##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R 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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘biomvRCNS.Rnw’ using Sweave
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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
Loading required package: GenomicRanges
Loading required package: Seqinfo
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' ...
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 '1' in column '1' ...
[ hsmmRun ] seq '1' column 'Coriell.05296' iteration: 1
Building HSMM for seq '1' in column '2' ...
Building HSMM for seq '2' in column '2' ...
[ hsmmRun ] seq '1' column 'Coriell.13330' iteration: 1
[ hsmmRun ] seq '2' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq '3' ...
Building HSMM for seq '3' in column '1' ...
Preparing sojourn prior for seq '4' ...
[ hsmmRun ] seq '3' column 'Coriell.05296' iteration: 1
Building HSMM for seq '4' in column '1' ...
[ hsmmRun ] seq '4' 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 '5' ...
Building HSMM for seq '4' in column '2' ...
[ hsmmRun ] seq '4' column 'Coriell.13330' iteration: 1
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 '7' ...
Building HSMM for seq '7' in column '1' ...
[ hsmmRun ] seq '7' column 'Coriell.05296' 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
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
Preparing sojourn prior for seq '9' ...
Building HSMM for seq '8' in column '2' ...
[ hsmmRun ] seq '8' column 'Coriell.13330' iteration: 1
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
Preparing sojourn prior for seq '11' ...
Building HSMM for seq '11' in column '1' ...
Building HSMM for seq '10' in column '2' ...
[ hsmmRun ] seq '11' column 'Coriell.05296' iteration: 1
[ hsmmRun ] seq '10' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq '12' ...
Building HSMM for seq '11' in column '2' ...
[ hsmmRun ] seq '11' column 'Coriell.13330' iteration: 1
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 '14' ...
Preparing sojourn prior for seq '13' ...
Building HSMM for seq '14' in column '1' ...
[ hsmmRun ] seq '14' column 'Coriell.05296' iteration: 1
Building HSMM for seq '13' in column '1' ...
[ hsmmRun ] seq '13' column 'Coriell.05296' iteration: 1
Building HSMM for seq '14' in column '2' ...
[ hsmmRun ] seq '14' column 'Coriell.13330' iteration: 1
Building HSMM for seq '13' in column '2' ...
[ hsmmRun ] seq '13' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq '15' ...
Preparing sojourn prior for seq '16' ...
Building HSMM for seq '15' in column '1' ...
Building HSMM for seq '16' in column '1' ...
[ hsmmRun ] seq '15' column 'Coriell.05296' iteration: 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
Building HSMM for seq '15' in column '2' ...
[ hsmmRun ] seq '15' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq '17' ...
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 '17' in column '1' ...
[ hsmmRun ] seq '17' column 'Coriell.05296' iteration: 1
Building HSMM for seq '18' in column '2' ...
[ hsmmRun ] seq '18' column 'Coriell.13330' iteration: 1
Building HSMM for seq '17' in column '2' ...
[ hsmmRun ] seq '17' column 'Coriell.13330' iteration: 1
Preparing sojourn prior for seq '19' ...
Preparing sojourn prior for seq '20' ...
Building HSMM for seq '19' in column '1' ...
[ hsmmRun ] seq '19' column 'Coriell.05296' iteration: 1
Building HSMM for seq '20' in column '1' ...
[ hsmmRun ] seq '20' column 'Coriell.05296' iteration: 1
Building HSMM for seq '19' in column '2' ...
[ hsmmRun ] seq '19' column 'Coriell.13330' 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
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 '21' in column '2' ...
[ hsmmRun ] seq '21' column 'Coriell.13330' 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.
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.
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' ...
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 'chr1' in column '1' ...
[ hsmmRun ] seq 'chr1' column 'meth.diff' iteration: 1
Building HSMM for seq 'chr2' in column '2' ...
[ hsmmRun ] seq 'chr2' column 'p.val' iteration: 1
Building HSMM for seq 'chr1' in column '2' ...
[ hsmmRun ] seq 'chr1' 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' ...
Preparing sojourn prior for seq 'chr2' ...
Building HSMM for group '1' ...
[ hsmmRun ] seq 'chr2' column 'meth.diff+p.val' iteration: 1
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: backsolve(dec, t(x) - mean, transpose = TRUE)
2: dmvnorm(x, mean = emis$mu[[j]], sigma = emis$var[[j]])
3: FUN(X[[i]], ...)
