1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
|
# These tests are intended to be run under valgrind so we can make sure there
# are no compiled code issues. It's basically impossible to run the full test
# suite under valgrind because there are lots of false positives from the PCRE
# library.
#
# Orinally these were the ses tests, but even the testthat overhead caused too
# many issues so we're just running the code without checking results.
writeLines("basic")
# expect_equal(ses(letters[1:10], letters[1:10]), character())
ses(letters[1:10], letters[1:10])
# expect_equal(ses(letters[1:10], LETTERS[1:10]), "1,10c1,10")
ses(letters[1:10], LETTERS[1:10])
# expect_equal(ses(letters[1:5], LETTERS[1:10]), "1,5c1,10")
ses(letters[1:5], LETTERS[1:10])
# expect_equal(ses(letters[1:10], LETTERS[1:5]), "1,10c1,5")
ses(letters[1:10], LETTERS[1:5])
# expect_equal(ses(letters[2:10], letters[1:7]), c("0a1", "7,9d7"))
ses(letters[2:10], letters[1:7])
# expect_equal(ses(letters[c(1:5, 1:5, 1:5)], c("e", "d", "a",
# "b", "c")), c("1,4d0", "6,8d1", "10d2", "14,15d5"))
ses(letters[c(1:5, 1:5, 1:5)], c("e", "d", "a", "b", "c"))
# expect_equal(ses(c("e", "d", "a", "b", "c"), letters[c(1:5, 1:5,
# 1:5)]), c("0a1,4", "1a6,8", "2a10", "5a14,15"))
ses(c("e", "d", "a", "b", "c"), letters[c(1:5, 1:5, 1:5)])
writeLines("trigger edit distance 1 branches")
# expect_equal(ses("a", c("a", "b")), "1a2")
ses("a", c("a", "b"))
# expect_equal(ses(c("a", "b"), "a"), "2d1")
ses(c("a", "b"), "a")
# expect_equal(ses("c", c("b", "c")), "0a1")
ses("c", c("b", "c"))
# expect_equal(ses(c("b", "c"), "c"), "1d0")
ses(c("b", "c"), "c")
# expect_equal(ses("a", character()), "1d0")
ses("a", character())
# expect_equal(ses(character(), "a"), "0a1")
ses(character(), "a")
# expect_equal(ses(character(), character()), character())
ses(character(), character())
## this is from the atomic tests, haven't dug into why they actually trigger
## the desired branches, but it is fairly complex
set.seed(2)
w1 <- sample(c("carrot", "cat", "cake", "eat", "rabbit", "holes",
"the", "a", "pasta", "boom", "noon", "sky", "hat", "blah",
"paris", "dog", "snake"), 25, replace = TRUE)
w4 <- w3 <- w2 <- w1
w2[sample(seq_along(w1), 5)] <- LETTERS[1:5]
w3 <- w1[8:15]
w4 <- c(w1[1:5], toupper(w1[1:5]), w1[6:15], toupper(w1[1:5]))
# expect_equal(ses(w1, w4), c("5a6,10", "15,21d19", "23,25c21,25"))
ses(w1, w4)
writeLines("longer strings")
# A bigger string
string <- do.call(paste0, expand.grid(LETTERS, LETTERS, LETTERS))
# expect_equal(ses(string, c("hello", string[-c(5, 500, 1000)],
# "goodbye")), c("0a1", "5d5", "500d499", "1000d998", "17576a17575"))
ses(string, c("hello", string[-c(5, 500, 1000)], "goodbye"))
# expect_equal(ses(c(string[200:500], "hello", string[-(1:400)][-c(5,
# 500, 1000)]), string), c("0a1,199", "207,306d405", "800a900",
# "1299a1400"))
ses(c(string[200:500], "hello", string[-(1:400)][-c(5, 500, 1000)]),
string)
writeLines("max diffs")
# expect_warning(ses(letters[1:10], LETTERS[1:10], max.diffs = 5),
# "Exceeded `max.diffs`")
suppressWarnings(ses(letters[1:10], LETTERS[1:10], max.diffs = 5))
# expect_equal(ses(letters[1:10], LETTERS[1:10], max.diffs = 5,
# warn = FALSE), "1,10c1,10")
ses(letters[1:10], LETTERS[1:10], max.diffs = 5, warn = FALSE)
# expect_equal(ses(letters[1:10], c(letters[1], LETTERS[2:5], letters[6:10]),
# max.diffs = 5, warn = FALSE), "2,5c2,5")
ses(letters[1:10], c(letters[1], LETTERS[2:5], letters[6:10]),
max.diffs = 5, warn = FALSE)
# expect_equal(ses(letters[1:10], c(letters[1], LETTERS[2:5], letters[6:8],
# LETTERS[9], letters[10]), max.diffs = 5, warn = FALSE), c("2,5c2,5",
# "9c9"))
ses(letters[1:10], c(letters[1], LETTERS[2:5], letters[6:8],
LETTERS[9], letters[10]), max.diffs = 5, warn = FALSE)
writeLines("corner cases?")
