[med-svn] [r-bioc-genomeinfodbdata] 01/03: New upstream version 1.0.0

[Graham Inggs]

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ginggs pushed a commit to branch master
in repository r-bioc-genomeinfodbdata.

commit 768c4aa204fba0a4e22d32f7415821dccd70480e
Author: Graham Inggs <ginggs at debian.org>
Date:   Tue Dec 19 20:49:02 2017 +0200

    New upstream version 1.0.0
---
 DESCRIPTION                           |  4 ++--
 inst/scripts/updateGenomeInfoDbData.R |  8 ++++----
 man/GenomeInfoDbData-package.Rd       | 14 +++++++-------
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4735e28..19f4baa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,11 +2,11 @@ Package: GenomeInfoDbData
 Title: Species and taxonomy ID look up tables used by GenomeInfoDb
 Description: Files for mapping between NCBI taxonomy ID and species. Used
         by functions in the GenomeInfoDb package.
-Version: 0.99.1
+Version: 1.0.0
 Author: Bioconductor Core Team 
 Maintainer: Bioconductor Maintainer <maintainer at bioconductor.org>
 Depends: R (>= 3.3)
 biocViews: AnnotationData, Organism
 License: Artistic-2.0
 NeedsCompilation: no
-Packaged: 2017-10-26 14:18:36 UTC; da42327_ca
+Packaged: 2017-12-14 12:34:59 UTC; lori
diff --git a/inst/scripts/updateGenomeInfoDbData.R b/inst/scripts/updateGenomeInfoDbData.R
index d688958..5e7cedc 100644
--- a/inst/scripts/updateGenomeInfoDbData.R
+++ b/inst/scripts/updateGenomeInfoDbData.R
@@ -1,6 +1,6 @@
 ## Scripts for updating specData, speciesMap and validTaxId
 
-## Download and unpack mapping file: 
+## Download and unpack mapping file:
 ## ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
 
 ## Generates specData
@@ -21,7 +21,7 @@
     keep <- grepl('scientific name', species[[3]])
     keep2 <- grepl('synonym', species[[3]])
     species <- species[(keep | keep2), 1:2]
-    
+
     ## split second column by first space:
     rawSpec <- species[[2]]
     spltSpec <- strsplit(rawSpec, split=" ")
@@ -54,9 +54,9 @@
     splt <- splt[idx]
     ## and keep only 1st two elements
     taxon <-  as.integer(unlist(lapply(splt, function(x){x[1]})))
-    species <- unlist(lapply(splt, function(x){x[2]})) 
+    species <- unlist(lapply(splt, function(x){x[2]}))
     speciesMap <- data.frame(taxon,    ## integer
-                             species,  ## character 
+                             species,  ## character
                              stringsAsFactors=FALSE)
     save(speciesMap, file='speciesMap.rda', compress="xz")
 
diff --git a/man/GenomeInfoDbData-package.Rd b/man/GenomeInfoDbData-package.Rd
index c80a8a5..a810a17 100644
--- a/man/GenomeInfoDbData-package.Rd
+++ b/man/GenomeInfoDbData-package.Rd
@@ -9,14 +9,14 @@
 
 \description{
   This package contains three mapping objects:
-  \itemize{ 
+  \itemize{
     \item speciesMap: A data frame with columns \sQuote{tax_id},
-          \sQuote{genus}, and \sQuote{species}. Used to retrieve taxonomy
-          ID by species and returns list of available species.
+	  \sQuote{genus}, and \sQuote{species}. Used to retrieve taxonomy
+	  ID by species and returns list of available species.
     \item validTaxIds: An integer vector of valid taxonomy IDs created from
-          \code{speciesMap}. Used internally for quick taxonomy ID look ups.
+	  \code{speciesMap}. Used internally for quick taxonomy ID look ups.
     \item specData: A data frame with columns \sQuote{taxon} and
-          \sQuote{species}. Used internally to retrieve species by taxonomy ID.
+	  \sQuote{species}. Used internally to retrieve species by taxonomy ID.
   }
 }
 
@@ -34,8 +34,8 @@ data(specData)
 
 \examples{
 data(speciesMap)
-sapply(speciesMap, class)   #       taxon     species 
-                            #    "integer" "character" 
+sapply(speciesMap, class)   #       taxon     species
+			    #    "integer" "character"
 subset(speciesMap, species=="Homo sapiens")$taxon # [1] 9606
 }
 

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