4: lapply(X = X, FUN = FUN, ...)
5: sapply(1:J, function(j) dmvnorm(x, mean = emis$mu[[j]], sigma = emis$var[[j]]))
6: initEmis(emis = emis, x = x)
7: hsmmRun(x[r, gi], xid[gi], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(hsmmRun(x[r, gi], xid[gi], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e)})
12: FUN(X[[i]], ...)
13: lapply(X = S, FUN = FUN, ...)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
18: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
19: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
20: FUN(X[[i]], ...)
21: lapply(seq_len(cores), inner.do)
22: mylapply(seq_along(seqs), function(s) { r <- which(as.character(seqnames(xRange)) == seqs[s]) if (length(r) < 2) { warning("Region too short for seq ", s, " skipped!") if (iterative) { runout <- sapply(seq_len(nc), function(c) list(NA)) } else { runout <- sapply(unique(grp), function(g) list(NA)) } } else { runout <- list() message(sprintf("Preparing sojourn prior for seq '%s' ...", seqs[s])) if (is.null(soj$maxk)) { ssoj <- append(soj, initDposV(xPos[r], maxbp)) if (is.null(ssoj$fttypes)) { ssoj <- append(ssoj, list(d = unifMJ(ssoj$maxk * length(r), J))) } } else { ssoj <- append(soj, list(d = unifMJ(min(soj$maxk, length(r)), J))) ssoj$maxk <- min(soj$maxk, length(r)) } ssoj <- initSojDd(ssoj) for (g in unique(grp)) { gi <- grp == g if (iterative) { for (ci in which(gi)) { message(sprintf("Building HSMM for seq '%s' in column '%s' ...", seqs[s], ci)) if (com.emis) { semis <- emis[[ci]] } else { if (spRle) { semis <- estEmis(x[, ci][[1]][r], J = J, prior.m = prior.m, emis.type = emis.type, q.alpha = q.alpha, r.var = r.var) } else { semis <- estEmis(x[r, ci], J = J, prior.m = prior.m, emis.type = emis.type, q.alpha = q.alpha, r.var = r.var) } } if (spRle) { grunout <- tryCatch(hsmmRun(x[, ci][[1]][r], xid[ci], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e) }) } else { grunout <- tryCatch(hsmmRun(x[r, ci], xid[ci], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e) }) } if (length(grep("error", class(grunout), ignore.case = T)) != 0) { warning("Model failed for seq ", s, " and column ", c, ".\n", grunout) runout <- append(runout, list(NA)) } else { runout <- append(runout, list(grunout)) } } } else { message(sprintf("Building HSMM for group '%s' ...", g)) if (com.emis) { semis <- emis[[g]] } else { if (spRle) { stop("Rle like structure is not currently supported for mvnorm / mvt!") } else { semis <- estEmis(x[r, gi], J = J, prior.m = prior.m, emis.type = emis.type, q.alpha = q.alpha, r.var = r.var) } } grunout <- tryCatch(hsmmRun(x[r, gi], xid[gi], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e) }) if (length(grep("error", class(grunout), ignore.case = T)) != 0) { warning("Model failed for seq ", s, " and group ", g, ".\n", grunout) runout <- append(runout, list(NA)) } else { runout <- append(runout, list(grunout)) } } } } return(runout)})
23: biomvRhsmm(x = variosm, J = 6, maxbp = 100, emis.type = "mvnorm", prior.m = "cluster", maxgap = 100, com.emis = T)
24: eval(expr, .GlobalEnv)
25: eval(expr, .GlobalEnv)
26: withVisible(eval(expr, .GlobalEnv))
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
31: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
32: evalFunc(ce, options)
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
35: driver$runcode(drobj, chunk, chunkopts)
36: utils::Sweave(...)
37: engine$weave(file, quiet = quiet, encoding = enc)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
42: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Building HSMM for group '1' ...
[ hsmmRun ] seq 'chr1' column 'meth.diff+p.val' iteration: 1
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: backsolve(dec, t(x) - mean, transpose = TRUE)
2: dmvnorm(x, mean = emis$mu[[j]], sigma = emis$var[[j]])
3: FUN(X[[i]], ...)
4: lapply(X = X, FUN = FUN, ...)
