version 0.9.3

DESCRIPTION

@@ -9,15 +9,15 @@ 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 download NCBI data dumps and create a local database for fast and local taxonomic assignment.
-Version: 0.9.2
-Date: 2022-06-23
+Version: 0.9.3
+Date: 2022-06-24
 Suggests: testthat, knitr, rmarkdown
 Depends: R (>= 3.0.0)
 Imports: RSQLite, R.utils, data.table, curl
 Encoding: UTF-8
 RoxygenNote: 7.2.0
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2022-06-23 18:35:50 UTC; scott
+Packaged: 2022-06-24 20:55:55 UTC; scott
 Repository: CRAN
-Date/Publication: 2022-06-23 19:30:02 UTC
+Date/Publication: 2022-06-26 21:40:02 UTC

MD5

@@ -1,12 +1,12 @@
-68e46dd96d8a8df5b6c8e77f92a77420 *DESCRIPTION
+0d24392099f9d49499e15fb2a0a76f65 *DESCRIPTION
 b234ee4d69f5fce4486a80fdaf4a4263 *LICENSE
 a4c6776aa0fdd71651b87d2dcbb60744 *NAMESPACE
 f3f0a7be9a6575a065a79eb84b6a82a4 *R/taxa.R
-e842aea2b0b3380e4822294e53869f1c *README.md
+389f76970a35942fcdcd4e5b86e95ab9 *README.md
 64cfe0a58a5609893dd979375e77436a *build/vignette.rds
 12825a05701bc308a1fece1aefc44930 *inst/doc/usage.R
-7a5cf6631faec02b51b7faee07445877 *inst/doc/usage.Rmd
-12e8212008aab3c9aed59ef6bf744aa4 *inst/doc/usage.html
+4670cd60b44e3689e6180a7923ab1c96 *inst/doc/usage.Rmd
+cfb15e201916b6e45cb78bd929970dcf *inst/doc/usage.html
 2c6938a3b6c0303311c55f0e328ff746 *inst/testdata/fakeNamesNodes.tar.gz
 6f928eac975decb053a812bf58c4a3c1 *man/accessionToTaxa.Rd
 fc39f17d296a65ca038d98b5b3a69d28 *man/condenseTaxa.Rd
@@ -35,5 +35,5 @@ d47fc7ed590032dbfa141b6952d998d3 *man/trimTaxa.Rd
 c6f8208857cc84cc3694a2f4a566745f *src/taxaTrim.c
 1b509a76cc18244a3847a2ab27ab9f77 *src/taxonomizr-init.c
 09570ff5fc4fe1c8f81b47295a3faafb *tests/testthat.R
-a3959bfeba5442a57244147ca8f0b5bd *tests/testthat/test_taxa.R
-7a5cf6631faec02b51b7faee07445877 *vignettes/usage.Rmd
+e6b4e75ae88283666c90218e9b3c4494 *tests/testthat/test_taxa.R
+4670cd60b44e3689e6180a7923ab1c96 *vignettes/usage.Rmd

README.md

@@ -517,7 +517,7 @@ Note that taxa may be the most specific taxon for a given taxa in the taxonomy m
 
 ## Changelog
 ### v0.9.2
-  * Allow factors as input to accessionToTaxa
+  * Allow factors as input to `accessionToTaxa`
   * Document sqlite pragmas for `read.accession2taxid`
   * Inherit ... argument documentation for `prepareDatabase`
   * Catch input/output error while processing large files

inst/doc/usage.Rmd

@@ -463,6 +463,9 @@ Note that taxa may be the most specific taxon for a given taxa in the taxonomy m
 