# expect_equal(ses(letters[1:4], letters[1:3]), "4d3")
ses(letters[1:4], letters[1:3])
# expect_equal(ses(letters[1:3], letters[1:4]), "3a4")
ses(letters[1:3], letters[1:4])
#
ses(1, 2:9, max.diffs = 8)
# h/t @gadenbui, data is extracted from palmerpenguins@0.1.0::penguins
#
# comparison <- subset(penguins, year == 2007 | flipper_length_mm > 220)
# test <- subset(penguins, year == 2008)
# a <- test$bill_length_mm
# b <- comparison$bill_length_mm
a <- c(39.6, 40.1, 35, 42, 34.5, 41.4, 39, 40.6, 36.5, 37.6, 35.7,
41.3, 37.6, 41.1, 36.4, 41.6, 35.5, 41.1, 35.9, 41.8, 33.5, 39.7,
39.6, 45.8, 35.5, 42.8, 40.9, 37.2, 36.2, 42.1, 34.6, 42.9, 36.7,
35.1, 37.3, 41.3, 36.3, 36.9, 38.3, 38.9, 35.7, 41.1, 34, 39.6,
36.2, 40.8, 38.1, 40.3, 33.1, 43.2, 49.1, 48.4, 42.6, 44.4, 44,
48.7, 42.7, 49.6, 45.3, 49.6, 50.5, 43.6, 45.5, 50.5, 44.9, 45.2,
46.6, 48.5, 45.1, 50.1, 46.5, 45, 43.8, 45.5, 43.2, 50.4, 45.3,
46.2, 45.7, 54.3, 45.8, 49.8, 46.2, 49.5, 43.5, 50.7, 47.7, 46.4,
48.2, 46.5, 46.4, 48.6, 47.5, 51.1, 45.2, 45.2, 50.5, 49.5, 46.4,
52.8, 40.9, 54.2, 42.5, 51, 49.7, 47.5, 47.6, 52, 46.9, 53.5,
49, 46.2, 50.9, 45.5)
b <- c(39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2, 34.1, 42, 37.8,
37.8, 41.1, 38.6, 34.6, 36.6, 38.7, 42.5, 34.4, 46, 37.8, 37.7,
35.9, 38.2, 38.8, 35.3, 40.6, 40.5, 37.9, 40.5, 39.5, 37.2, 39.5,
40.9, 36.4, 39.2, 38.8, 42.2, 37.6, 39.8, 36.5, 40.8, 36, 44.1,
37, 39.6, 41.1, 37.5, 36, 42.3, 46.1, 50, 48.7, 50, 47.6, 46.5,
45.4, 46.7, 43.3, 46.8, 40.9, 49, 45.5, 48.4, 45.8, 49.3, 42,
49.2, 46.2, 48.7, 50.2, 45.1, 46.5, 46.3, 42.9, 46.1, 44.5, 47.8,
48.2, 50, 47.3, 42.8, 45.1, 59.6, 49.6, 50.5, 50.5, 50.1, 50.4,
46.2, 54.3, 49.8, 49.5, 50.7, 46.4, 48.2, 48.6, 45.2, 52.5, 50,
50.8, 52.1, 52.2, 49.5, 50.8, 46.9, 51.1, 55.9, 49.1, 49.8, 51.5,
55.1, 48.8, 50.4, 46.5, 50, 51.3, 45.4, 52.7, 45.2, 46.1, 51.3,
46, 51.3, 46.6, 51.7, 47, 52, 45.9, 50.5, 50.3, 58, 46.4, 49.2,
42.4, 48.5, 43.2, 50.6, 46.7, 52)
# In <0.3.4: Exceeded buffer for finding fake snake
ses(a[-c(15:38, 50:90)], b[-c(40:85, 100:125)], max.diffs=80)
# In <0.3.4: Faux Snake Process Failed
ses(a[-(18:38)], b[-(50:80)], max.diffs=115)
