RtmpoyrwC3/file222a4c13ecbe_counts_H3K27me3-SHR-rep2.wig.gz ... 0.18s
Writing to file /tmp/RtmpoyrwC3/file222a4c13ecbe_counts_H3K27me3-SHR-rep3.wig.gz ... 0.2s
Setting up parallel execution with 4 threads ... 0.37s
================
Binning the data
================
Obtaining chromosome length information from file /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0s
Making fixed-width bins for bin size 1000 ... 0.05s
Making fixed-width bins for bin size 500 ... 0.07s
Binning data ... 14.1s
Binning control ... 2.15s
========================
Calling univariate peaks
========================
Univariate peak calling ... 8.67s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.04s
Extracting read counts ... 0.26s
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 ... 0.43s
Running multivariate ... 17.99s
Merging chromosomes ... 0.28s
Saving to file /tmp/RtmpoyrwC3/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.52s
Making plots ... 0.17s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.13s
Concatenating HMMs ... 0.09s
Making combinations ... 0.13s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.09s
Assigning combinatorial states ... 0.06s
Transferring counts and posteriors ... 0.08s
Making segmentation ... 0.17s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.1s
Redoing segmentation for each condition separately ... 0.61s
Saving to file /tmp/RtmpoyrwC3/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.35s
Plotting read count correlation ... 0.25s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpoyrwC3/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.03s
Writing to file /tmp/RtmpoyrwC3/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file /tmp/RtmpoyrwC3/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpoyrwC3/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/RtmpoyrwC3/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0.01s
==> Total time spent: 48s <==
Writing to file /tmp/RtmpoyrwC3/file222a74852f54_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/RtmpoyrwC3/file222a74852f54_peaks_H4K20me1-BN-rep2.bed.gz ... 0.01s
Writing to file /tmp/RtmpoyrwC3/file222a74852f54_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file /tmp/RtmpoyrwC3/file222a53e66f8f_counts_H4K20me1-BN-rep1.wig.gz ... 0.27s
Writing to file /tmp/RtmpoyrwC3/file222a53e66f8f_counts_H4K20me1-BN-rep2.wig.gz ... 0.2s
Writing to file /tmp/RtmpoyrwC3/file222a53e66f8f_counts_H4K20me1-SHR-rep1.wig.gz ... 0.2s
Writing to file /tmp/RtmpoyrwC3/file222a3da64051_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.4s
================
Binning the data
================
Obtaining chromosome length information from file /Library/Frameworks/R.framework/Versions/4.1/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.06s
Making fixed-width bins for bin size 500 ... 0.06s
Binning data ... 13.99s
Binning control ... 1.17s
========================
Calling univariate peaks
========================
Univariate peak calling ... 8.6s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.03s
Extracting read counts ... 0.44s
Getting combinatorial states ... 0.16s
Computing pre z-matrix ... 0.01s
Transfering values into z-matrix ... 0.05s
Computing inverse of correlation matrix ... 0.02s
Setting up parallel multivariate with 4 threads ... 0.44s
Running multivariate ... 18.36s
Merging chromosomes ... 0.29s
Saving to file /tmp/RtmpoyrwC3/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.77s
Making plots ... 0.19s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.23s
Concatenating conditions ... 0.07s
Reassigning levels ... 0s
Assigning transition groups ... 0.06s
Assigning combinatorial states ... 0.05s
Transferring counts and posteriors ... 0.08s
Making segmentation ... 0.4s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.12s
Redoing segmentation for each condition separately ... 0.05s
Saving to file /tmp/RtmpoyrwC3/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.55s
Plotting read count correlation ... 0.31s
=======================
Exporting browser files
=======================
Writing to file /tmp/RtmpoyrwC3/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.06s
Writing to file /tmp/RtmpoyrwC3/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/RtmpoyrwC3/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s
Writing to file /tmp/RtmpoyrwC3/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/RtmpoyrwC3/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s
==> Total time spent: 48s <==
Quitting from lines 377-397 (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.
http://may2012.archive.ensembl.org:80/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