updated readme table in test standards.

hugheylab · Jan 13, 2024 · fe86e93 · fe86e93
1 parent a88a290
commit fe86e93
Show file tree

Hide file tree

Showing 11 changed files with 40 additions and 8 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.18
-Date: 2023-12-01 04:59:09 UTC
-SHA: 03076df8196cf8fa678a75848abc1cf187ab2acf
+Version: 1.0.19
+Date: 2023-12-16 19:24:39 UTC
+SHA: a88a29050ece0185651b02cdeb9f855913d86b44
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pmparser
 Title: Create and Maintain a Relational Database of Data from PubMed/MEDLINE
-Version: 1.0.19
+Version: 1.0.20
 Authors@R: c(person('Jake', 'Hughey', , 'jakejhughey@gmail.com', c('aut', 'cre')),
   person('Josh', 'Schoenbachler', , 'josh.schoenbachler@gmail.com', 'aut'),
   person('Elliot', 'Outland', , 'ehoutland@gmail.com', 'aut'))
@@ -13,7 +13,7 @@ License: GPL-2
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Depends: R (>= 3.6)
 Imports:
   curl (>= 4.3.2),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# pmparser 1.0.20
+* Updated readme table in test standards.
+
 # pmparser 1.0.19
 * Updated test standards based on the annual update to PubMed XML files.
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -20,7 +20,7 @@
   Found the following files/directories:
     'lastMiKTeXException'
 
-See results for [Windows](https://builder.r-hub.io/status/pmparser_1.0.19.tar.gz-da4498bfdbad4e479b5cefc58b318ed9), [Ubuntu](https://builder.r-hub.io/status/pmparser_1.0.19.tar.gz-e3dc23cc69e1479d807cf853cfe1b3af), and [Fedora](https://builder.r-hub.io/status/pmparser_1.0.19.tar.gz-69efe91cf9a94f12bdf7f608674ec198).
+See results for [Windows](https://builder.r-hub.io/status/pmparser_1.0.20.tar.gz-7e6f8e826eaa4b6eb6080f32db868522), [Ubuntu](https://builder.r-hub.io/status/pmparser_1.0.20.tar.gz-88807a83f1024e20a79db5d5fa559fbb), and [Fedora](https://builder.r-hub.io/status/pmparser_1.0.20.tar.gz-6c2e2a4fbfc14a2c8792df295c01735d).
 
 ### GitHub Actions
 
@@ -30,4 +30,4 @@ See results for Mac, Windows, and Ubuntu [here]().
 
 ## Changes from current CRAN release
 
-* Updated test standards based on the annual update to PubMed XML files.
+* Updated readme table in test standards.
diff --git a/data-raw/wrap_get_test_standard.R b/data-raw/wrap_get_test_standard.R
@@ -1,7 +1,7 @@
 # before running this script, run "Clean and Install"
 foreach::registerDoSEQ() # to ensure reproducibility, do not parallelize
 
-options(timeout = 3600)
+options(timeout = 60 * 60 * 3)
 localDir = file.path('tests', 'testthat', 'pubmed_sample')
 tmpDir = tempfile()
 

diff --git a/tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db b/tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db
diff --git a/tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db b/tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db
diff --git a/tests/testthat/pubmed_sample/file_info_predown_all.csv b/tests/testthat/pubmed_sample/file_info_predown_all.csv
@@ -1227,3 +1227,32 @@ updatefiles,pubmed24n1225.xml.gz,pubmed24n1225.xml.gz.md5,,
 updatefiles,pubmed24n1226.xml.gz,pubmed24n1226.xml.gz.md5,,
 updatefiles,pubmed24n1227.xml.gz,pubmed24n1227.xml.gz.md5,,
 updatefiles,pubmed24n1228.xml.gz,pubmed24n1228.xml.gz.md5,,
+updatefiles,pubmed24n1229.xml.gz,pubmed24n1229.xml.gz.md5,,
+updatefiles,pubmed24n1230.xml.gz,pubmed24n1230.xml.gz.md5,,
+updatefiles,pubmed24n1231.xml.gz,pubmed24n1231.xml.gz.md5,,
+updatefiles,pubmed24n1232.xml.gz,pubmed24n1232.xml.gz.md5,,
+updatefiles,pubmed24n1233.xml.gz,pubmed24n1233.xml.gz.md5,,
+updatefiles,pubmed24n1234.xml.gz,pubmed24n1234.xml.gz.md5,,
+updatefiles,pubmed24n1235.xml.gz,pubmed24n1235.xml.gz.md5,,
+updatefiles,pubmed24n1236.xml.gz,pubmed24n1236.xml.gz.md5,,
+updatefiles,pubmed24n1237.xml.gz,pubmed24n1237.xml.gz.md5,,
+updatefiles,pubmed24n1238.xml.gz,pubmed24n1238.xml.gz.md5,,
+updatefiles,pubmed24n1239.xml.gz,pubmed24n1239.xml.gz.md5,,
+updatefiles,pubmed24n1240.xml.gz,pubmed24n1240.xml.gz.md5,,
+updatefiles,pubmed24n1241.xml.gz,pubmed24n1241.xml.gz.md5,,
+updatefiles,pubmed24n1242.xml.gz,pubmed24n1242.xml.gz.md5,,
+updatefiles,pubmed24n1243.xml.gz,pubmed24n1243.xml.gz.md5,,
+updatefiles,pubmed24n1244.xml.gz,pubmed24n1244.xml.gz.md5,,
+updatefiles,pubmed24n1245.xml.gz,pubmed24n1245.xml.gz.md5,,
+updatefiles,pubmed24n1246.xml.gz,pubmed24n1246.xml.gz.md5,,
+updatefiles,pubmed24n1247.xml.gz,pubmed24n1247.xml.gz.md5,,
+updatefiles,pubmed24n1248.xml.gz,pubmed24n1248.xml.gz.md5,,
+updatefiles,pubmed24n1249.xml.gz,pubmed24n1249.xml.gz.md5,,
+updatefiles,pubmed24n1250.xml.gz,pubmed24n1250.xml.gz.md5,,
+updatefiles,pubmed24n1251.xml.gz,pubmed24n1251.xml.gz.md5,,
+updatefiles,pubmed24n1252.xml.gz,pubmed24n1252.xml.gz.md5,,
+updatefiles,pubmed24n1253.xml.gz,pubmed24n1253.xml.gz.md5,,
+updatefiles,pubmed24n1254.xml.gz,pubmed24n1254.xml.gz.md5,,
+updatefiles,pubmed24n1255.xml.gz,pubmed24n1255.xml.gz.md5,,
+updatefiles,pubmed24n1256.xml.gz,pubmed24n1256.xml.gz.md5,,
+updatefiles,pubmed24n1257.xml.gz,pubmed24n1257.xml.gz.md5,,
diff --git a/tests/testthat/pubmed_sample/open_citation_collection.zip b/tests/testthat/pubmed_sample/open_citation_collection.zip
diff --git a/tests/testthat/pubmed_sample/pmdb_sample_create.db b/tests/testthat/pubmed_sample/pmdb_sample_create.db
diff --git a/tests/testthat/pubmed_sample/pmdb_sample_update.db b/tests/testthat/pubmed_sample/pmdb_sample_update.db