About a windows only error message

[Codezy99]

Hi @lawremi,

I am developing a Bioconductor package (m6Aboost) and I meet a windows only bug when I submit the package to bioconductor. The error message looks like this:

Warning in .local(con, format, text, ...) :
  Invalid argument
lseek(5, 366, invalid 'whence' value (1822621639)) failed
Error in .local(con, format, text, ...) : UCSC library operation failed
Calls: CtoTAssignment ... import -> import -> import -> import -> .local -> .Call
Execution halted
** running examples for arch 'x64' ... [33s] OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
m6Aboost 9.14   1.23   11.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [29s]
 [30s] ERROR
Running the tests in 'tests/testthat.R' failed.
Last 20 lines of output:
    7.       \-BiocIO::import(con, "BigWig", ...)
    8.         +-BiocIO::import(FileForFormat(con, format), ...)
    9.         \-rtracklayer::import(FileForFormat(con, format), ...)
   10.           \-rtracklayer:::.local(con, format, text, ...)
  -- Error (test_truncationAssignment.R:9:5): truncationAssignment works as expected --
  Error: UCSC library operation failed
  Backtrace:
       x
    1. +-m6Aboost::truncationAssignment(...) test_truncationAssignment.R:9:4
    2. \-m6Aboost::truncationAssignment(...)
    3.   \-m6Aboost:::.readBW(bw_positive, bw_negative)
    4.     +-rtracklayer::import.bw(con = file_P)
    5.     \-rtracklayer::import.bw(con = file_P)
    6.       +-BiocIO::import(con, "BigWig", ...)
    7.       \-BiocIO::import(con, "BigWig", ...)
    8.         +-BiocIO::import(FileForFormat(con, format), ...)
    9.         \-rtracklayer::import(FileForFormat(con, format), ...)
   10.           \-rtracklayer:::.local(con, format, text, ...)

I have tested the package on my windows machine, but it did not give me any error. I think the maintainer of "karyoploteR" package also met this issue. And the issue that he reported could be found in this link: https://stat.ethz.ch/pipermail/bioc-devel/2018-September/014119.html.

I was wondering whether you can give me some tipps to take care of this error message. Thank you : )

Best regards, You Zhou

[lawremi]

Perhaps @sanchit-saini has the time to look into this. Support for reading bigwigs on Windows is probably still a bit shaky.

[sanchit-saini]

Sure I will look into it.