# issue 157
# Arguably could match on 'A' instead of 'X' and be more comparct
a <- c('a', 'b', 'c', 'A', 'X', 'Y', 'Z', 'W')
b <- c('X', 'C', 'A', 'U', 1, 2, 3)
ses(a, b, max.diffs=13)
# segfault (but may have beend debugging code)
ses(letters[1:2], LETTERS[1:2], max.diffs = 4)
# snake overrun
ses(c("G", "C", "T", "C", "A", "C", "G", "C"), c("T", "G"), max.diffs=2)
# effect of max.diffs on compactness (waldo logical comparison)
ses(c('A','A','A','A','A'), c('B','A','B','A','B'), max.diffs=0)
ses(c('A','A','A','A','A'), c('B','A','B','A','B'), max.diffs=1)
ses(c('A','A','A','A','A'), c('B','A','B','A','B'), max.diffs=2)
# back snake all matches before faux snake triggered
ses_dat(
a=c("T", "A", "A", "C", "C", "A"),
b=c("A", "G", "A", "A"), max.diffs = 0
)
writeLines("errors")
# expect_error(ses("a", "b", max.diffs = "hello"), "must be scalar integer")
try(ses("a", "b", max.diffs = "hello"), silent=TRUE)
# expect_error(ses("a", "b", warn = "hello"), "must be TRUE or FALSE")
try(ses("a", "b", warn = "hello"), silent=TRUE)
# We want to have a test file that fully covers the C code in order to run
# valgrind with just that one. We were unable to isolate simple diffs that
# triggered all the code, but we were able to do it with the below in addition
# to the above.
# test_that("Repeat tests for full coverage in SES file", {
#
# From test.diffStr.R
# formula display changed
writeLines("model prep")
frm1 <- as.formula("Sepal.Length ~ Sepal.Width", env=.GlobalEnv)
frm2 <- as.formula("Sepal.Length ~ Sepal.Width + Species", env=.GlobalEnv)
mdl1 <- lm(frm1, iris)
mdl2 <- lm(frm2, iris)
writeLines("diff str")
# as.character(
# diffStr(mdl1, mdl2,
# extra = list(strict.width = "wrap"), line.limit = 30)
# )
## we captured the text being diffed above at the actual level, and
## also at the highest level
ses(
readLines('valgrind/mdl-tar.txt'), readLines('valgrind/mdl-cur.txt')
)
ses(
readLines('valgrind/mdl-tar-all.txt'),
readLines('valgrind/mdl-cur-all.txt')
)
# from testthat.warnings.R
writeLines("exceeded diff")
A3 <- c("a b c", "d e f A B C D", "g h i", "f")
B3 <- c("a b c", "xd e f E Q L S", "g h i", "q")
suppressWarnings(ses(A3, B3, max.diffs = 2))
writeLines("done")
|
