I am trying to use GEOquery to download the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39133. Based on the vignette, I should be able to just run the code:

gse <- getGEO('GSE39133')

This produces the following output:

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39133/matrix/
Found 1 file(s)
GSE39133_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39133/matrix/GSE39133_series_matrix.txt.gz'
ftp data connection made, file length 14943474 bytes
==================================================
downloaded 14.3 MB

Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) :
  cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full'

When I navigate in my web browser to the link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full, I can find it and it starts to download.

I am a bit confused as to what is happening. Because according to the getGEO documentation, it states:

 GSEMatrix: A boolean telling GEOquery whether or not to use GSE Series
           Matrix files from GEO.  The parsing of these files can be many
           orders-of-magnitude faster than parsing the GSE SOFT format
           files.  Defaults to TRUE, meaning that the SOFT format parsing
           will not occur; set to FALSE if you for some reason need other
           columns from the GSE records.

So if the SOFT file is not being parsed, why is it downloading it? Perhaps I am missing something here...

Any help would be appreciated. Many thanks in advance,

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin11.0.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
[1] GEOquery_2.38.4     Biobase_2.32.0      BiocGenerics_0.20.0
[4] nvimcom_0.9-14

loaded via a namespace (and not attached):
[1] httr_1.2.0     R6_2.1.2       tools_3.3.1    RCurl_1.95-4.8 bitops_1.0-6

Great question.  Sorry for the inconvenience, but NCBI recently changed all `http` links to be `https` only. You'll need to upgrade to at least 2.40 version of GEOquery; this version is associated with the 3.4 release of Bioconductor.  Prior to that, GEOquery used `http` and that is the issue you are seeing here.

Thanks for the reply.

I see. Any chance the conda package of bioconductor-geoquery can be updated with version 2.4? I've switched over to using conda for managing all my r package dependencies and the current version is only 2.38.4 on conda cloud hence explaining the problems...