diff --git a/DESCRIPTION b/DESCRIPTION index 793f5ee..7aac344 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: ensembldb Type: Package Title: Utilities to create and use Ensembl-based annotation databases -Version: 2.37.1 +Version: 2.37.2 Authors@R: c(person(given = "Johannes", family = "Rainer", email = "johannes.rainer@eurac.edu", role = c("aut", "cre"), diff --git a/R/functions-create-EnsDb.R b/R/functions-create-EnsDb.R index 55c4503..01e2e9f 100644 --- a/R/functions-create-EnsDb.R +++ b/R/functions-create-EnsDb.R @@ -33,10 +33,10 @@ ## retrieve Ensembl data ## save all files to local folder. ## returns the path where files have been saved to. -fetchTablesFromEnsembl <- function(version, ensemblapi, user="anonymous", - host="ensembldb.ensembl.org", pass="", - port=5306, species="human"){ - if(missing(version)) +fetchTablesFromEnsembl <- function(version, ensemblapi, user = "anonymous", + host = "ensembldb.ensembl.org", pass = "", + port = 5306, species = "human"){ + if (missing(version)) stop("The version of the Ensembl database has to be provided!") ## setting the stage for perl: fn <- system.file("perl", "get_gene_transcript_exon_tables.pl", @@ -45,8 +45,10 @@ fetchTablesFromEnsembl <- function(version, ensemblapi, user="anonymous", ## replacing white spaces with _ species <- gsub(species, pattern=" ", replacement="_") - cmd <- paste0("perl ", fn, " -s ", species," -e ", version, - " -U ", user, " -H ", host, " -p ", port, " -P ", pass) + cmd <- paste0("perl ", fn, " -s ", shQuote(species), + " -e ", shQuote(version), " -U ", shQuote(user), + " -H ", shQuote(host), " -p ", shQuote(port), + " -P ", shQuote(pass)) if(!missing(ensemblapi)){ Sys.setenv(ENS=ensemblapi) } diff --git a/inst/NEWS b/inst/NEWS index 3516ef5..357e966 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -1,3 +1,8 @@ +Changes in version 2.37.2 + +- Fix first security issues reported by the Bioconductor Security Audit: + - `fetchTablesFromEnsembl()`: fix potential command injection issue. + Changes in version 2.33.3 - Add `genome<-` method to support manually setting the genome build version.