Hello,
I tried downloading that file using 'utils::download.file' (which worked), but then continued to complain about "damaged archive" when trying to use 'utils::untar'. However, it seemed to work when I downloaded the archive manually. Finally, the solution I found is that you have to specify the mode in which you're downloading the file. Something like: URL <- " https://ftp.ncbi.nlm.nih.gov/geo/series/GSE162nnn/GSE162562/suppl/GSE162562_RAW.tar " FILE <- file.path(tempdir(), basename(URL)) utils::download.file(URL, FILE, mode = "wb") utils::untar(FILE, exdir = dirname(FILE)) worked perfectly for me. It seems to also work still on Ubuntu, but you can let us know if you find it doesn't. I hope this helps! On Mon, Aug 23, 2021 at 3:20 PM Anas Jamshed <anasjamshed1...@gmail.com> wrote: > I am trying this URL: " > https://ftp.ncbi.nlm.nih.gov/geo/series/GSE162nnn/GSE162562/suppl/GSE162562_RAW.tar > " > > but it is not giving me any file > > On Mon, Aug 23, 2021 at 11:42 PM Andrew Simmons <akwsi...@gmail.com> > wrote: > >> Hello, >> >> >> I don't think you need to use a system command directly, I think >> 'utils::untar' is all you need. I tried the same thing myself, something >> like: >> >> >> URL <- "https://exiftool.org/Image-ExifTool-12.30.tar.gz"; >> FILE <- file.path(tempdir(), basename(URL)) >> >> >> utils::download.file(URL, FILE) >> utils::untar(FILE, exdir = dirname(FILE)) >> >> >> and it makes a folder "Image-ExifTool-12.30". It seems to work perfectly >> fine in Windows 10 x64 build 19042. Can you send the specific file (or >> provide a URL to the specific file) that isn't working for you? >> >> On Mon, Aug 23, 2021 at 12:53 PM Anas Jamshed <anasjamshed1...@gmail.com> >> wrote: >> >>> I have the file GSE162562_RAW. First I untar them >>> by untar("GSE162562_RAW.tar") >>> then I am running like: >>> system("gunzip ~/Desktop/GSE162562_RAW/*.gz") >>> >>> >>> This is running fine in Linux but not in windows. What changes I >>> should make to run this command in windows as well >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