5: sapply(1:J, function(j) dmvnorm(x, mean = emis$mu[[j]], sigma = emis$var[[j]]))
6: initEmis(emis = emis, x = x)
7: hsmmRun(x[r, gi], xid[gi], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(hsmmRun(x[r, gi], xid[gi], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e)})
12: FUN(X[[i]], ...)
13: lapply(X = S, FUN = FUN, ...)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
18: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
19: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
20: FUN(X[[i]], ...)
21: lapply(seq_len(cores), inner.do)
22: mylapply(seq_along(seqs), function(s) { r <- which(as.character(seqnames(xRange)) == seqs[s]) if (length(r) < 2) { warning("Region too short for seq ", s, " skipped!") if (iterative) { runout <- sapply(seq_len(nc), function(c) list(NA)) } else { runout <- sapply(unique(grp), function(g) list(NA)) } } else { runout <- list() message(sprintf("Preparing sojourn prior for seq '%s' ...", seqs[s])) if (is.null(soj$maxk)) { ssoj <- append(soj, initDposV(xPos[r], maxbp)) if (is.null(ssoj$fttypes)) { ssoj <- append(ssoj, list(d = unifMJ(ssoj$maxk * length(r), J))) } } else { ssoj <- append(soj, list(d = unifMJ(min(soj$maxk, length(r)), J))) ssoj$maxk <- min(soj$maxk, length(r)) } ssoj <- initSojDd(ssoj) for (g in unique(grp)) { gi <- grp == g if (iterative) { for (ci in which(gi)) { message(sprintf("Building HSMM for seq '%s' in column '%s' ...", seqs[s], ci)) if (com.emis) { semis <- emis[[ci]] } else { if (spRle) { semis <- estEmis(x[, ci][[1]][r], J = J, prior.m = prior.m, emis.type = emis.type, q.alpha = q.alpha, r.var = r.var) } else { semis <- estEmis(x[r, ci], J = J, prior.m = prior.m, emis.type = emis.type, q.alpha = q.alpha, r.var = r.var) } } if (spRle) { grunout <- tryCatch(hsmmRun(x[, ci][[1]][r], xid[ci], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e) }) } else { grunout <- tryCatch(hsmmRun(x[r, ci], xid[ci], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e) }) } if (length(grep("error", class(grunout), ignore.case = T)) != 0) { warning("Model failed for seq ", s, " and column ", c, ".\n", grunout) runout <- append(runout, list(NA)) } else { runout <- append(runout, list(grunout)) } } } else { message(sprintf("Building HSMM for group '%s' ...", g)) if (com.emis) { semis <- emis[[g]] } else { if (spRle) { stop("Rle like structure is not currently supported for mvnorm / mvt!") } else { semis <- estEmis(x[r, gi], J = J, prior.m = prior.m, emis.type = emis.type, q.alpha = q.alpha, r.var = r.var) } } grunout <- tryCatch(hsmmRun(x[r, gi], xid[gi], xRange[r], ssoj, semis, cMethod, maxit, maxgap, tol, avg.m = avg.m, trim = trim, na.rm = na.rm, com.emis = com.emis), error = function(e) { return(e) }) if (length(grep("error", class(grunout), ignore.case = T)) != 0) { warning("Model failed for seq ", s, " and group ", g, ".\n", grunout) runout <- append(runout, list(NA)) } else { runout <- append(runout, list(grunout)) } } } } return(runout)})
23: biomvRhsmm(x = variosm, J = 6, maxbp = 100, emis.type = "mvnorm", prior.m = "cluster", maxgap = 100, com.emis = T)
24: eval(expr, .GlobalEnv)
25: eval(expr, .GlobalEnv)
26: withVisible(eval(expr, .GlobalEnv))
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
31: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
32: evalFunc(ce, options)
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
35: driver$runcode(drobj, chunk, chunkopts)
36: utils::Sweave(...)
37: engine$weave(file, quiet = quiet, encoding = enc)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
42: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Warning in mylapply(seq_along(seqs), function(s) { :
scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected
Building HSMM complete, preparing output ...
Error: processing vignette 'biomvRCNS.Rnw' failed with diagnostics:
chunk 24 (label = varioHsmmrun2)
Error in if (!is.na(mcres[[s]][[g]][1])) { : argument is of length zero
--- failed re-building 'biomvRCNS.Rnw'
SUMMARY: processing the following file failed:
'biomvRCNS.Rnw'
Error: Vignette re-building failed.
Execution halted