Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-05-10 11:36:54 -0400 (Fri, 10 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4662
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4393
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4424
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

Package 208/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomvRCNS 1.45.0  (landing page)
Yang Du
Snapshot Date: 2024-05-08 14:05:06 -0400 (Wed, 08 May 2024)
git_url: https://git.bioconductor.org/packages/biomvRCNS
git_branch: devel
git_last_commit: 03672c7
git_last_commit_date: 2024-04-30 11:53:14 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

BUILD results for biomvRCNS on palomino4


To the developers/maintainers of the biomvRCNS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomvRCNS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biomvRCNS
Version: 1.45.0
Command: chmod a+r biomvRCNS -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data biomvRCNS
StartedAt: 2024-05-08 17:13:16 -0400 (Wed, 08 May 2024)
EndedAt: 2024-05-08 17:15:25 -0400 (Wed, 08 May 2024)
EllapsedTime: 128.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r biomvRCNS -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data biomvRCNS
###
##############################################################################
##############################################################################


* checking for file 'biomvRCNS/DESCRIPTION' ... OK
* preparing 'biomvRCNS':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'biomvRCNS.Rnw' using Sweave
Loading required package: IRanges
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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Checking input ...
xAnno is not present or not supported, try to use maxbp/maxk in the uniform prior for the sojourn distribution.
Estimating common emission prior ...
Warning in var(x, na.rm = na.rm) * f.var :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.
Warning in var(x, na.rm = na.rm) * f.var :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.
Loading required package: parallel
Preparing sojourn prior for seq  '1' ...
Building HSMM for seq '1' in column '1' ...
[ hsmmRun ] seq '1' column 'Coriell.05296' iteration: 1
Building HSMM for seq '1' in column '2' ...
[ hsmmRun ] seq '1' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '2' ...
Building HSMM for seq '2' in column '1' ...
[ hsmmRun ] seq '2' column 'Coriell.05296' iteration: 1
Building HSMM for seq '2' in column '2' ...
[ hsmmRun ] seq '2' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '3' ...
Building HSMM for seq '3' in column '1' ...
[ hsmmRun ] seq '3' column 'Coriell.05296' iteration: 1
Building HSMM for seq '3' in column '2' ...
[ hsmmRun ] seq '3' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '4' ...
Building HSMM for seq '4' in column '1' ...
[ hsmmRun ] seq '4' column 'Coriell.05296' iteration: 1
Building HSMM for seq '4' in column '2' ...
[ hsmmRun ] seq '4' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '5' ...
Building HSMM for seq '5' in column '1' ...
[ hsmmRun ] seq '5' column 'Coriell.05296' iteration: 1
Building HSMM for seq '5' in column '2' ...
[ hsmmRun ] seq '5' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '6' ...
Building HSMM for seq '6' in column '1' ...
[ hsmmRun ] seq '6' column 'Coriell.05296' iteration: 1
Building HSMM for seq '6' in column '2' ...
[ hsmmRun ] seq '6' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '7' ...
Building HSMM for seq '7' in column '1' ...
[ hsmmRun ] seq '7' column 'Coriell.05296' iteration: 1
Building HSMM for seq '7' in column '2' ...
[ hsmmRun ] seq '7' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '8' ...
Building HSMM for seq '8' in column '1' ...
[ hsmmRun ] seq '8' column 'Coriell.05296' iteration: 1
Building HSMM for seq '8' in column '2' ...
[ hsmmRun ] seq '8' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '9' ...
Building HSMM for seq '9' in column '1' ...
[ hsmmRun ] seq '9' column 'Coriell.05296' iteration: 1
Building HSMM for seq '9' in column '2' ...
[ hsmmRun ] seq '9' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '10' ...
Building HSMM for seq '10' in column '1' ...
[ hsmmRun ] seq '10' column 'Coriell.05296' iteration: 1
Building HSMM for seq '10' in column '2' ...
[ hsmmRun ] seq '10' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '11' ...
Building HSMM for seq '11' in column '1' ...
[ hsmmRun ] seq '11' column 'Coriell.05296' iteration: 1
Building HSMM for seq '11' in column '2' ...
[ hsmmRun ] seq '11' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '12' ...
Building HSMM for seq '12' in column '1' ...
[ hsmmRun ] seq '12' column 'Coriell.05296' iteration: 1
Building HSMM for seq '12' in column '2' ...
[ hsmmRun ] seq '12' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '13' ...
Building HSMM for seq '13' in column '1' ...
