I am trying to rerun the simulation in the CSAW paper, but the autosim.R file (http://bioinf.wehi.edu.au/csaw/autosim.R) does not seem to work.

I run autosim.R with the following line added:

is.tf = FALSE

and I get the error 

Error in crunch2BAM(fnames) : failed to sort BAM file

How do I fix this?

I'm guessing that you're using the latest version of SAMtools, where it seems that the legacy options for sort are no longer supported. Specifically, instead of:

samtools sort <INPUT.BAM> <OUT>

... the new call is now:

samtools sort <INPUT.BAM> -o <OUT.BAM>

Note the extra "-o" flag and the use of the full output file name rather than just the prefix in the legacy version. You can just change the relevant line in crunch2BAM to:

system(paste("samtools sort", temp, "-o", paste0(prefix, ".bam")), ignore.stderr=TRUE)

... and then re-install the xscss package. I'll also update the package on the WEHI page (now version 1.1.3).

P.S. This question is about the paper, not the package, so it's probably best to email me directly rather than putting it on the support site.

I changed crunch2bam to the following:

crunch2BAM<-function(sam.files, dir=".")
# This crunches a set of SAM files to sorted & indexed BAM files using the samtools command.
# We avoid calling Rsamtools because of strange errors with 'invalid cross-device link'. I
# think it's putting things in /tmp when that might be full, and I can't see any option to
# change the temporary directory.
#
# written by Aaron Lun
{
    out<-NULL
    for (sam.file in sam.files) {
        prefix<-file.path(dir, sub("\\.sam$", "", basename(sam.file)))
        temp<-tempfile(tmpdir=dir, fileext=".bam")
        if (system(paste("samtools view -bS -h", sam.file, "-o", temp), ignore.stderr=TRUE)) {
            stop("failed to compress to BAM")
        }

    # system(paste("samtools sort", temp, prefix), ignore.stderr=TRUE)
        if (system(paste("samtools sort", temp, "-o", paste0(prefix, ".bam")), ignore.stderr=TRUE)) {
            stop("failed to sort BAM file")
        }
        bam.file<-paste0(prefix, ".bam")
        indexBam(bam.file)
        unlink(temp)
        out<-append(out, bam.file)
    }
    return(out);
}

and then created a new tar.gz with

tar -cvzf xscss_1.1.2.tar.gz xscss/**

But when I try to install it I get

> install.packages("xscss_1.1.2.tar.gz", repos=NULL, type="source")
Installing package into '/local/home/endrebak/R/x86_64-pc-linux-gnu-library/3.2'
(as 'lib' is unspecified)
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
Warning in file.link(name2, name) :
  cannot link 'xscss/man/fillGenome.Rd' to 'xscss/man/fillGenome.Rd', reason 'No such file or directory'
... long list of similar messages ...
* installing *source* package 'xscss' ...
** libs
Warning: no source files found
** help
No man pages found in package  'xscss'
*** installing help indices
** building package indices
** testing if installed package can be loaded
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
Note: the specification for S3 class "AsIs" in package 'DBI' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Error in library.dynam(lib, package, package.lib) :
  shared object 'xscss.so' not found
Error: loading failed
Execution halted
ERROR: loading failed