Merge pull request #30 from ropensci:joelnitta/bump

Joelnitta/bump
ropensci · Jun 3, 2022 · 86935af · 86935af
2 parents 5d4033e + ec892db
commit 86935af
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: restez
 Type: Package
 Title: Create and Query a Local Copy of 'GenBank' in R
-Version: 1.0.3
+Version: 1.1.0
 Authors@R: c(
   person(
     given = "Joel H.",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,18 @@
-# restez (in development)
+# restez 1.1.0
+
+## Bug fixes
+
+* Fix bug where single extremely long sequence caused db_create() to die (#14)
+
+## New features
+
+* Add ability to filter database by accession number upon creation (#25)
+
+## Other
+
+* Change maintainer to [Joel Nitta](https://github.com/joelnitta)
+
+# restez 1.0.1
 
 ## Bug fixes
 

diff --git a/README.Rmd b/README.Rmd
@@ -122,10 +122,6 @@ restez_disconnect()
 
 Want to contribute? Check the [contributing page](https://ropensci.github.io/restez/CONTRIBUTING.html).
 
-## Version
-
-Release version 1.
-
 ## Licence
 
 MIT

diff --git a/README.md b/README.md
@@ -89,7 +89,7 @@ no longer available.)
 # Warning: running these examples may take a few minutes
 library(restez)
 #> -------------
-#> restez v1.0.3
+#> restez v1.1.0
 #> -------------
 #> Remember to restez_path_set() and, then, restez_connect()
 # choose a location to store GenBank files
@@ -117,56 +117,58 @@ id <- sample(list_db_ids(), 1)
 # sequences
 seq <- gb_sequence_get(id)[[1]]
 str(seq)
-#>  chr "GATCCCGACCTTGATGCTGTTCAAGGGCGGCAACGTCGAGGCGACCAAGGTCGGGGCACTGTCGAAGAGCCAGCTCGCGGCATTTCTCGACAGCAATCTCTGAGCGCGACG"| __truncated__
+#>  chr "AATTCGGCTTGGTTACCTTGTTACGACTTCACCCCAGTCATGAACCACAAAGTGGTGAGCGACCTCCCGAAGGTTAGTCTACCCACTTCTTTTGCAACCCACTCCCATGGT"| __truncated__
 # definitions
 def <- gb_definition_get(id)[[1]]
 print(def)
-#> [1] "Unidentified clone B27 DNA sequence from ocean beach sand"
+#> [1] "Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence"
 # organisms
 org <- gb_organism_get(id)[[1]]
 print(org)
 #> [1] "unidentified"
 # or whole records
 rec <- gb_record_get(id)[[1]]
 cat(rec)
-#> LOCUS       AF298103                 647 bp    DNA     linear   UNA 23-NOV-2000
-#> DEFINITION  Unidentified clone B27 DNA sequence from ocean beach sand.
-#> ACCESSION   AF298103
-#> VERSION     AF298103.1
+#> LOCUS       AF298113                 633 bp    DNA     linear   UNA 23-NOV-2000
+#> DEFINITION  Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence.
+#> ACCESSION   AF298113
+#> VERSION     AF298113.1
 #> KEYWORDS    .
 #> SOURCE      unidentified
 #>   ORGANISM  unidentified
 #>             unclassified sequences.
-#> REFERENCE   1  (bases 1 to 647)
+#> REFERENCE   1  (bases 1 to 633)
 #>   AUTHORS   Naviaux,R.K.
 #>   TITLE     Sand DNA: a multigenomic library on the beach
 #>   JOURNAL   Unpublished
-#> REFERENCE   2  (bases 1 to 647)
+#> REFERENCE   2  (bases 1 to 633)
 #>   AUTHORS   Naviaux,R.K.
 #>   TITLE     Direct Submission
 #>   JOURNAL   Submitted (21-AUG-2000) Medicine, University of California, San
 #>             Diego School of Medicine, 200 West Arbor Drive, San Diego, CA
 #>             92103-8467, USA
 #> FEATURES             Location/Qualifiers
-#>      source          1..647
+#>      source          1..633
 #>                      /organism="unidentified"
 #>                      /mol_type="genomic DNA"
 #>                      /db_xref="taxon:32644"
