Error using getGEO - error reading from the connection

Question

[bautin]

Hi, I've been trying to open GEO data in R studio. So far I have the following code, copied from a tutorial:

#tutorial for analysing data from GEO
library(GEOquery)

my_id <- "GSE33126"

gse <- getGEO(my_id)

However, I get the following error when running this code:

Found 1 file(s)
GSE33126_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3658664 bytes (3.5 MB)
downloaded 3.5 MB
File stored at: 
C:\Users\mark\AppData\Local\Temp\RtmpovALno/GPL6947.soft.gz
Error in readLines(con, 100) : error reading from the connection
In addition: Warning message:
In for (i in seq_len(n)) { :
  closing unused connection 3 (C:\Users\mark\AppData\Local\Temp\RtmpovALno/GPL6246.soft.gz)

For reference, I have a fresh R studio and R installation with R version 4.1.2. The packages I have installed are:

install.packages("BiocManager")
install.packages("forcats")
install.packages("stringr")
install.packages("ggplot2")
install.packages("ggrepel")
install.packages("readr")
install.packages("tidyr")
install.packages("survminer")
BiocManager::install("GEOquery")
BiocManager::install("limma")
BiocManager::install("pheatmap")
BiocManager::install("org.Hs.eg.db")

It seems that the file is downloaded correctly, but something is going wrong afterwards. Does anyone have an idea what could be the problem here?

[zx8754]

Related GitHub issue - https://github.com/seandavi/GEOquery/issues/118