The EBI GWAS catalog is large -- now the download is over 100MB for 179K associations. A "bug" in the package was reported, so I acquired the file by hand.
> nn = read.delim("gwas_catalog_v1.0.2-associations_e98_r2020-03-08.tsv", sep="\t") *Warning message:* *In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :* * EOF within quoted string* > dim(nn) [1] 35264 38 The "bug" is the number 35264 ... > [1]+ Stopped R %vjcair> wc gwas_cat*tsv 179365 13243516 120140148 gwas_catalog_v1.0.2-associations_e98_r2020-03-08.tsv %vjcair> vi gwas_cat*tsv %vjcair> fg R > tail(nn) *Error: C stack usage 98161262 is too close to the limit* *Maybe my R needs to be updated.* *If I use data.table::fread to consume the tsv over HTTP all seems well, and perhaps* *I will switch to that.* -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel