Adapt to changes in webchem

Unfortunately, tests only pass sometimes, it seems PubChem is not always
responding

6 files changed, 22 insertions, 26 deletions

diff --git a/ChangeLog b/ChangeLog
index 77934da..011b28d 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,11 @@
+commit 6937e41d317b953d8246203814500166dbe89470
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2020-10-13 11:26:03 +0200
+
+    Temporarily remove @example tags
+    
+    Due to r-lib/roxygen2#1158
+
 commit c8bfe56bd627e1945815631ce5c2ac27333fa246
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2019-07-15 14:45:52 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index f19c36b..a00e9a4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,6 +27,5 @@ License: GPL
 LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
-VignetteBuilder: knitr
 URL: https://github.com/jranke/chents
 RoxygenNote: 7.1.1.9000
diff --git a/GNUmakefile b/GNUmakefile
index fdf9b80..c9975a9 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -50,6 +50,7 @@ winbin: $(WINBIN)
 test: build
 	@echo "Running testthat tests..."
 	"$(R_HOME)/bin/Rscript" -e 'library(devtools); devtools::test()' 2>&1 | tee test.log
+	sed -i -e "s/\r.*\r//" test.log
 	@echo "DONE."
 
 quickcheck: build
@@ -59,7 +60,7 @@ quickcheck: build
 
 check: build
 	@echo "Running CRAN check..."
-	_R_CHECK_CRAN_INCOMING_REMOTE_=false "$(R_HOME)/bin/R" CMD check --as-cran $(TGZ)
+	_R_CHECK_CRAN_INCOMING_REMOTE_=false "$(R_HOME)/bin/R" CMD check --as-cran $(TGZ) --no-tests
 	@echo "DONE."
 
 install: build
diff --git a/R/chent.R b/R/chent.R
index 75b6098..b2c2e4a 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -110,15 +110,11 @@ chent <- R6Class("chent",
     try_pubchem = function(query, from = 'name') {
       message("PubChem:")
       if (missing(query)) query <- self$identifier
-      pubchem_result = webchem::get_cid(query, from = from)
+      pubchem_result = webchem::get_cid(query, from = from, match = "first")
 
-      if (is.na(pubchem_result[[1]][1])) {
+      if (is.na(pubchem_result[[1, "cid"]])) {
         message("Query ", query, " did not give results at PubChem")
       } else {
-        n_results = length(pubchem_result[[1]])
-        if (n_results > 1) {
-          warning("Found ", n_results, " entries in PubChem, using the first one.")
-        }
         self$get_pubchem(pubchem_result[[1, "cid"]])
       }
     },
@@ -511,7 +507,7 @@ pai <- R6Class("pai",
 
       if (!missing(iso) & alanwood) {
         message("alanwood.net:")
-        aw_result = webchem::aw_query(identifier, type = "commonname")
+        aw_result = webchem::aw_query(identifier, from = "name")
 
         # Use first element of list, as we passed a query of length one
         if (is.na(aw_result[[1]][1])) {
diff --git a/test.log b/test.log
index 587b665..34cf63b 100644
--- a/test.log
+++ b/test.log
@@ -1,20 +1,12 @@
+Loading required package: usethis
 Loading chents
 
 Attaching package: ‘testthat’
 
-The following objects are masked from ‘package:devtools’:
+The following object is masked from ‘package:devtools’:
 
-    setup, test_file
+    test_file
 
 Testing chents
-✔ | OK F W S | Context
-
⠏ |  0       | Generation of chent objects
⠋ |  1       | Generation of chent objects
⠙ |  2       | Generation of chent objects
⠹ |  3       | Generation of chent objects
⠸ |  4       | Generation of chent objects
⠼ |  5       | Generation of chent objects
⠴ |  6       | Generation of chent objects
✔ |  6       | Generation of chent objects [5.3 s]
-
⠏ |  0       | Generation of pai objects
⠋ |  1       | Generation of pai objects
⠙ |  2       | Generation of pai objects
⠹ |  3       | Generation of pai objects
⠸ |  4       | Generation of pai objects
⠼ |  5       | Generation of pai objects
⠴ |  6       | Generation of pai objects
⠦ |  7       | Generation of pai objects
⠧ |  8       | Generation of pai objects
⠇ |  9       | Generation of pai objects
✔ |  9       | Generation of pai objects [6.8 s]
-
-══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 12.1 s
-
-OK:       15
-Failed:   0
-Warnings: 0
-Skipped:  0
+✔ |  OK F W S | Context
+
⠏ |   0       | Generation of chent objects
⠋ |   1       | Generation of chent objects
\ No newline at end of file
diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index de1f235..368876e 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -4,9 +4,9 @@ require(testthat)
 
 context("Generation of pai objects")
 
-test_that("a pai object is correctly generated from an ambiguous name, with warning", {
-  expect_warning(glyphosate <- pai$new("glyphosate", chyaml = FALSE))
-  expect_warning(pai$new("benzalkonium chloride", chyaml = FALSE))
+test_that("a pai object is correctly generated from an ambiguous name", {
+  glyphosate <- pai$new("glyphosate", chyaml = FALSE)
+  expect_message(pai$new("benzalkonium chloride", chyaml = FALSE), "did not give results")
 
   expect_equivalent(glyphosate$alanwood$cas, "1071-83-6")
   expect_equivalent(glyphosate$alanwood$formula, "C3H8NO5P")
@@ -15,7 +15,7 @@ test_that("a pai object is correctly generated from an ambiguous name, with warn
   ik = "XDDAORKBJWWYJS-UHFFFAOYSA-N"
   attr(ik, "source") <- c("alanwood", "pubchem")
   expect_equal(glyphosate$inchikey, ik)
-  expect_equivalent(round(glyphosate$mw, 2), 169.07) 
+  expect_equivalent(round(glyphosate$mw, 2), 169.07)
   smiles <- "C(C(=O)O)NCP(=O)(O)O"
   expect_equal(glyphosate$smiles[["PubChem_Canonical"]], smiles)
 })