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BioC 3.6: BUILD report for chromstaR on malbec1

This page was generated on 2017-08-16 13:24:41 -0400 (Wed, 16 Aug 2017).

Package 222/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.3.1
Aaron Taudt
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chromstaR
Last Changed Rev: 131423 / Revision: 131943
Last Changed Date: 2017-07-20 05:30:00 -0400 (Thu, 20 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromstaR
Version: 1.3.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data chromstaR
StartedAt: 2017-08-15 20:31:14 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 20:33:51 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 156.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-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
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,
    cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get,
    grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K4me3-BN-male-bio2-tech1.bam ... 0.04s
Making fixed-width bins for bin size 1000 ... 0.42s
Counting overlaps for binsize 1000 with offset 0 ... 0.17s
Counting overlaps for binsize 1000 with offset 500 ... 0.12s
Making bins with offsets ... 1.14s
Replaced read counts > 500 by 500 in 97 bins to enhance performance (option 'read.cutoff').
Running Baum-Welch for offset = 0 ... 2.28s
Collecting counts and posteriors ... 0.58s
Obtaining states for offset = 500 ... 0.64s
Calculating states from posteriors ... 0.06s
Making segmentation ... 0.26s
Calculating states from peakScores ... 0s
Making segmentation ... 0.43s
Writing to file /tmp/Rtmp9640QB/file31a452cd0830_peaks_track-1.bed.gz ... 0.04s
Writing to file /tmp/Rtmp9640QB/file31a468bfc8d0_counts_track-1.wig.gz ... 0.31s
Reading header from /home/biocbuild/bbs-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-BN-male-bio2-tech1.bam ... 0.09s
Making fixed-width bins for bin size 1000 ... 0.08s
Counting overlaps for binsize 1000 with offset 0 ... 0.22s
Counting overlaps for binsize 1000 with offset 500 ... 0.2s
Making bins with offsets ... 0.7s
Running Baum-Welch for offset = 0 ... 1.31s
Collecting counts and posteriors ... 0.06s
Obtaining states for offset = 500 ... 0.1s
Calculating states from posteriors ... 0.23s
Making segmentation ... 0.04s
Calculating states from peakScores ... 0.01s
Making segmentation ... 0.06s
Writing to file /tmp/Rtmp9640QB/file31a4835adfe_peaks_track-1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a433507db9_counts_track-1.wig.gz ... 0.21s
Reading header from /home/biocbuild/bbs-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-BN-male-bio1-tech1.bam ... 0.04s
Making fixed-width bins for bin size 1000 ... 0.07s
Counting overlaps for binsize 1000 with offset 0 ... 0.61s
Counting overlaps for binsize 1000 with offset 500 ... 0.67s
Making bins with offsets ... 0.69s
Running Baum-Welch for offset = 0 ... 1.86s
Collecting counts and posteriors ... 0.09s
Obtaining states for offset = 500 ... 0.14s
Calculating states from posteriors ... 0.04s
Making segmentation ... 0.04s
Reading header from /home/biocbuild/bbs-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech1.bam ... 0.04s
Making fixed-width bins for bin size 1000 ... 0.09s
Counting overlaps for binsize 1000 with offset 0 ... 0.14s
Counting overlaps for binsize 1000 with offset 500 ... 0.14s
Reading header from /home/biocbuild/bbs-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio2-tech2.bam ... 0.03s
Making fixed-width bins for bin size 1000 ... 0.09s
Counting overlaps for binsize 1000 with offset 0 ... 0.23s
Counting overlaps for binsize 1000 with offset 500 ... 0.21s
Reading header from /home/biocbuild/bbs-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H3K27me3-SHR-male-bio3-tech1.bam ... 0.03s
Making fixed-width bins for bin size 1000 ... 0.6s
Counting overlaps for binsize 1000 with offset 0 ... 0.33s
Counting overlaps for binsize 1000 with offset 500 ... 0.3s
Reading header from /home/biocbuild/bbs-3.6-bioc/R/library/chromstaRData/extdata/euratrans/lv-H4K20me1-SHR-male-bio1-tech1.bam ... 0.04s
