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authorJohannes Ranke <jranke@uni-bremen.de>2020-10-13 15:10:03 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-13 15:10:03 +0200
commit898d598bcbb022ac767e0105e868798130f2c74c (patch)
tree8a079442d27df08ed8ee7659f508f62e544f8b32
parent6937e41d317b953d8246203814500166dbe89470 (diff)
Adapt to changes in webchemHEADmaster
Unfortunately, tests only pass sometimes, it seems PubChem is not always responding
-rw-r--r--ChangeLog8
-rw-r--r--DESCRIPTION1
-rw-r--r--GNUmakefile3
-rw-r--r--R/chent.R10
-rw-r--r--test.log18
-rw-r--r--tests/testthat/test_pai.R8
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)
})

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