Hi Val, I think I achieved some resolution, if not total clarity. It's to do with the encoding of the of the two path variables:
> Encoding(path1) [1] "unknown" > Encoding(path2) [1] "UTF-8" I don't understand why recursive calls to normalizePath() changes the encoding, but the combination of HDF5 & Windows fails when given UTF-8 paths. I've updated rhdf5 to try and ensure paths are encoded in Latin-1 which Windows is fine with, but it'll still go awry if you use characters outside that set. I'm still searching for a more comprehensive solution. Thanks, Mike On Thu, 31 May 2018 at 20:09, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Mike, > Is this still an issue or has it been resolved? > Val > > > On 05/22/2018 02:19 PM, Mike Smith wrote: > > In trying to diagnose this issue athttps://support.bioconductor.org/p/108548/ > I've found some weird behaviour > with Windows, normalizePath(), and non-ASCII characters. Essentially, if I > run normalizePath() recursively on a path that contains 'é' (I haven't > tried other characters) something 'changes' in the string, but I can't work > out what, and it breaks a subsequent .Call() which uses the path. > > The example below tries to demonstrate this in a fairly concise manner. It > works fine if normalizePath() is run once, but fails after it's run a > second time on itself. > > However, change "éxample" for "example" and both instances work. Similarly, > both run fine on my Linux machine with the non-ASCII character inplace. > > I'd be grateful if anyone else with a Windows machine could verify this > behaviour, or to shed any light on what might be the difference between path1 > and path2 below. > > Thank, > Mike > > ------------------------------ > > ## setup some HDF5 components required later > flags <- rhdf5:::h5checkConstants("H5F_ACC", h5default("H5F_ACC")) > fcpl <- rhdf5:::h5checktypeAndPLC(NULL, "H5P_FILE_CREATE", allowNULL = TRUE) > fapl <- rhdf5::H5Pcreate("H5P_FILE_ACCESS") > > ## create a folder with non-ASCII character > dir.create('éxample') > setwd("éxample") > > ## create two normalized paths recursively - these are 'identical' > path1 <- normalizePath('test.h5', mustWork = FALSE) > path2 <- normalizePath(path1, mustWork = FALSE) > identical(path1, path2) > > ## create an HDF5 file using path1 - this works > fid <- .Call("_H5Fcreate", path1, flags, fcpl@ID, fapl@ID, > PACKAGE = "rhdf5") > .Call("_H5Fclose", fid, PACKAGE = "rhdf5") > file.remove(path1) > > ## create an HDF5 file using path2 - this fails > fid <- .Call("_H5Fcreate", path2, flags, fcpl@ID, fapl@ID, > PACKAGE = "rhdf5") > if(exists('fid2')) { > .Call("_H5Fclose", fid2, PACKAGE = "rhdf5") > file.remove(path2) > } > > ## tidy up > rhdf5::h5closeAll() > setwd("../") > > [[alternative HTML version deleted]] > > _______________________________________________bioc-de...@r-project.org > mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