[ hsmmRun ] seq '13' column 'Coriell.05296' iteration: 1
Building HSMM for seq '13' in column '2' ...
[ hsmmRun ] seq '13' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '14' ...
Building HSMM for seq '14' in column '1' ...
[ hsmmRun ] seq '14' column 'Coriell.05296' iteration: 1
Building HSMM for seq '14' in column '2' ...
[ hsmmRun ] seq '14' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '15' ...
Building HSMM for seq '15' in column '1' ...
[ hsmmRun ] seq '15' column 'Coriell.05296' iteration: 1
Building HSMM for seq '15' in column '2' ...
[ hsmmRun ] seq '15' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '16' ...
Building HSMM for seq '16' in column '1' ...
[ hsmmRun ] seq '16' column 'Coriell.05296' iteration: 1
Building HSMM for seq '16' in column '2' ...
[ hsmmRun ] seq '16' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '17' ...
Building HSMM for seq '17' in column '1' ...
[ hsmmRun ] seq '17' column 'Coriell.05296' iteration: 1
Building HSMM for seq '17' in column '2' ...
[ hsmmRun ] seq '17' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '18' ...
Building HSMM for seq '18' in column '1' ...
[ hsmmRun ] seq '18' column 'Coriell.05296' iteration: 1
Building HSMM for seq '18' in column '2' ...
[ hsmmRun ] seq '18' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '19' ...
Building HSMM for seq '19' in column '1' ...
[ hsmmRun ] seq '19' column 'Coriell.05296' iteration: 1
Building HSMM for seq '19' in column '2' ...
[ hsmmRun ] seq '19' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '20' ...
Building HSMM for seq '20' in column '1' ...
[ hsmmRun ] seq '20' column 'Coriell.05296' iteration: 1
Building HSMM for seq '20' in column '2' ...
[ hsmmRun ] seq '20' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '21' ...
Building HSMM for seq '21' in column '1' ...
[ hsmmRun ] seq '21' column 'Coriell.05296' iteration: 1
Building HSMM for seq '21' in column '2' ...
[ hsmmRun ] seq '21' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '22' ...
Building HSMM for seq '22' in column '1' ...
[ hsmmRun ] seq '22' column 'Coriell.05296' iteration: 1
Building HSMM for seq '22' in column '2' ...
[ hsmmRun ] seq '22' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq  '23' ...
Building HSMM for seq '23' in column '1' ...
[ hsmmRun ] seq '23' column 'Coriell.05296' iteration: 1
Building HSMM for seq '23' in column '2' ...
[ hsmmRun ] seq '23' column 'Coriell.13330' iteration: 1
Building HSMM complete, preparing output ...
Processing sequence 1
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 1 complete.
Processing sequence 2
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 2 complete.
Processing sequence 3
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 3 complete.
Processing sequence 4
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 4 complete.
Processing sequence 5
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 5 complete.
Processing sequence 6
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 6 complete.
Processing sequence 7
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 7 complete.
Processing sequence 8
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 8 complete.
Processing sequence 9
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 9 complete.
Processing sequence 10
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 10 complete.
Processing sequence 11
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 11 complete.
Processing sequence 12
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 12 complete.
Processing sequence 13
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 13 complete.
Processing sequence 14
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 14 complete.
Processing sequence 15
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 15 complete.
Processing sequence 16
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 16 complete.
Processing sequence 17
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 17 complete.
Processing sequence 18
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 18 complete.
Processing sequence 19
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 19 complete.
Processing sequence 20
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 20 complete.
Processing sequence 21
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 21 complete.
Processing sequence 22
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 22 complete.
Processing sequence 23
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
No need to run step 2 merging, processing complete for column 1 from group 1.
Building segmentation model for group 1 complete.
Step 1 building segmentation model for group 2 ...
Step 1 building segmentation model for group 2 complete.
No need to run step 2 merging, processing complete for column 2 from group 2.
Building segmentation model for group 2 complete.
Processing sequence 23 complete.
Processing sequence 1

