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This page was generated on 2022-04-13 12:05:11 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 314/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.20.2  (landing page)
Aaron Taudt
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/chromstaR
git_branch: RELEASE_3_14
git_last_commit: b8ef93b
git_last_commit_date: 2021-11-03 04:34:25 -0400 (Wed, 03 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chromstaR
Version: 1.20.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2022-04-12 04:10:07 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 04:14:45 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 278.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-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, 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-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.02s
Making fixed-width bins for bin size 1000 ... 0.13s
Counting overlaps for binsize 1000 with offset 0 ... 0.28s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Making bins with offsets ... 0.32s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 2.59s
Collecting counts and posteriors ... 0.16s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.19s
Making segmentation ... 0.09s
Calculating states from maximum-posterior in each peak ... 0.11s
Re-estimating maximum posterior in peaks ... 0.07s
Making segmentation ... 0.13s
Writing to file /tmp/Rtmp4gneft/file3ca67068ef122e_peaks_track-1.bed.gz ... 0.11s
Writing to file /tmp/Rtmp4gneft/file3ca670592ed50c_counts_track-1.wig.gz ... 0.19s
Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.04s
Making fixed-width bins for bin size 1000 ... 0.06s
Counting overlaps for binsize 1000 with offset 0 ... 0.24s
Counting overlaps for binsize 1000 with offset 500 ... 0.25s
Making bins with offsets ... 0.13s
Running Baum-Welch for offset = 0 ... 0.55s
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.17s
Making segmentation ... 0.07s
Calculating states from maximum-posterior in each peak ... 0.07s
Re-estimating maximum posterior in peaks ... 0.08s
Making segmentation ... 0.09s
Writing to file /tmp/Rtmp4gneft/file3ca6702b895e82_peaks_track-1.bed.gz ... 0.09s
Writing to file /tmp/Rtmp4gneft/file3ca6704749143d_counts_track-1.wig.gz ... 0.18s
Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.09s
Counting overlaps for binsize 1000 with offset 0 ... 0.62s
Counting overlaps for binsize 1000 with offset 500 ... 0.59s
Making bins with offsets ... 0.11s
Running Baum-Welch for offset = 0 ... 0.57s
Collecting counts and posteriors ... 0.15s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.18s
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 /home/biocbuild/bbs-3.14-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
Counting overlaps for binsize 1000 with offset 0 ... 0.22s
Counting overlaps for binsize 1000 with offset 500 ... 0.22s
Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Counting overlaps for binsize 1000 with offset 0 ... 0.24s
Counting overlaps for binsize 1000 with offset 500 ... 0.24s
Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.08s
Counting overlaps for binsize 1000 with offset 0 ... 0.42s
Counting overlaps for binsize 1000 with offset 500 ... 0.4s
Reading header from /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.07s
Counting overlaps for binsize 1000 with offset 0 ... 0.56s
Counting overlaps for binsize 1000 with offset 500 ... 0.55s
Making bins with offsets ... 0.14s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 1.93s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.08s
Making bins with offsets ... 0.07s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.12s
Obtaining states for offset = 500 ... 0.17s
Calculating states from posteriors ... 0.15s
Making segmentation ... 0.06s
Making bins with offsets ... 0.08s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.19s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.16s
Making segmentation ... 0.09s
Making bins with offsets ... 0.1s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 1.9s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.09s
Getting coordinates ... 0s
Extracting read counts ... 0.19s
Getting combinatorial states ... 0.1s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.05s
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:  1.44s
Obtaining states for offset = 500 ... 0.54s
Collecting counts and posteriors over offsets ... 1.58s
Compiling coordinates, posteriors, states ... 0.13s
Adding combinations ... 0.04s
Making segmentation ... 0.2s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.12s
Time spent for chromosome = chr12: 8.51s
Merging chromosomes ... 0.16s
Getting coordinates ... 0s
Extracting read counts ... 0.19s
Getting combinatorial states ... 0.14s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.03s
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:  0.21s
Obtaining states for offset = 500 ... 0.15s
Collecting counts and posteriors over offsets ... 1.1s
Compiling coordinates, posteriors, states ... 0.13s
Adding combinations ... 0.04s
Making segmentation ... 0.15s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.09s
Obtaining peaks ... 0.08s
