version 0.5.1

DESCRIPTION

@@ -1,21 +1,22 @@
 Package: taxonomizr
 Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>
-License: GPL-2
+License: GPL (>= 2) | file LICENSE
 Title: Functions to Work with NCBI Accessions and Taxonomy
 Type: Package
 LazyLoad: yes
 Author: Scott Sherrill-Mix [aut, cre]
 Authors@R: c(person("Scott", "Sherrill-Mix", role = c("aut", "cre"),
                      email = "shescott@upenn.edu"))
+BugReports: https://github.com/sherrillmix/taxonomizr/issues
 Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
-Version: 0.2.2
-Date: 2017-03-08
+Version: 0.5.1
+Date: 2018-08-31
 Suggests: testthat, knitr, rmarkdown
 Depends: R (>= 3.0.0)
 Imports: parallel, RSQLite, data.table, R.utils
 RoxygenNote: 6.0.1
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2017-03-08 16:28:47 UTC; scott
+Packaged: 2018-08-31 20:05:46 UTC; scott
 Repository: CRAN
-Date/Publication: 2017-03-09 08:18:40
+Date/Publication: 2018-08-31 20:50:03 UTC

MD5

@@ -1,27 +1,36 @@
-62dd06fd710dba97ee279a89409cfe15 *DESCRIPTION
-8a4caaee399dcb1fddde3a025e5eaee3 *NAMESPACE
-4279a71de096e8915427ddd6d2757ee4 *R/taxa.R
-04eb33dc0d5b6aa6be127051577023a6 *README.md
-e4a51d030e435d56ce75836fdd3220b2 *build/vignette.rds
-1b90cfd8fa1b486a6a28386d33ce3462 *inst/doc/usage.R
-3c856fee9facd38b1026ff18fa9dd777 *inst/doc/usage.Rmd
-537381f14ddaed8c165df096ddcba4cf *inst/doc/usage.html
-13d0bde45c8c16a6b9b98abc9bd1c2d2 *man/accessionToTaxa.Rd
-40a8f619bdae98f77d841e515dd3d58d *man/condenseTaxa.Rd
-f7296ef498ab1380d619d7cc636f0f6e *man/getAccession2taxid.Rd
-a85c107799e511b6bf26c3fe095ef63f *man/getId.Rd
-0fc65f288dcae4ac732a6217ebda16e9 *man/getNamesAndNodes.Rd
-98cfdf24259b07e79f880eadb733fbc5 *man/getTaxonomy.Rd
+0cb81087ee9a9c9e13f93ee1f8f6455f *DESCRIPTION
+b234ee4d69f5fce4486a80fdaf4a4263 *LICENSE
+7bd5a2024023fcdc3e56246fede69169 *NAMESPACE
+a4dc51bda75b22027162408f28cc41e4 *R/taxa.R
+19f81903072e403d63f69f7a613c5dc2 *README.md
+fcf3c6caf0d0dd0a9b926ed36c95e470 *build/vignette.rds
+14b6e1db194ff18f1fadabaf830c04a0 *inst/doc/usage.R
+a25b8ed785ad9a3819c6a439ba6c5639 *inst/doc/usage.Rmd
+01a9e61092c47c18c0d7f94ce5f2626e *inst/doc/usage.html
+68387ebc183536fcefb27616ef5de18e *man/accessionToTaxa.Rd
+fc39f17d296a65ca038d98b5b3a69d28 *man/condenseTaxa.Rd
+e05a27da96d9eaeec0a3ab74437418c5 *man/getAccession2taxid.Rd
+f45d1ede2cc22a697cab44ea01b21f7b *man/getAccessions.Rd
+0e28b5f644daca47d88b18d505948669 *man/getId.Rd
+552082d7d53e19e9754c99d666fcaa17 *man/getId2.Rd
+c86cadc2fddc68e701044bf9bf97d0e5 *man/getNamesAndNodes.Rd
+00605228ae8f11848491341529906238 *man/getTaxonomy.Rd
+69eb3ce54dce2802545d337794564c0c *man/getTaxonomy2.Rd
 8420a5306860a41886c0da14e1bf47b0 *man/lastNotNa.Rd
-91ce383d20e7daf897a44193c6f261a3 *man/read.accession2taxid.Rd
-12f35e0ff0f0fbf8ccbf0fd7f94bf323 *man/read.names.Rd
-ecdcd5b39012aa4458a4b3eb6a189833 *man/read.nodes.Rd
-4de9fac0202c014e1267084e38a5766c *man/streamingRead.Rd
-14137ee1cf1eddd029976d0ea3901333 *man/trimTaxa.Rd
-a7ed2d70251d676a986945f19b456602 *src/taxaTrim.c
-b7d3c5c239cb16ad1d8e4c68f43e5d09 *src/taxaTrim.h
+47b86f075854e98ec479a4fbfa4fe073 *man/prepareDatabase.Rd
+dbf8bf8dbcebfb85405709e7af6e7385 *man/read.accession2taxid.Rd
+1e155828aed61000b228f43577e00846 *man/read.names.Rd
+507d3c41836c5b6c6efebec94862d88c *man/read.names.sql.Rd
+bcc485c9bb1dee0463a07ab9f8472ad5 *man/read.nodes.Rd
+8746dd71ef08324d519db790f61f4f7e *man/read.nodes.sql.Rd
+5d8ea142c3bfff486547b8479f2d52a3 *man/streamingRead.Rd
+5e3d2fb08aa1d61618a136e8e56c69c7 *man/taxonomizr-package.Rd
+f9f540122f8ba96b91d56226eebc9026 *man/taxonomizrSwitch.Rd
+d47fc7ed590032dbfa141b6952d998d3 *man/trimTaxa.Rd
+973c222136ffbf4008ff747d643bc6a3 *src/taxaTrim.c
 1b509a76cc18244a3847a2ab27ab9f77 *src/taxonomizr-init.c
 09570ff5fc4fe1c8f81b47295a3faafb *tests/testthat.R
-822e81b3c55ffe8f62e66e6e92e410f6 *tests/testthat/fakeNamesNodes.tar.gz
-887945d7d4ac31cba8105fffe13fa730 *tests/testthat/test_taxa.R
-3c856fee9facd38b1026ff18fa9dd777 *vignettes/usage.Rmd
+2c6938a3b6c0303311c55f0e328ff746 *tests/testthat/fakeNamesNodes.tar.gz
+ee7e47ac573f20970c95c7d71522bbcf *tests/testthat/test_taxa.R
+a25b8ed785ad9a3819c6a439ba6c5639 *vignettes/usage.Rmd
+0cd93bfeaacc55b489c2238496ae6ddc *vignettes/usage.md

NAMESPACE

@@ -3,13 +3,19 @@
 export(accessionToTaxa)
 export(condenseTaxa)
 export(getAccession2taxid)
+export(getAccessions)
 export(getId)
+export(getId2)
 export(getNamesAndNodes)
 export(getTaxonomy)
+export(getTaxonomy2)
 export(lastNotNa)
+export(prepareDatabase)
 export(read.accession2taxid)
 export(read.names)
+export(read.names.sql)
 export(read.nodes)
+export(read.nodes.sql)
 export(streamingRead)
 import(data.table)
 useDynLib(taxonomizr, .registration=TRUE)