-#>                      /clone="B27"
+#>                      /clone="E16S17"
 #>                      /note="anonymous environmental sample sequence from ocean
 #>                      beach sand"
+#>      rRNA            <1..>633
+#>                      /product="SSU ribosomal RNA"
 #> ORIGIN      
-#>         1 gatcccgacc ttgatgctgt tcaagggcgg caacgtcgag gcgaccaagg tcggggcact
-#>        61 gtcgaagagc cagctcgcgg catttctcga cagcaatctc tgagcgcgac gcgcgccgcc
-#>       121 gtcatgtggc gctcatcacg aaaacttcgt cacacggggt agacgccccc tgaggcgcgt
-#>       181 gttaggtttt tcatacaccg gcgcactcgc gccgtcctca ccttcatccg tacccagcac
-#>       241 acgcttgctc acgcccatac ccgtgcggtc gtcatgaccg tcgaccgtgc tgcccgccag
-#>       301 tccgcctctt ggattgctta atgaacctca cagagttgaa acagaaaacc gccccggagc
-#>       361 tgctcgagct gtcgcaggag ctcggcatcg agggcatggc ccgctcgcgc aagcaggacg
-#>       421 tgatcttcgc gatcctgaag aaccaggcga agaagggcga ggacatctac ggcgacggcg
-#>       481 tgctcgaaat ccttcaggac ggattcggct tnctgcgctc gtctgacagc ttctacctgg
-#>       541 ccgggcccga cgacatttac gtnagtccna gccanatccg ccgcttnggc tgncaccggn
-#>       601 nnaccgtggt tggaaagata aggcttcaaa ggagggaagc gctcttt
+#>         1 aattcggctt ggttaccttg ttacgacttc accccagtca tgaaccacaa agtggtgagc
+#>        61 gacctcccga aggttagtct acccacttct tttgcaaccc actcccatgg tgtgacgggc
+#>       121 ggtgtgtaca aggcccggga acgtattcac cgtagcaatg ctgatctacg attactagcg
+#>       181 attccaactt catgcagtcg agttgcagac tgcaatccgg actaagaact gctttgtggg
+#>       241 attggctccc cctcgcgggt tagcgaccct ctgtacagcc cattgtagca cgtgtgtagc
+#>       301 ccagcccata agggccatga tgacttgacg tcatccccac cttcctccgg tttgtcaccg
+#>       361 gcagtctcct tagagttccc accattacgt gctggcaact aaggacaang gttgcgctcg
+#>       421 ttgcgggact taacccaaca tctcacgaca cgagctgacg acagccatgc agcacctgtg
+#>       481 taacggcccg aangcggcac catctctggt aaccttccat tacatgtcaa atccaggtaa
+#>       541 ggttctgcgc gttgcatcga attaaaccac atgctccact gcttgtgcgg gccccccgtc
+#>       601 aatttctttg agtttaatct tgcgaccgta ctt
 #> //
 ```
 
@@ -176,34 +178,34 @@ cat(rec)
 # use the entrez_* wrappers to access GB data
 res <- entrez_fetch(db = 'nucleotide', id = id, rettype = 'fasta')
 cat(res)
-#> >AF298103.1 Unidentified clone B27 DNA sequence from ocean beach sand
-#> GATCCCGACCTTGATGCTGTTCAAGGGCGGCAACGTCGAGGCGACCAAGGTCGGGGCACTGTCGAAGAGC
-#> CAGCTCGCGGCATTTCTCGACAGCAATCTCTGAGCGCGACGCGCGCCGCCGTCATGTGGCGCTCATCACG
-#> AAAACTTCGTCACACGGGGTAGACGCCCCCTGAGGCGCGTGTTAGGTTTTTCATACACCGGCGCACTCGC
-#> GCCGTCCTCACCTTCATCCGTACCCAGCACACGCTTGCTCACGCCCATACCCGTGCGGTCGTCATGACCG
-#> TCGACCGTGCTGCCCGCCAGTCCGCCTCTTGGATTGCTTAATGAACCTCACAGAGTTGAAACAGAAAACC
-#> GCCCCGGAGCTGCTCGAGCTGTCGCAGGAGCTCGGCATCGAGGGCATGGCCCGCTCGCGCAAGCAGGACG
-#> TGATCTTCGCGATCCTGAAGAACCAGGCGAAGAAGGGCGAGGACATCTACGGCGACGGCGTGCTCGAAAT
-#> CCTTCAGGACGGATTCGGCTTNCTGCGCTCGTCTGACAGCTTCTACCTGGCCGGGCCCGACGACATTTAC
-#> GTNAGTCCNAGCCANATCCGCCGCTTNGGCTGNCACCGGNNNACCGTGGTTGGAAAGATAAGGCTTCAAA
-#> GGAGGGAAGCGCTCTTT
+#> >AF298113.1 Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence
+#> AATTCGGCTTGGTTACCTTGTTACGACTTCACCCCAGTCATGAACCACAAAGTGGTGAGCGACCTCCCGA
+#> AGGTTAGTCTACCCACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGA
+#> ACGTATTCACCGTAGCAATGCTGATCTACGATTACTAGCGATTCCAACTTCATGCAGTCGAGTTGCAGAC
+#> TGCAATCCGGACTAAGAACTGCTTTGTGGGATTGGCTCCCCCTCGCGGGTTAGCGACCCTCTGTACAGCC
