sir after that I want to run:
#get the list of sample names
GSMnames <- t(list.files("~/Desktop/GSE162562_RAW", full.names =
F))
#remove .txt from file/sample names
GSMnames <- gsub(pattern = ".txt", replacement = "",
GSMnames)
#make a vector of the list of files to aggregate
files <- list.files("~/Desktop/GSE162562_RAW", full.names = TRUE)
but it is not running as after running utils::untar(FILE, exdir dirname(FILE))
it creates another 108 archieves
On Tue, Aug 24, 2021 at 2:03 AM Andrew Simmons <akwsimmo at gmail.com>
wrote:
> 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]]
>>>>
>>>> ______________________________________________
>>>> R-help at 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.
>>>>
>>>
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