I asked about /media/ because 'usually' this is where one mounts removable media like thumb drives and so on. I guess when you reported available space it was from a command like df -h /media/nat/entain/toy3/Bioconductor/data

You could try and debug by using `debug()` and then stepping through individual functions until something goes wrong; here's my session... I start by debugging some likely functions, one exported the other not...

> debug(parseGEO)
> debug(GEOquery:::parseGPL)

I then evaluate the function, where 'fl' is the file path to my cached file. The function runs until it calls parseGEO

> gseEset2 <- getGEO('GSE76896', destdir=fl)[[1]]
Found 1 file(s)
GSE76896_series_matrix.txt.gz
Using locally cached version: /tmp/Rtmpe4NWji/file4e3d1576c470/GSE76896_series_matrix.txt.gz
Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_character()
)
See spec(...) for full column specifications.
|=================================================================| 100%   84 MB
Using locally cached version of GPL570 found here:
/tmp/Rtmpe4NWji/file4e3d1576c470/GPL570.soft
debugging in: parseGEO(filename, GSElimits, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL)
debug: {
    con <- fileOpen(fname)
    first.entity <- findFirstEntity(con)
    close(con)
    ret <- switch(as.character(first.entity[1]), sample = {
        parseGSM(fname)
    }, series = parseGSE(fname, GSElimits), dataset = {
        parseGDS(fname)
    }, platform = {
        parseGPL(fname)
    }, `0` = {
        parseGSEMatrix(fname, destdir = destdir, AnnotGPL = AnnotGPL,
            getGPL = getGPL)$eset
    }, )
    return(ret)
}

I then look at the help page ?browser and type 'n' to go to the next line of code

Browse[2]> n
debug: con <- fileOpen(fname)
Browse[2]> n
debug: first.entity <- findFirstEntity(con)
Browse[2]> n
debug: close(con)
Browse[2]> n
debug: ret <- switch(as.character(first.entity[1]), sample = {
    parseGSM(fname)
}, series = parseGSE(fname, GSElimits), dataset = {
    parseGDS(fname)
}, platform = {
    parseGPL(fname)
}, `0` = {
    parseGSEMatrix(fname, destdir = destdir, AnnotGPL = AnnotGPL,
        getGPL = getGPL)$eset
}, )
Browse[2]> n

until I get to the next place I'd put a debug call, and then step through some more, eventually exiting

debug: parseGPL(fname)
Browse[2]> n
debugging in: parseGPL(fname)
debug: {
    if (getOption("GEOquery.inmemory.gpl")) {
        info <- file.info(fname, extra_cols = FALSE)
        cache <- get0(fname, envir = GPLcache, inherits = FALSE)
        if (!is.null(cache) && cache$info$mtime == info$mtime) {
            message("Using GPL object found in memory from locally cached version.")
            return(cache$gpl)
        }
    }
    txt = read_lines(fname)
    txt = txt[txt != ""]
    return(.parseGPLTxt(txt))
}
Browse[3]> n
debug: if (getOption("GEOquery.inmemory.gpl")) {
    info <- file.info(fname, extra_cols = FALSE)
    cache <- get0(fname, envir = GPLcache, inherits = FALSE)
    if (!is.null(cache) && cache$info$mtime == info$mtime) {
        message("Using GPL object found in memory from locally cached version.")
        return(cache$gpl)
    }
}
Browse[3]> n
debug: txt = read_lines(fname)
Browse[3]> n
|=================================================================| 100%   80 MB
debug: txt = txt[txt != ""]
Browse[3]> n
debug: return(.parseGPLTxt(txt))
Browse[3]> n
|=================================================================| 100%   75 MB
exiting from: parseGPL(fname)
debug: return(ret)
Browse[2]> n
exiting from: parseGEO(filename, GSElimits, destdir, AnnotGPL = AnnotGPL, getGPL = getGPL)

At some point your own code will freeze. You can then break, debug() that function, and try again. Repeat until you get to what seems like a basic function (e.g., read_csv) that seems like it 'should' work; you can print out things like variables while in the Browser> , so occasionally you will want to do a 'sanity check'.