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 <anasjamshed1994 at
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 <akwsimmo at
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 <anasjamshed1994 at
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]]
>>>
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>>
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