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|
#!perl -T
use 5.010;
use strict;
use warnings FATAL => 'all';
use Test::More tests => 54;
use Test::Fatal;
use Statistics::R::IO::Parser qw(:all);
use Statistics::R::IO::ParserState;
use Statistics::R::IO::QapEncoding qw(:all);
use lib 't/lib';
use ShortDoubleVector;
use TestCases;
sub check_qap {
my ($file, $expected, $message) = @_;
my $filename = $file . '.qap';
open (my $f, $filename) or die $! . " $filename";
binmode $f;
my ($data, $rc) = '';
while ($rc = read($f, $data, 8192, length $data)) {}
die $! unless defined $rc;
subtest 'qap - ' . $message => sub {
plan tests => 2;
my ($actual, $state) = @{ decode($data) };
## NOTE: I'm switching the order of comparisons to ensure
## ShortDoubleVector's 'eq' overload is used
is($expected, $actual, $message) or diag explain $actual;
ok($state->eof, $message . ' - parse complete')
}
}
sub check_padding {
my ($data, $expected, $message) = @_;
subtest 'padding - ' . $message => sub {
plan tests => 2;
my ($value, $state) = @{ decode($data) };
is($value, $expected, $message) or diag explain $value;
ok($state->eof, $message . ' - parse complete')
}
}
subtest 'integer vectors' => sub {
plan tests => 2;
## serialize 1:3, XDR: true
check_qap('t/data/noatt-123l',
Statistics::R::REXP::Integer->new([ 1, 2, 3 ]),
'int vector no atts');
## serialize a=1L, b=2L, c=3L, XDR: true
check_qap('t/data/abc-123l',
Statistics::R::REXP::Integer->new(
elements => [ 1, 2, 3 ],
attributes => {
names => Statistics::R::REXP::Character->new(['a', 'b', 'c'])
}),
'int vector names att');
# ## handling of negative integer vector length
# like(exception {
# unserialize("\x58\x0a\0\0\0\2\0\3\0\2\0\2\3\0\0\0\0\x0d\xff\xff\xff\xff" .
# "\0\0\0\0" . "\0\0\0\1")
# }, qr/TODO: Long vectors are not supported/, 'long length');
# like(exception {
# unserialize("\x58\x0a\0\0\0\2\0\3\0\2\0\2\3\0\0\0\0\x0d\xff\xff\xff\x0")
# }, qr/Negative length/, 'negative length');
};
subtest 'double vectors' => sub {
plan tests => 2;
## serialize 1:3, XDR: true
check_qap('t/data/noatt-123456',
ShortDoubleVector->new([ 1234.56 ]),
'double vector no atts');
## serialize foo=1234.56, XDR: true
check_qap('t/data/foo-123456',
ShortDoubleVector->new(
elements => [ 1234.56 ],
attributes => {
names => Statistics::R::REXP::Character->new(['foo'])
}),
'double vector names att');
};
subtest 'character vectors' => sub {
plan tests => 3;
## serialize letters[1:3], XDR: true
check_qap('t/data/noatt-abc',
Statistics::R::REXP::Character->new([ 'a', 'b', 'c' ]),
'character vector no atts');
## serialize A='a', B='b', C='c', XDR: true
check_qap('t/data/ABC-abc',
Statistics::R::REXP::Character->new(
elements => [ 'a', 'b', 'c' ],
attributes => {
names => Statistics::R::REXP::Character->new(['A', 'B', 'C'])
}),
'character vector names att');
check_padding("\x0a\x0c\0\0\x22\x08\0\0\x61\0\x62\0\x63\0\1\1",
Statistics::R::REXP::Character->new(['a', 'b', 'c']),
'c("a", "b", "c")');
};
subtest 'raw vectors' => sub {
plan tests => 4;
## serialize as.raw(c(1:3, 255, 0), XDR: true
check_qap('t/data/noatt-raw',
Statistics::R::REXP::Raw->new([ 1, 2, 3, 255, 0 ]),
'raw vector');
check_padding("\x0a\x0c\0\0\x25\x08\0\0\1\0\0\0\x78\0\0\0",
Statistics::R::REXP::Raw->new([120]),
'charToRaw("x")');
check_padding("\x0a\x0c\0\0\x25\x08\0\0\3\0\0\0\x66\x6f\x6f\0",
Statistics::R::REXP::Raw->new([102, 111, 111]),
'charToRaw("foo")');
check_padding("\x0a\x0c\0\0\x25\x08\0\0\4\0\0\0\x66\x72\x65\x64",
Statistics::R::REXP::Raw->new([102, 114, 101, 100]),
'charToRaw("fred")');
};
subtest 'logical vectors' => sub {
plan tests => 5;
check_qap('t/data/noatt-true',
Statistics::R::REXP::Logical->new([ 1 ]),
'logical vector - singleton');
check_qap('t/data/noatt-tfftf',
Statistics::R::REXP::Logical->new([ 1, 0, 0, 1, 0 ]),
'logical vector');
check_qap('t/data/ABCDE-tfftf',
Statistics::R::REXP::Logical->new(
elements => [ 1, 0, 0, 1, 0 ],
attributes => {
names => Statistics::R::REXP::Character->new(['A', 'B', 'C', 'D', 'E'])
}),
