Hi Folks

I ran DEXSeqHTML and something has gone wrong with the filenames of the output. In stead of saving the files to DEXSeqReport/file/ENSG000000003.10count.htm, all the files were saved as: DEXSeqReport/fileENSG000000003.10count.htm, i.e. the slash between the subdirectory file and ENSG disappeared. Apart from setting my working directory I have not specified any directory names. Why did this happen and how should I fix it? If I need to provide any more information to make sense of this, please just ask.

All help will be appreciated.

Kind Regards
Jannetta

This is my first post, so I apologize if it's a little unorthodox or inappropriately formatted. 

I am running into the same error as Jannetta, and I believe that I have identified the problem. 

When exporting the report with DEXSeqHTML(), the .html and .svg files have "files" appended to the name and are not written in the "files" directory.  I believe the problem is with line # 66 in the source code for the DEXSeqHTML function.  It reads:

ptowrite <- file.path(path, "files/")

On windows, for R versions < 3.1.0, trailing "/" characters are removed when using the file.path function: https://stat.ethz.ch/R-manual/R-devel/library/base/html/file.path.html.

The result is that instead of writing the html and .svg files to the "files" directory, they now simply all have "files" appended to the beginning of the names for windows users. This issue is demonstrated below:

> path = "yourfilepath"
> ptowrite <- file.path(path, "files/")
> ptowrite
[1] "yourfilepath/files"

The trailing "/" is removed, which I think causes problems later when the ptowrite character string is used to write files into the "files" sub-directory.  To get around this issue, windows users might edit the code by entering in their R console

trace("DEXSeqHTML",edit=TRUE)

This will bring up the code for the DEXSeqHTML function for editing. Change line # 66 of the DEXSeqHTML function to:

ptowrite <- paste0(path, "/files/")

Please note that I changed the function used and added an additional "/". 
After that change I was able to export the html report on my windows machine without issues. 

-Joseph

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.16.1              DESeq2_1.10.0              RcppArmadillo_0.5.400.2.0  Rcpp_0.12.1               
 [5] SummarizedExperiment_1.0.1 GenomicRanges_1.22.1       GenomeInfoDb_1.6.1         IRanges_2.4.1             
 [9] S4Vectors_0.8.2            Biobase_2.30.0             BiocGenerics_0.16.1        BiocParallel_1.4.0        
[13] RevoUtilsMath_3.2.2    

Thanks a lot for the catch, I have implemented your fix to the latest version of DEXSeq in the svn.

Alejandro