I did this:
makeOrgPackageFromNCBI(version = "0.1", author = "Marco Chiapello <firstname.lastname@example.org>", maintainer = "Some One <email@example.com>", outputDir = ".", tax_id = "3880", genus = "Medicago", species = "truncatula")
And I get this output error:
If this is the 1st time you have run this function, it may take a long time (over an hour) to download needed files and assemble a 12 GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day. Getting data for gene2pubmed.gz Loading required package: RCurl Loading required package: bitops extracting only data for our organism from : gene2pubmed Getting data for gene2accession.gz extracting only data for our organism from : gene2accession Getting data for gene2refseq.gz extracting only data for our organism from : gene2refseq Getting data for gene2unigene extracting only data for our organism from : gene2unigene getting all data for our organism from : gene2unigene Getting data for gene_info.gz extracting only data for our organism from : gene_info Getting data for gene2go.gz extracting only data for our organism from : gene2go Error in function (type, msg, asError = TRUE) : FTP response timeout
Any idea how to fix it?
Thank you very much in advance,
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.1 (El Capitan) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  grid tools stats graphics grDevices utils datasets methods base other attached packages:  gridExtra_2.0.0 tidyr_0.3.1 ggplot2_1.0.1 HSAUR_1.3-7 cluster_2.0.3  mvtnorm_1.0-3 gss_2.1-5 loaded via a namespace (and not attached):  Rcpp_0.12.1 magrittr_1.5 MASS_7.3-44 munsell_0.4.2 colorspace_1.2-6  R6_2.1.1 stringr_1.0.0 plyr_1.8.3 dplyr_0.4.3 parallel_3.2.2  gtable_0.1.2 DBI_0.3.1 lazyeval_0.1.10 digest_0.6.8 assertthat_0.1  reshape2_1.4.1 labeling_0.3 stringi_1.0-1 scales_0.3.0 proto_0.3-10