I'm getting an error when running runSeqsumm to read a file.  Here's my code and the error message:

> library(seqCNA)
> runSeqsumm(file='C1.sam')
Reading records from C1.sam
Summarizing in windows of 50000 bps.
sh: c®Ä: command not found

Writing results to disk...

Done!
>

Naturally I've checked that the file in question (C1.sam) exists and is a valid sam file. The program creates a file with a garbage name (eg, '%E7%D4I???') containing just a header line:

chrom	win.start	reads.gc	reads.mapq	counts

The guts of runSeqsumm is a C++ function. It kind of feels like the R-C++ linkage is not right. I'm not an R package developer and don't know how to "remake" the package (other than by reinstalling it from scratch), but if someone can point me in that direction I'm happy to give it a try.

Here's the sessionInfo

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] seqCNA_1.16.0       seqCNA.annot_1.6.0  adehabitatLT_0.3.20
 [4] CircStats_0.2-4     boot_1.3-17         MASS_7.3-45
 [7] adehabitatMA_0.3.10 ade4_1.7-3          sp_1.2-2
[10] doSNOW_1.0.14       snow_0.4-1          iterators_1.0.8
[13] foreach_1.4.3       GLAD_2.34.0

loaded via a namespace (and not attached):
[1] codetools_0.2-14 grid_3.2.3       lattice_0.20-33

Thanks for trying out seqCNA, I´m really sorry to hear that you have run into problems.

I have looked into it and here are some comments that might help us in the troubleshooting:

- seqCNA does not use samtools for the processing of files in SAM format, but I have tried replicating the error in a system without samtools, just in case, without luck.

- I have also tried to replicate the error using the same R, package and OS (10.8 though), as well as with other combinations of package version (1.10), OS (Linux), R (3.1) and various SAM files. Still no luck.

- Now, the closest I have come to replicating the error is when I try to analyze a BAM file without the function knowing where samtools is:

> runSeqsumm(file=sam)
Warning in runSeqsumm(file = sam) :
  A seqsumm output file already exists in the folder and will be overwritten.
Reading records from alignments.REF_21.bam
Summarizing in windows of 50000 bps.
sh: samtools: command not found

Writing results to disk...

Done!

Those symbols are really odd. As a typical troubleshooting approach, could you please reinstall the package and/or try on a different machine?