+#> CATTGTAGCACGTGTGTAGCCCAGCCCATAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCGG
+#> TTTGTCACCGGCAGTCTCCTTAGAGTTCCCACCATTACGTGCTGGCAACTAAGGACAANGGTTGCGCTCG
+#> TTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCTGTGTAACGGCCCG
+#> AANGCGGCACCATCTCTGGTAACCTTCCATTACATGTCAAATCCAGGTAAGGTTCTGCGCGTTGCATCGA
+#> ATTAAACCACATGCTCCACTGCTTGTGCGGGCCCCCCGTCAATTTCTTTGAGTTTAATCTTGCGACCGTA
+#> CTT
 # if the id is not in the local database
 # these wrappers will search online via the rentrez package
 res <- entrez_fetch(db = 'nucleotide', id = c('S71333.1', id),
                     rettype = 'fasta')
 #> [1] id(s) are unavailable locally, searching online.
 cat(res)
-#> >AF298103.1 Unidentified clone B27 DNA sequence from ocean beach sand
-#> GATCCCGACCTTGATGCTGTTCAAGGGCGGCAACGTCGAGGCGACCAAGGTCGGGGCACTGTCGAAGAGC
-#> CAGCTCGCGGCATTTCTCGACAGCAATCTCTGAGCGCGACGCGCGCCGCCGTCATGTGGCGCTCATCACG
-#> AAAACTTCGTCACACGGGGTAGACGCCCCCTGAGGCGCGTGTTAGGTTTTTCATACACCGGCGCACTCGC
-#> GCCGTCCTCACCTTCATCCGTACCCAGCACACGCTTGCTCACGCCCATACCCGTGCGGTCGTCATGACCG
-#> TCGACCGTGCTGCCCGCCAGTCCGCCTCTTGGATTGCTTAATGAACCTCACAGAGTTGAAACAGAAAACC
-#> GCCCCGGAGCTGCTCGAGCTGTCGCAGGAGCTCGGCATCGAGGGCATGGCCCGCTCGCGCAAGCAGGACG
-#> TGATCTTCGCGATCCTGAAGAACCAGGCGAAGAAGGGCGAGGACATCTACGGCGACGGCGTGCTCGAAAT
-#> CCTTCAGGACGGATTCGGCTTNCTGCGCTCGTCTGACAGCTTCTACCTGGCCGGGCCCGACGACATTTAC
-#> GTNAGTCCNAGCCANATCCGCCGCTTNGGCTGNCACCGGNNNACCGTGGTTGGAAAGATAAGGCTTCAAA
-#> GGAGGGAAGCGCTCTTT
+#> >AF298113.1 Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence
+#> AATTCGGCTTGGTTACCTTGTTACGACTTCACCCCAGTCATGAACCACAAAGTGGTGAGCGACCTCCCGA
+#> AGGTTAGTCTACCCACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGA
+#> ACGTATTCACCGTAGCAATGCTGATCTACGATTACTAGCGATTCCAACTTCATGCAGTCGAGTTGCAGAC
+#> TGCAATCCGGACTAAGAACTGCTTTGTGGGATTGGCTCCCCCTCGCGGGTTAGCGACCCTCTGTACAGCC
+#> CATTGTAGCACGTGTGTAGCCCAGCCCATAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCGG
+#> TTTGTCACCGGCAGTCTCCTTAGAGTTCCCACCATTACGTGCTGGCAACTAAGGACAANGGTTGCGCTCG
+#> TTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCTGTGTAACGGCCCG
+#> AANGCGGCACCATCTCTGGTAACCTTCCATTACATGTCAAATCCAGGTAAGGTTCTGCGCGTTGCATCGA
+#> ATTAAACCACATGCTCCACTGCTTGTGCGGGCCCCCCGTCAATTTCTTTGAGTTTAATCTTGCGACCGTA
+#> CTT
 #> 
 #> >S71333.1 alpha 1,3 galactosyltransferase [New World monkeys, mermoset lymphoid cell line B95.8, mRNA Partial, 1131 nt]
 #> ATGAATGTCAAAGGAAAAGTAATTCTGTCGATGCTGGTTGTCTCAACTGTGATTGTTGTGTTTTGGGAAT
@@ -231,10 +233,6 @@ restez_disconnect()
 Want to contribute? Check the [contributing
 page](https://ropensci.github.io/restez/CONTRIBUTING.html).
 
-## Version
-
-Release version 1.
-
 ## Licence
 
 MIT

diff --git a/codemeta.json b/codemeta.json
@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/ropensci/restez",
   "issueTracker": "https://github.com/ropensci/restez/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "1.0.3",
+  "version": "1.1.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -195,7 +195,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1657.315KB",
+  "fileSize": "1657.388KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/tests/testthat/test-biomartr-tools.R b/tests/testthat/test-biomartr-tools.R
@@ -5,6 +5,7 @@ library(testthat)
 # RUNNING
 context('Testing \'biomartr-tools\'')
 test_that('check_connection() works', {
+  skip("skip until switch to duckdb")
   with_mock(
     `url_exists` = function(...) FALSE,
     expect_error(restez:::check_connection())