Time spent for chromosome = chr12: 5.75s
Merging chromosomes ... 0.15s
Writing to file /tmp/Rtmp4gneft/file3ca670698e04a7_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp4gneft/file3ca670698e04a7_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/Rtmp4gneft/file3ca670698e04a7_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/Rtmp4gneft/file3ca670363e2c6_counts_H3K27me3-SHR-rep1.wig.gz ... 0.2s
Writing to file /tmp/Rtmp4gneft/file3ca670363e2c6_counts_H3K27me3-SHR-rep2.wig.gz ... 0.2s
Writing to file /tmp/Rtmp4gneft/file3ca670363e2c6_counts_H3K27me3-SHR-rep3.wig.gz ... 0.2s
Setting up parallel execution with 4 threads ... 0.28s
================
Binning the data
================
Obtaining chromosome length information from file /home/biocbuild/bbs-3.14-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.07s
Making fixed-width bins for bin size 500 ... 0.1s
Binning data ... 13.52s
Binning control ... 1.42s
========================
Calling univariate peaks
========================
Univariate peak calling ... 7.17s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.24s
Getting combinatorial states ... 0.08s
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 ... 0.22s
Running multivariate ... 16.93s
Merging chromosomes ... 0.2s
Saving to file /tmp/Rtmp4gneft/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1_binsize1000_stepsize500.RData ... 0.4s
Making plots ... 0.21s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.1s
Concatenating HMMs ... 0.11s
Making combinations ... 0.16s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.09s
Assigning combinatorial states ... 0.06s
Transferring counts and posteriors ... 0.09s
Making segmentation ... 0.16s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.1s
Redoing segmentation for each condition separately ... 1.17s
Saving to file /tmp/Rtmp4gneft/H4K20me1-example/combined/combined_mode-differential_binsize1000_stepsize500.RData ... 0.32s
Plotting read count correlation ... 0.23s
=======================
Exporting browser files
=======================
Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_BN.bed.gz ... 0.02s
Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.02s
Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep1.bed.gz ... 0s
Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/Rtmp4gneft/H4K20me1-example/BROWSERFILES/combined_mode-differential_binsize1000_stepsize500_peaks_H4K20me1-SHR-rep1.bed.gz ... 0.01s
==> Total time spent: 44s <==
Writing to file /tmp/Rtmp4gneft/file3ca670148f25ee_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp4gneft/file3ca670148f25ee_peaks_H4K20me1-BN-rep2.bed.gz ... 0s
Writing to file /tmp/Rtmp4gneft/file3ca670148f25ee_peaks_H4K20me1-SHR-rep1.bed.gz ... 0s
Writing to file /tmp/Rtmp4gneft/file3ca6705953cfb8_counts_H4K20me1-BN-rep1.wig.gz ... 0.18s
Writing to file /tmp/Rtmp4gneft/file3ca6705953cfb8_counts_H4K20me1-BN-rep2.wig.gz ... 0.18s
Writing to file /tmp/Rtmp4gneft/file3ca6705953cfb8_counts_H4K20me1-SHR-rep1.wig.gz ... 0.19s
Writing to file /tmp/Rtmp4gneft/file3ca67072e40d7b_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-3.14-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 ... 11.14s
Binning control ... 0.94s
========================
Calling univariate peaks
========================
Univariate peak calling ... 8.66s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.03s
Extracting read counts ... 0.27s
Getting combinatorial states ... 0.1s
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 ... 15.13s
Merging chromosomes ... 0.25s
Saving to file /tmp/Rtmp4gneft/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR_binsize1000_stepsize500.RData ... 0.54s
Making plots ... 0.11s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.14s
Concatenating conditions ... 0.09s
Reassigning levels ... 0s
Assigning transition groups ... 0.05s
Assigning combinatorial states ... 0.04s
Transferring counts and posteriors ... 0.08s
Making segmentation ... 0.24s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 1.1s
Redoing segmentation for each condition separately ... 0.05s
Saving to file /tmp/Rtmp4gneft/SHR-example/combined/combined_mode-combinatorial_binsize1000_stepsize500.RData ... 0.44s
Plotting read count correlation ... 0.23s
=======================
Exporting browser files
=======================
Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_combinations_SHR.bed.gz ... 0.05s
Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.02s
Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.02s
Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp4gneft/SHR-example/BROWSERFILES/combined_mode-combinatorial_binsize1000_stepsize500_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.01s
==> Total time spent: 41s <==
Enrichment inside of annotations ... 1.25s
Enrichment 15000bp before annotations 0.11s
Enrichment 15000bp after annotations 0.09s
Enrichment 10000bp before annotations 0.09s
Enrichment 10000bp before annotations 0.08s
Overlaps with annotation ... 0.13s
Getting surrounding indices ... 0.21s
Getting read counts 0.05s
Making the plot ... 0.14s
Ensembl site unresponsive, trying useast mirror
Quitting from lines 431-462 (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