Adapt to new SMILES names at PubChem

This may break some code using the old smiles names "PubChem_Canonical"
and "PubChem_Isomeric" instead of the new smiles names "PubChem"
(including isotopic and stereochemical information) and
"PubChem_Connectivity" (only containing connectivity, but still
canonical).

Further changes in this commit:
- A fix to the test target in the makefile
- Use markdown syntax for link to objects from other packages in the
  documentation
- Adapt the tests
- Increase test coverage a bit

1 files changed, 7 insertions, 4 deletions

diff --git a/tests/testthat/test_pai.R b/tests/testthat/test_pai.R
index 518fc56..f38672d 100644
--- a/tests/testthat/test_pai.R
+++ b/tests/testthat/test_pai.R
@@ -4,10 +4,13 @@ require(testthat)
 
 context("Generation of pai objects")
 
-test_that("a pai object is correctly generated from an ambiguous name", {
+test_that("a pai object is correctly generated", {
   skip_on_travis() # server certificate verification failed in curl_fetch_memory()
-  glyphosate <- pai$new("glyphosate", chyaml = FALSE)
-  expect_message(pai$new("benzalkonium chloride", chyaml = FALSE), "did not give results")
+  glyphosate <- pai$new("glyphosate")
+  
+  # This did not give results at BCPC in previous times, so it was used to test
+  # the corresponding warning.
+  #bc <- pai$new("benzalkonium chloride") 
 
   expect_equivalent(glyphosate$bcpc$cas, "1071-83-6")
   expect_equivalent(glyphosate$bcpc$formula, "C3H8NO5P")
@@ -18,5 +21,5 @@ test_that("a pai object is correctly generated from an ambiguous name", {
   expect_equal(glyphosate$inchikey, ik)
   expect_equivalent(round(glyphosate$mw, 2), 169.07)
   smiles <- "C(C(=O)O)NCP(=O)(O)O"
-  expect_equal(glyphosate$smiles[["PubChem_Canonical"]], smiles)
+  expect_equal(glyphosate$smiles[["PubChem"]], smiles)
 })