Tag Archives: R language learning

Error: The size of the connection buffer (131072) was not large enough

R language, carry out geo data mining and analysis, Download geo data online,

gset <- getGEO("GSE94994", GSEMatrix =TRUE, AnnotGPL=FALSE)

The following error is reported:

Found 1 file(s)
GSE94994_series_matrix.txt.gz
Using locally cached version: C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GSE94994_series_matrix.txt.gz
Error: The size of the connection buffer (131072) was not large enough
to fit a complete line:
  * Increase it by setting `Sys.setenv("VROOM_CONNECTION_SIZE")`

Rstido’s default link cache is 131072 bytes. After conversion, it is 131kb, 0.131mb

  But the size of the data you downloaded & gt; 131072 bytes, so we need to adjust the default connection cache for normal download

resolvent:

Sys.setenv("VROOM_CONNECTION_SIZE"=99999999)

  Code implementation:

> gset <- getGEO("GSE94994", GSEMatrix =TRUE, AnnotGPL=FALSE)
Found 1 file(s)
GSE94994_series_matrix.txt.gz
Using locally cached version: C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GSE94994_series_matrix.txt.gz
Error: The size of the connection buffer (111) was not large enough
to fit a complete line:
  * Increase it by setting `Sys.setenv("VROOM_CONNECTION_SIZE")`
> Sys.setenv("VROOM_CONNECTION_SIZE"=99999999)
> gset <- getGEO("GSE94994", GSEMatrix =TRUE, AnnotGPL=FALSE)
Found 1 file(s)
GSE94994_series_matrix.txt.gz
Using locally cached version: C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GSE94994_series_matrix.txt.gz
Rows: 18 Columns: 160                                                                                                         
 0s-- Column specification --------------------------------------------------------------------------------------------------------
Delimiter: "\t"
chr   (1): ID_REF
dbl (159): GSM2493904, GSM2493905, GSM2493906, GSM2493907, GSM2493908, GSM2493909, GSM2493910, GSM2493911, GSM2493912, GSM24...

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
Using locally cached version of GPL23075 found here:
C:\Users\ENMONS~1\AppData\Local\Temp\Rtmpe27iLR/GPL23075.soft