THIS IS MEANT TO REFERENCE A COMMENT I MADE IN MY QUESTION ABOUT WHAT I WAS ORIGINALLY TRYING TO DO:

By the way, for anybody who came here because you are also trying this with yeast, or other non-human model organism, by providing the correct species name, but still encountering the error:

Error in .normargSeqlengths(value, seqnames(x)) : 
  when the supplied 'seqlengths' vector is named, the names must match the seqnames

I think you get that because your chromosomes supplied are out of order, and the solution to address this was in Leonardo's reply -> C: derfinder: fullCoverage() problems. You need to find out the order and formats `GenomeInfoDb` has by installing, loading, and querying `GenomeInfoDb` in R.

Leonardo's reply showed it for a couple of chromosomes for Populus trichocarpa .

Here I'll show the updated result for Populus and illustrate doing that for Saccharomyces cervisiae with the evaluated R code below:

> source("https://bioconductor.org/biocLite.R")
> biocLite("GenomeInfoDbData")
> library(GenomeInfoDb)
...
> genomeStyles()$Populus_trichocarpa[c(2, 11), ]
   circular auto   sex NCBI JGI2.F Ensembl
2     FALSE TRUE FALSE LGII      2       2
11    FALSE TRUE FALSE LGXI     11      11

> genomeStyles()$Saccharomyces_cerevisiae
   circular  auto   sex NCBI    UCSC Ensembl
1     FALSE  TRUE FALSE    I    chrI       I
2     FALSE  TRUE FALSE   II   chrII      II
3     FALSE  TRUE FALSE  III  chrIII     III
4     FALSE  TRUE FALSE   IV   chrIV      IV
5     FALSE  TRUE FALSE    V    chrV       V
6     FALSE  TRUE FALSE   VI   chrVI      VI
7     FALSE  TRUE FALSE  VII  chrVII     VII
8     FALSE  TRUE FALSE VIII chrVIII    VIII
9     FALSE  TRUE FALSE   IX   chrIX      IX
10    FALSE  TRUE FALSE    X    chrX       X
11    FALSE  TRUE FALSE   XI   chrXI      XI
12    FALSE  TRUE FALSE  XII  chrXII     XII
13    FALSE  TRUE FALSE XIII chrXIII    XIII
14    FALSE  TRUE FALSE  XIV  chrXIV     XIV
15    FALSE  TRUE FALSE   XV   chrXV      XV
16    FALSE  TRUE FALSE  XVI  chrXVI     XVI
17     TRUE FALSE FALSE   MT    chrM    Mito
18     TRUE FALSE  TRUE  2uM 2micron    <NA>
> 

This will tell you what order to supply them and allow you to determine what style matches your chromosome names. See unevaluated code example here --> (derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle').

The rest of this post is about getting things to behave when you are providing a non-model organism name.

Versions 1.10.1 and 1.11.1 now have better documentation for extendedMapSeqlevels(). See https://github.com/lcolladotor/derfinder/commit/9913ff01fd129705e5fcf9e410c51fc26fc2d546 for details.

Okay I tried this command below:

## Load libraries
library('derfinder')
library('GenomicRanges')
file_designations <- c("WT1","WT2","WT3", "MT1", "MT2", "MT3")
chrs_all = c('I', 'II','III','IV', 'IX', 'V', 'VI', 'VII', 'VIII', 'X', 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI', 'XVII')
## Load the data from disk
files <- file.path("/data/alignments", file_designations , paste0(file_designations,"Aligned.sorted.bam"))
system.time(fullCov <- fullCoverage(files = files, chrs = chrs_all, totalMapped = sapply(files,getTotalMapped, chrs = chrs_all), targetSize = 8e+07, currentStyle = 'UCSC'))
system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75))

Still got same issue when it hit the tenth chromosome in the regionMatrix() command:

...lots of lines before this of it working....
2017-05-04 19:23:41 getRegionCoverage: processing VIII
2017-05-04 19:23:41 getRegionCoverage: done processing VIII
2017-05-04 19:23:41 regionMatrix: calculating coverageMatrix
2017-05-04 19:23:42 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-04 19:23:42 regionMatrix: processing X
2017-05-04 19:23:43 filterData: originally there were 745751 rows, now there are 694290 rows. Meaning that 6.90000000000001 percent was filtered.
2017-05-04 19:23:43 findRegions: identifying potential segments
2017-05-04 19:23:43 findRegions: segmenting information
2017-05-04 19:23:43 findRegions: identifying candidate regions
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
2017-05-04 19:23:43 findRegions: identifying region clusters
Error in .normargSeqlengths(value, seqnames(x)) :
  when the supplied 'seqlengths' vector is named, the names must match the seqnames
Timing stopped at: 19.4 0.064 19.463
> 

Even with that setting, regionMatrix() seems to ignore the fact it shouldn't touch the chromosome names when it gets to that one.
I just tried using the test data and put `fullCov <- fullCoverage(files=files[1], chrs=c('21','X', '22'), currentStyle = 'UCSC')` to see if the regionMatrix() command. `system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 76))` then says `extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens`, but it didn't. It also find no regions and so I don't know if it is a valid comparison?
Unevaluated code:

library(derfinder)
datadir <- system.file('extdata', 'genomeData', package='derfinder')
files <- rawFiles(datadir=datadir, samplepatt='*accepted_hits.bam$',
     fileterm=NULL)
## Shorten the column names
names(files) <- gsub('_accepted_hits.bam', '', names(files))
## Read and filter the data, only for 1 file
fullCov <- fullCoverage(files=files[1], chrs=c('21','X','22'), currentStyle = 'UCSC')
system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 76))

Here is the result:

> system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 76))
2017-05-04 21:05:05 regionMatrix: processing 21
2017-05-04 21:05:05 filterData: originally there were 48129895 rows, now there are  rows. Meaning that  percent was filtered.
2017-05-04 21:05:05 findRegions: identifying potential segments
2017-05-04 21:05:05 regionMatrix: processing X
2017-05-04 21:05:05 filterData: originally there were 155270560 rows, now there are  rows. Meaning that  percent was filtered.
2017-05-04 21:05:05 findRegions: identifying potential segments
2017-05-04 21:05:05 regionMatrix: processing 22
2017-05-04 21:05:05 filterData: originally there were 51304566 rows, now there are  rows. Meaning that  percent was filtered.
2017-05-04 21:05:05 findRegions: identifying potential segments
   user  system elapsed 
  0.052   0.000   0.049 
Warning messages:
1: In findRegions(position = filt$position, fstats = filt$meanCoverage,  :
  Found no regions
2: In findRegions(position = filt$position, fstats = filt$meanCoverage,  :
  Found no regions
3: In findRegions(position = filt$position, fstats = filt$meanCoverage,  :
  Found no regions

>