Making fixed-width bins for bin size 1000 ... 0.06s
Counting overlaps for binsize 1000 with offset 0 ... 0.43s
Counting overlaps for binsize 1000 with offset 500 ... 0.42s
Making bins with offsets ... 0.1s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.1s
Obtaining states for offset = 500 ... 0.1s
Calculating states from posteriors ... 0.03s
Making segmentation ... 0.03s
Making bins with offsets ... 0.17s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.54s
Obtaining states for offset = 500 ... 0.1s
Calculating states from posteriors ... 0.02s
Making segmentation ... 0.03s
Making bins with offsets ... 0.48s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.06s
Obtaining states for offset = 500 ... 0.1s
Calculating states from posteriors ... 0.02s
Making segmentation ... 0.02s
Making bins with offsets ... 0.09s
------------------------------------ Try 1 of 1 -------------------------------------
Collecting counts and posteriors ... 0.07s
Obtaining states for offset = 500 ... 0.47s
Calculating states from posteriors ... 0.02s
Making segmentation ... 0.02s
Getting coordinates ... 0s
Extracting read counts ... 0.03s
Getting combinatorial states ... 0.05s
Computing pre z-matrix ... 0.01s
Transfering values into z-matrix ... 0.03s
Computing inverse of correlation matrix ... 0.03s
------------------
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:  1.53s
Obtaining states for offset = 500 ... 0.41s
Collecting counts and posteriors over offsets ... 0.36s
Compiling coordinates, posteriors, states ... 0.07s
Calculating peak scores ... 0.26s
Adding combinations ... 0.01s
Making segmentation ... 0.08s
Obtaining peaks ... 0.03s
Time spent for chromosome = chr12: 4.02s
Merging chromosomes ... 0.15s
Getting coordinates ... 0s
Extracting read counts ... 0.02s
Getting combinatorial states ... 0.04s
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:  0.17s
Obtaining states for offset = 500 ... 0.1s
Collecting counts and posteriors over offsets ... 0.41s
Compiling coordinates, posteriors, states ... 0.06s
Calculating peak scores ... 0.23s
Adding combinations ... 0.01s
Making segmentation ... 0.07s
Obtaining peaks ... 0.02s
Time spent for chromosome = chr12: 2.45s
Merging chromosomes ... 0.11s
Writing to file /tmp/Rtmp9640QB/file31a4641b0c0c_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a4641b0c0c_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a4641b0c0c_peaks_H3K27me3-SHR-rep3.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a4e4f5885_counts_H3K27me3-SHR-rep1.wig.gz ... 0.87s
Writing to file /tmp/Rtmp9640QB/file31a4e4f5885_counts_H3K27me3-SHR-rep2.wig.gz ... 0.4s
Writing to file /tmp/Rtmp9640QB/file31a4e4f5885_counts_H3K27me3-SHR-rep3.wig.gz ... 0.4s
Setting up parallel execution with 4 threads ... 0.96s
================
Binning the data
================
Obtaining chromosome length information from file /home/biocbuild/bbs-3.6-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 ... 0.09s
Binning data ... 10.24s
Binning input ... 1.39s
========================
Calling univariate peaks
========================
Univariate peak calling ... 10.83s
==========================
Calling multivariate peaks
==========================
mode = differential
---------------
mark = H4K20me1
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.06s
Getting combinatorial states ... 0.04s
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 ... 1.02s
Running multivariate ... 12s
Merging chromosomes ... 0.18s
Saving to file /tmp/Rtmp9640QB/H4K20me1-example/multivariate/multivariate_mode-differential_mark-H4K20me1.RData ... 0.44s
Making plots ... 0.19s
===========================
Combining multivariate HMMs
===========================
Processing HMM 1 ... 0.16s
Concatenating HMMs ... 0.11s
Making combinations ... 0.14s
Reassigning levels ... 0.01s
Assigning transition groups ... 0.05s
Redoing segmentation for all conditions combined ... 0.06s
Redoing segmentation for each condition separately ... 0.05s
