Displaying 5 results from an estimated 5 matches for "checkchiptyp".
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checkchiptypes
2018 May 02
7
download.file does not process gz files correctly (truncates them?)
...if I download using
download.file("
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz
",
destfile = "GSM907811.CEL.gz")
The file is downloaded, but oligo::read.celfiles() returns the following
error:
Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
End of gz file reached unexpectedly. Perhaps this file is truncated.
Moreover, if I try to delete it after using download.file(), I get a
warning that permission is denied. I can only remove it using Windows file
explorer after I closed the R...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...destfile = "GSM907811.CEL.gz")
On windows, the 'mode' argument to download.file() needs to be "wb"
(write binary) for binary files.
Martin
>
> The file is downloaded, but oligo::read.celfiles() returns the following
> error:
>
> Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
> End of gz file reached unexpectedly. Perhaps this file is truncated.
>
> Moreover, if I try to delete it after using download.file(), I get a
> warning that permission is denied. I can only remove it using Windows file
> exp...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...>
> https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz
> ",
> destfile = "GSM907811.CEL.gz")
>
> The file is downloaded, but oligo::read.celfiles() returns the following
> error:
>
> Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
> End of gz file reached unexpectedly. Perhaps this file is truncated.
>
> Moreover, if I try to delete it after using download.file(), I get a
> warning that permission is denied. I can only remove it using Windows file
> explo...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...ot;)
>>
>
> On windows, the 'mode' argument to download.file() needs to be "wb" (write
> binary) for binary files.
>
> Martin
>
>
>> The file is downloaded, but oligo::read.celfiles() returns the following
>> error:
>>
>> Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
>> End of gz file reached unexpectedly. Perhaps this file is truncated.
>>
>> Moreover, if I try to delete it after using download.file(), I get a
>> warning that permission is denied. I can only remove it using Window...
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
...ile("https://www.ncbi.nlm.nih.gov/geo/download/
> ?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz",
> destfile = "GSM907811.CEL.gz")
>
> The file is downloaded, but oligo::read.celfiles() returns the following
> error:
>
> Error in checkChipTypes(filenames, verbose, "affymetrix", TRUE) :
> End of gz file reached unexpectedly. Perhaps this file is truncated.
>
> Moreover, if I try to delete it after using download.file(), I get a
> warning that permission is denied. I can only remove it using Windows file
> explo...