bugfix for compact ellipsis on windows system

[FelixErnst]

On windows the compact ellipsis is now shown correctly due to encoding change in S4Vectors::safeExplode. Solution works both on Windows and Linux. macOS was not tested.

[FelixErnst]

The windows specific error of the Modstrings package on devel is caused by the compact_ellipsis incompatibility on windows system triggered by the show method.

http://bioconductor.org/checkResults/3.11/bioc-LATEST/Modstrings/tokay2-buildsrc.html

Modstrings relies currently on the toSeqSnippet function from Biostrings. In this function the compact_ellipsis is added, but the encoding does not stick, so that the character get two additional letters breaking a offset calculation, which then turns negative. This raises the invalid times argument error, since times must be positive.

Should implement toSeqSnippet myself in the Modstrings package?

[FelixErnst]

Hi Herve @hpages

just wanted to bump this PR. Any comments?

I had to investigate some other encoding issue in BiocPkgTools package and by accident got a bit more insight intos the underlying issue.

1. the compact ellipsis has a different raw value on windows systems. Therefore rawToChar(as.raw(c(0xe2, 0x80, 0xa6))) isn't working as expected.
2. strsplit(xi,"")[[1L]] preserves the boundary of individual characters, whereas safeExplode(xi) relies on the correct lenght of the character vector being returned by LENGTH or XLENGTH in the C code. What I didn't realize initially is that even on Linux safeExplode(xi) destroys the ellipsis character. However, paste0 can stich it back together on Linux, which doesn't work on Windows.

Felix

[hpages]

Thanks Felix. I'm no longer using the compact ellipsis (see commit 567d8c3). Yes it saves 2 characters but it's hard to see so I'm back using the 3 dots.