Back to Multiple platform build/check report for BioC 3.15
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-22 11:09:57 -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 merida1


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: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2022-01-21 17:07:56 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 17:10:46 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 170.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/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

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 /Library/Frameworks/R.framework/Versions/4.2/Resources/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.03s
Making fixed-width bins for bin size 1000 ... 0.18s
Counting overlaps for binsize 1000 with offset 0 ... 0.38s
Counting overlaps for binsize 1000 with offset 500 ... 0.27s
Making bins with offsets ... 0.29s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 1.36s
Collecting counts and posteriors ... 0.8s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.16s
Making segmentation ... 0.12s
Calculating states from maximum-posterior in each peak ... 0.07s
Re-estimating maximum posterior in peaks ... 0.05s
Making segmentation ... 0.13s
Writing to file /tmp/Rtmpp8lUVy/file1487277ccad58_peaks_track-1.bed.gz ... 0.09s
Writing to file /tmp/Rtmpp8lUVy/file148721e88a9da_counts_track-1.wig.gz ... 0.3s
Reading header from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.07s
Making fixed-width bins for bin size 1000 ... 0.09s
Counting overlaps for binsize 1000 with offset 0 ... 0.29s
Counting overlaps for binsize 1000 with offset 500 ... 0.3s
Making bins with offsets ... 0.12s
Running Baum-Welch for offset = 0 ... 0.68s
Collecting counts and posteriors ... 0.14s
Obtaining states for offset = 500 ... 0.22s
Calculating states from posteriors ... 0.16s
Making segmentation ... 0.08s
Calculating states from maximum-posterior in each peak ... 0.07s
Re-estimating maximum posterior in peaks ... 0.07s
Making segmentation ... 0.08s
Writing to file /tmp/Rtmpp8lUVy/file1487213f4ac9b_peaks_track-1.bed.gz ... 0.08s
Writing to file /tmp/Rtmpp8lUVy/file14872246ffe59_counts_track-1.wig.gz ... 0.31s
Reading header from /Library/Frameworks/R.framework/Versions/4.2/Resources/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 ... 0.83s
Counting overlaps for binsize 1000 with offset 500 ... 0.81s
Making bins with offsets ... 0.1s
Running Baum-Welch for offset = 0 ... 0.92s
Collecting counts and posteriors ... 0.16s
Obtaining states for offset = 500 ... 0.19s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.08s
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/4.2/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.06s
Counting overlaps for binsize 1000 with offset 0 ... 0.27s
Counting overlaps for binsize 1000 with offset 500 ... 0.27s
Reading header from /Library/Frameworks/R.framework/Versions/4.2/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 ... 0.3s
Counting overlaps for binsize 1000 with offset 500 ... 0.3s
Reading header from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.06s
Counting overlaps for binsize 1000 with offset 0 ... 0.53s
Counting overlaps for binsize 1000 with offset 500 ... 0.54s
Reading header from /Library/Frameworks/R.framework/Versions/4.2/Resources/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 ... 0.75s
Counting overlaps for binsize 1000 with offset 500 ... 0.75s
Making bins with offsets ... 0.11s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.16s
Making segmentation ... 0.08s
Making bins with offsets ... 0.12s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.13s
Obtaining states for offset = 500 ... 0.2s
Calculating states from posteriors ... 0.14s
Making segmentation ... 0.1s
Making bins with offsets ... 0.11s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.15s
Obtaining states for offset = 500 ... 0.87s
Calculating states from posteriors ... 0.13s
Making segmentation ... 0.1s
Making bins with offsets ... 0.09s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.15s
Obtaining states for offset = 500 ... 0.18s
Calculating states from posteriors ... 0.14s
Making segmentation ... 0.08s
Getting coordinates ... 0s
Extracting read counts ... 0.22s
Getting combinatorial states ... 0.11s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.06s
Computing inverse of correlation matrix ... 0.04s
------------------
Chromosome = chr12
Starting multivariate HMM with 16 combinatorial states
Making bins with offsets ... 0.01s
Fitting Hidden Markov Model for offset = 0
Time spent in multivariate HMM:  1.5s
Obtaining states for offset = 500 ... 0.61s
Collecting counts and posteriors over offsets ... 0.71s
Compiling coordinates, posteriors, states ... 0.14s
Adding combinations ... 0.04s
Making segmentation ... 0.36s
Adding differential score ... 0.03s
Getting maximum posterior in peaks ... 0.11s
Obtaining peaks ... 0.13s
Time spent for chromosome = chr12: 5.7s
Merging chromosomes ... 0.14s
Getting coordinates ... 0s
Extracting read counts ... 0.19s
Getting combinatorial states ... 0.11s
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 ... 0s
Fitting Hidden Markov Model for offset = 0
Time spent in multivariate HMM:  0.26s
Obtaining states for offset = 500 ... 0.17s
Collecting counts and posteriors over offsets ... 0.66s
Compiling coordinates, posteriors, states ... 0.11s
Adding combinations ... 0.03s
Making segmentation ... 0.26s
Adding differential score ... 0.02s
Getting maximum posterior in peaks ... 0.1s
Obtaining peaks ... 0.1s
Time spent for chromosome = chr12: 3.81s
Merging chromosomes ... 0.13s
Writing to file /tmp/Rtmpp8lUVy/file1487210d56c5e_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmpp8lUVy/file1487210d56c5e_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/Rtmpp8lUVy/file1487210d56c5e_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/Rtmpp8lUVy/file148722bbd97f4_counts_H3K27me3-SHR-rep1.wig.gz ... 0.31s
Writing to file /tmp/Rtmpp8lUVy/file148722bbd97f4_counts_H3K27me3-SHR-rep2.wig.gz ... 0.32s
Writing to file /tmp/Rtmpp8lUVy/file148722bbd97f4_counts_H3K27me3-SHR-rep3.wig.gz ... 0.34s
Setting up parallel execution with 4 threads ... 0.5s
================
Binning the data
================
Obtaining chromosome length information from file /Library/Frameworks/R.framework/Versions/4.2/Resources/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.01s
Making fixed-width bins for bin size 1000 ... 0.05s
Making fixed-width bins for bin size 500 ... 0.08s
Binning data ... 18.24s
Binning control ... 1.98s
========================
Calling univariate peaks
========================
Univariate peak calling ...Quitting from lines 289-295 (chromstaR.Rnw) 
Error: processing vignette 'chromstaR.Rnw' failed with diagnostics:
task 1 failed - "Graphics API version mismatch"
--- failed re-building ‘chromstaR.Rnw’

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

Error: Vignette re-building failed.
Execution halted