 
 ## Changelog
+### v0.9.3
+  * Fix bug in testing script
+
 ### v0.9.2
   * Allow factors as input to `accessionToTaxa`
   * Document sqlite pragmas for `read.accession2taxid`

inst/doc/usage.html

@@ -583,6 +583,12 @@ <h3>Convert taxonomy to Newick tree</h3>
 </div>
 <div id="changelog" class="section level2">
 <h2>Changelog</h2>
+<div id="v0.9.3" class="section level3">
+<h3>v0.9.3</h3>
+<ul>
+<li>Fix bug in testing script</li>
+</ul>
+</div>
 <div id="v0.9.2" class="section level3">
 <h3>v0.9.2</h3>
 <ul>

tests/testthat/test_taxa.R

@@ -109,7 +109,7 @@ test_that("Test streamingRead",{
 
 test_that("Test trimTaxa",{
   expect_error(taxonomizr:::trimTaxa('NotARealFile','test'),'file')
-  expect_error(.C('taxaTrim',c('NotARealFile','test'),PACKAGE='taxonomizr'),'file')
+  expect_error(.C('taxaTrim',c('NotARealFile','test'),1:2,2,PACKAGE='taxonomizr'),'file')
   tmp<-tempfile()
   out<-c(
     'head\t1\t2\t3',
@@ -121,18 +121,18 @@ test_that("Test trimTaxa",{
   tmpDir<-tempfile()
   dir.create(tmpDir)
   #should error (can't write to directory)
-  expect_error(.C('taxaTrim',c(tmp,tmpDir),PACKAGE='taxonomizr'),'output file')
+  expect_error(.C('taxaTrim',c(tmp,tmpDir),1:2,2,PACKAGE='taxonomizr'),'output file')
   file.remove(tmpDir)
   tmpPerm<-tempfile()
   file.create(tmpPerm)
   #some systems can't set permissions
   if(Sys.chmod(tmpPerm,'0000') && file.access(tmpPerm,6)==-1 && any(class(tryCatch(readLines(tmpPerm),error=function(xx)xx))=='error') && any(class(tryCatch(writeLines('ABC',tmpPerm),error=function(xx)xx))=='error')){
-    expect_error(.C('taxaTrim',c(tmpPerm,tmp),PACKAGE='taxonomizr'),'input file')
-    expect_error(.C('taxaTrim',c(tmp,tmpPerm),PACKAGE='taxonomizr'),'output file')
+    expect_error(.C('taxaTrim',c(tmpPerm,tmp),1:2,2,PACKAGE='taxonomizr'),'input file')
+    expect_error(.C('taxaTrim',c(tmp,tmpPerm),1:2,2,PACKAGE='taxonomizr'),'output file')
   }
   file.remove(tmpPerm) 
   if(file.exists('/dev/full')){
-    expect_error(.C('taxaTrim',c(tmp,'/dev/full'),PACKAGE='taxonomizr'),'write')
+    expect_error(.C('taxaTrim',c(tmp,'/dev/full'),1:2,2,PACKAGE='taxonomizr'),'write')
     expect_error(taxonomizr:::trimTaxa(tmp,'/dev/full'),'write')
   }
   tmp2<-tempfile()
@@ -163,15 +163,15 @@ test_that("Test trimTaxa",{
     'c\t4\t5\t6'
   )
   writeLines(out,tmp)
-  expect_error(.C('taxaTrim',c(tmp,tmp2),PACKAGE='taxonomizr'),'Malformed.*3')
+  expect_error(.C('taxaTrim',c(tmp,tmp2),1:2,2,PACKAGE='taxonomizr'),'Malformed.*3')
   out<-c(
     'head\t1\t2\t3',
     'a\t2\t3\t4',
     'b\t3\t4\t5',
     'c\t4\t5'
   )
   writeLines(out,tmp)
-  expect_error(.C('taxaTrim',c(tmp,tmp2),PACKAGE='taxonomizr'),'Malformed.*4')
+  expect_error(.C('taxaTrim',c(tmp,tmp2),1:2,2,PACKAGE='taxonomizr'),'Malformed.*4')
 })
 
 test_that("Test read.accession2taxid",{

vignettes/usage.Rmd

@@ -463,6 +463,9 @@ Note that taxa may be the most specific taxon for a given taxa in the taxonomy m
 
 
 ## Changelog
+### v0.9.3
+  * Fix bug in testing script
+
 ### v0.9.2
   * Allow factors as input to `accessionToTaxa`
   * Document sqlite pragmas for `read.accession2taxid`