Saving to file /tmp/Rtmp9640QB/H4K20me1-example/combined/combined_mode-differential.RData ... 0.28s
Plotting read count correlation ... 0.56s
=======================
Exporting browser files
=======================
Writing to file /tmp/Rtmp9640QB/H4K20me1-example/BROWSERFILES/combined_mode-differential_combinations_BN.bed.gz ... 0.02s
Writing to file /tmp/Rtmp9640QB/H4K20me1-example/BROWSERFILES/combined_mode-differential_combinations_SHR.bed.gz ... 0.06s
Writing to file /tmp/Rtmp9640QB/H4K20me1-example/BROWSERFILES/combined_mode-differential_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/H4K20me1-example/BROWSERFILES/combined_mode-differential_peaks_H4K20me1-BN-rep2.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/H4K20me1-example/BROWSERFILES/combined_mode-differential_peaks_H4K20me1-SHR-rep1.bed.gz ... 0.01s
==> Total time spent: 39s <==
Writing to file /tmp/Rtmp9640QB/file31a478974564_peaks_H4K20me1-BN-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a478974564_peaks_H4K20me1-BN-rep2.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a478974564_peaks_H4K20me1-SHR-rep1.bed.gz ... 0.01s
Writing to file /tmp/Rtmp9640QB/file31a443e8c252_counts_H4K20me1-BN-rep1.wig.gz ... 0.84s
Writing to file /tmp/Rtmp9640QB/file31a443e8c252_counts_H4K20me1-BN-rep2.wig.gz ... 0.39s
Writing to file /tmp/Rtmp9640QB/file31a443e8c252_counts_H4K20me1-SHR-rep1.wig.gz ... 0.39s
Writing to file /tmp/Rtmp9640QB/file31a428bac95d_combinations.bed.gz ... 0s
Setting up parallel execution with 4 threads ... 0.89s
================
Binning the data
================
Obtaining chromosome length information from file /home/biocbuild/bbs-3.6-bioc/R/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 ... 0.09s
Binning data ... 8.96s
Binning input ... 0.72s
========================
Calling univariate peaks
========================
Univariate peak calling ... 9.75s
==========================
Calling multivariate peaks
==========================
mode = combinatorial
---------------
condition = SHR
---------------
Getting coordinates ... 0.02s
Extracting read counts ... 0.11s
Getting combinatorial states ... 0.05s
Computing pre z-matrix ... 0s
Transfering values into z-matrix ... 0.04s
Computing inverse of correlation matrix ... 0.01s
Setting up parallel multivariate with 4 threads ... 0.9s
Running multivariate ... 12.71s
Merging chromosomes ... 0.19s
Saving to file /tmp/Rtmp9640QB/SHR-example/multivariate/multivariate_mode-combinatorial_condition-SHR.RData ... 0.57s
Making plots ... 0.17s
===========================
Combining multivariate HMMs
===========================
Processing condition 1 ... 0.2s
Concatenating conditions ... 0.56s
Reassigning levels ... 0s
Assigning transition groups ... 0.11s
Redoing segmentation for all conditions combined ... 0.12s
Redoing segmentation for each condition separately ... 0.02s
Saving to file /tmp/Rtmp9640QB/SHR-example/combined/combined_mode-combinatorial.RData ... 0.41s
Plotting read count correlation ... 0.32s
=======================
Exporting browser files
=======================
Writing to file /tmp/Rtmp9640QB/SHR-example/BROWSERFILES/combined_mode-combinatorial_combinations_SHR.bed.gz ... 0.06s
Writing to file /tmp/Rtmp9640QB/SHR-example/BROWSERFILES/combined_mode-combinatorial_peaks_H3K27me3-SHR-rep1.bed.gz ... 0.03s
Writing to file /tmp/Rtmp9640QB/SHR-example/BROWSERFILES/combined_mode-combinatorial_peaks_H3K27me3-SHR-rep2.bed.gz ... 0.04s
Writing to file /tmp/Rtmp9640QB/SHR-example/BROWSERFILES/combined_mode-combinatorial_peaks_H3K4me3-SHR-rep1.bed.gz ... 0.03s
Writing to file /tmp/Rtmp9640QB/SHR-example/BROWSERFILES/combined_mode-combinatorial_peaks_H3K4me3-SHR-rep2.bed.gz ... 0.02s
==> Total time spent: 38s <==
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://may2012.archive.ensembl.org:80/biomart/martservice?type=datasets&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
Quitting from lines 356-373 (chromstaR.Rnw) 
Error: processing vignette 'chromstaR.Rnw' failed with diagnostics:
invalid 'text' argument
Execution halted