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 1 complete.
Processing sequence 2

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 2 complete.
Processing sequence 3

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 3 complete.
Processing sequence 4

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 4 complete.
Processing sequence 5

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 5 complete.
Processing sequence 6

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 6 complete.
Processing sequence 7

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 7 complete.
Processing sequence 8

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 8 complete.
Processing sequence 9

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 9 complete.
Processing sequence 10

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 10 complete.
Processing sequence 11

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
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Building segmentation model for group 2 complete.
Processing sequence 11 complete.
Processing sequence 12

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 12 complete.
Processing sequence 13

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 13 complete.
Processing sequence 14

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 14 complete.
Processing sequence 15

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 15 complete.
Processing sequence 16

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 16 complete.
Processing sequence 17

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 17 complete.
Processing sequence 18

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 18 complete.
Processing sequence 19

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 19 complete.
Processing sequence 20

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 20 complete.
Processing sequence 21

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
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Building segmentation model for group 2 complete.
Processing sequence 21 complete.
Processing sequence 22

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 22 complete.
Processing sequence 23

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 23 complete.
Processing sequence 1

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 1 complete.
Processing sequence 2

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 2 complete.
Processing sequence 3

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 3 complete.
Processing sequence 4

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 4 complete.
Processing sequence 5

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 5 complete.
Processing sequence 6

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 6 complete.
Processing sequence 7

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 7 complete.
Processing sequence 8

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 8 complete.
Processing sequence 9

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 9 complete.
Processing sequence 10

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 10 complete.
Processing sequence 11

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 11 complete.
Processing sequence 12

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 12 complete.
Processing sequence 13

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 13 complete.
Processing sequence 14

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 14 complete.
Processing sequence 15

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 15 complete.
Processing sequence 16

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 16 complete.
Processing sequence 17

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 17 complete.
Processing sequence 18

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 18 complete.
Processing sequence 19

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 19 complete.
Processing sequence 20

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 20 complete.
Processing sequence 21

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 21 complete.
Processing sequence 22

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 22 complete.
Processing sequence 23

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Building segmentation model for group 2 ...
Building segmentation model for group 2 complete.
Processing sequence 23 complete.
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Checking input ...
Estimated state number from xAnno: J = 3
Estimating common emission prior ...
Preparing sojourn prior for seq  'chr17' ...
Building HSMM for seq 'chr17' in column '1' ...
[ hsmmRun ] seq 'chr17' column 'Gm12878' iteration: 1
Building HSMM for seq 'chr17' in column '2' ...
[ hsmmRun ] seq 'chr17' column 'K562' iteration: 1
Building HSMM complete, preparing output ...
Processing sequence chr17
 ...
Step 1 building segmentation model for group 1 ...
Step 1 building segmentation model for group 1 complete.
Step 2 merging for column 1 from group 1

Step 2 merging for column 1 from group 1 complete.
Step 2 merging for column 2 from group 1

Step 2 merging for column 2 from group 1 complete.
Building segmentation model for group 1 complete.
Processing sequence chr17 complete.
Processing sequence chr17

Building segmentation model for group 1 ...
Building segmentation model for group 1 complete.
Processing sequence chr17 complete.
Checking input ...
Loading required package: cluster
xAnno is not present or not supported, try to use maxbp/maxk in the uniform prior for the sojourn distribution.
Estimating common emission prior ...
Preparing sojourn prior for seq  'chr1' ...
Building HSMM for seq 'chr1' in column '1' ...
[ hsmmRun ] seq 'chr1' column 'meth.diff' iteration: 1
Building HSMM for seq 'chr1' in column '2' ...
[ hsmmRun ] seq 'chr1' column 'p.val' iteration: 1
Preparing sojourn prior for seq  'chr2' ...
Building HSMM for seq 'chr2' in column '1' ...
[ hsmmRun ] seq 'chr2' column 'meth.diff' iteration: 1
Building HSMM for seq 'chr2' in column '2' ...
[ hsmmRun ] seq 'chr2' column 'p.val' iteration: 1
Building HSMM complete, preparing output ...
Checking input ...
xAnno is not present or not supported, try to use maxbp/maxk in the uniform prior for the sojourn distribution.
Estimating common emission prior ...
Preparing sojourn prior for seq  'chr1' ...
Building HSMM for group '1' ...
[ hsmmRun ] seq 'chr1' column 'meth.diff+p.val' iteration: 1
Preparing sojourn prior for seq  'chr2' ...
Building HSMM for group '1' ...
[ hsmmRun ] seq 'chr2' column 'meth.diff+p.val' iteration: 1
Building HSMM complete, preparing output ...
texify: major issue: User/administrator updates are out-of-sync.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "biomvRCNS.tex" --max-iterations=20 -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/tex/latex" -I "F:/biocbuild/bbs-3.20-bioc/R/share/texmf/bibtex/bst"' had status 1033
Error: processing vignette 'biomvRCNS.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'biomvRCNS.pdf' for vignette with name 'biomvRCNS' and engine 'utils::Sweave'. The following files exist in working directory 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkRP8A8\Rbuildcd8bb1676b\biomvRCNS\vignettes': 'biomvRCNS-coriellHsmmplot.pdf' (16640 bytes), 'biomvRCNS-plotENCODEHsmmG.pdf' (93641 bytes), 'biomvRCNS-plotENCODEHsmmK.pdf' (94188 bytes), 'biomvRCNS-plotdmr.pdf' (46589 bytes), 'biomvRCNS-plotdmr2.pdf' (47067 bytes), 'biomvRCNS-plotdmr3.pdf' (47295 bytes), 'biomvRCNS.Rnw' (25683 bytes), 'biomvRCNS.bib' (9134 bytes), 'biomvRCNS.tex' (40583 bytes)
--- failed re-building 'biomvRCNS.Rnw'

SUMMARY: processing the following file failed:
  'biomvRCNS.Rnw'

Error: Vignette re-building failed.
Execution halted