Hi, I'm trying to use the code provided by GEO2R for my own purposes, but run into an error while loading the ncbi annotations. I'm using a locally downloaded copy of the series matrix for GSE50397 (I'm unable to get getGEO to download the file from the internet). Here is the relevant portion of my code :

################################################################
#   Differential expression analysis with limma
library(Biobase)
library(GEOquery)
library(limma)

## load series and platform data from GEO
gset <- getGEO(filename = "data/GSE50397_series_matrix.txt.gz", GSEMatrix=TRUE, AnnotGPL=TRUE)

...

# load NCBI platform annotation
gpl <- annotation(gset)
platf <- getGEO(gpl, AnnotGPL=TRUE)
ncbifd <- data.frame(attr(dataTable(platf), "table"))

Error thrown on line gset <- getGEO(filename ... )and platf <- getGEO(gpl, AnnotGPL=TRUE) :

Using locally cached version of GPL6244 found here:
/tmp/RtmpE2RbXC/GPL6244.annot.gz 
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) : 
  invalid 'nlines' argument

The temporary files created show GPL6244.soft (48MB) and GPL6244.annot.gz (0B). I don't know if I should be downloading GPL6244.annot.gz from someplace on the internet.

Here's the output of sessionInfo() :

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

locale:
[1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8  
[5] LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C               
[9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] limma_3.26.3        GEOquery_2.36.0     Biobase_2.30.0      BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] tools_3.2.2    RCurl_1.95-4.7 bitops_1.0-6   XML_3.98-1.3