'logical vector names att');
check_padding("\x0a\x0c\0\0\x24\x08\0\0\1\0\0\0\1\xff\xff\xff",
Statistics::R::REXP::Logical->new([1]),
'TRUE');
check_padding("\x0a\x0c\0\0\x24\x08\0\0\4\0\0\0\1\0\0\1",
Statistics::R::REXP::Logical->new([1, 0, 0, 1]),
'c(TRUE, FALSE, FALSE, TRUE)');
};
subtest 'generic vector (list)' => sub {
plan tests => 2;
## serialize list(1:3, list('a', 'b', 11), 'foo'), XDR: true
check_qap('t/data/noatt-list',
Statistics::R::REXP::List->new([
Statistics::R::REXP::Integer->new([ 1, 2, 3]),
Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new(['a']),
Statistics::R::REXP::Character->new(['b']),
ShortDoubleVector->new([11]) ]),
Statistics::R::REXP::Character->new(['foo']) ]),
'generic vector no atts');
## serialize list(foo=1:3, list('a', 'b', 11), bar='foo'), XDR: true
check_qap('t/data/foobar-list',
Statistics::R::REXP::List->new(
elements => [
Statistics::R::REXP::Integer->new([ 1, 2, 3]),
Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new(['a']),
Statistics::R::REXP::Character->new(['b']),
ShortDoubleVector->new([11]) ]),
Statistics::R::REXP::Character->new(['foo']) ],
attributes => {
names => Statistics::R::REXP::Character->new(['foo', '', 'bar'])
}),
'generic vector names att');
};
subtest 'symbol' => sub {
plan tests => 3;
check_padding("\x0a\x08\0\0\x13\4\0\0\x78\0\0\0",
Statistics::R::REXP::Symbol->new('x'),
'as.name("x")');
check_padding("\x0a\x08\0\0\x13\4\0\0\x66\x6f\x6f\0",
Statistics::R::REXP::Symbol->new('foo'),
'as.name("foo")');
check_padding("\x0a\x0c\0\0\x13\x08\0\0\x66\x72\x65\x64\0\0\0\0",
Statistics::R::REXP::Symbol->new('fred'),
'as.name("fred")');
};
subtest 'matrix' => sub {
plan tests => 2;
## serialize matrix(-1:4, 2, 3), XDR: true
check_qap('t/data/noatt-mat',
Statistics::R::REXP::Integer->new(
elements => [ -1, 0, 1, 2, 3, 4 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([2, 3]),
}),
'int matrix no atts');
## serialize matrix(-1:4, 2, 3, dimnames=list(c('a', 'b'))), XDR: true
check_qap('t/data/ab-mat',
Statistics::R::REXP::Integer->new(
elements => [ -1, 0, 1, 2, 3, 4 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([2, 3]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new(['a', 'b']),
Statistics::R::REXP::Null->new
]),
}),
'int matrix rownames');
};
subtest 'data frames' => sub {
plan tests => 3;
## serialize head(cars)
check_qap('t/data/cars',
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 4, 4, 7, 7, 8, 9]),
ShortDoubleVector->new([ 2, 10, 4, 22, 16, 10]),
],
attributes => {
names => Statistics::R::REXP::Character->new(['speed', 'dist']),
class => Statistics::R::REXP::Character->new(['data.frame']),
'row.names' => Statistics::R::REXP::Integer->new([
1, 2, 3, 4, 5, 6
]),
}),
'the cars data frame');
## serialize head(mtcars)
check_qap('t/data/mtcars',
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 21.0, 21.0, 22.8, 21.4, 18.7, 18.1 ]),
ShortDoubleVector->new([ 6, 6, 4, 6, 8, 6 ]),
ShortDoubleVector->new([ 160, 160, 108, 258, 360, 225 ]),
ShortDoubleVector->new([ 110, 110, 93, 110, 175, 105 ]),
ShortDoubleVector->new([ 3.90, 3.90, 3.85, 3.08, 3.15, 2.76 ]),
ShortDoubleVector->new([ 2.620, 2.875, 2.320, 3.215, 3.440, 3.460 ]),
ShortDoubleVector->new([ 16.46, 17.02, 18.61, 19.44, 17.02, 20.22 ]),
ShortDoubleVector->new([ 0, 0, 1, 1, 0, 1 ]),
ShortDoubleVector->new([ 1, 1, 1, 0, 0, 0 ]),
ShortDoubleVector->new([ 4, 4, 4, 3, 3, 3 ]),
ShortDoubleVector->new([ 4, 4, 1, 1, 2, 1 ]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'mpg' , 'cyl', 'disp', 'hp', 'drat', 'wt', 'qsec',
'vs', 'am', 'gear', 'carb']),
class => Statistics::R::REXP::Character->new(['data.frame']),
'row.names' => Statistics::R::REXP::Character->new([
'Mazda RX4', 'Mazda RX4 Wag', 'Datsun 710',
'Hornet 4 Drive', 'Hornet Sportabout', 'Valiant'
]),
}),
'the mtcars data frame');
## serialize head(iris)
check_qap('t/data/iris',
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 5.1, 4.9, 4.7, 4.6, 5.0, 5.4 ]),
ShortDoubleVector->new([ 3.5, 3.0, 3.2, 3.1, 3.6, 3.9 ]),
ShortDoubleVector->new([ 1.4, 1.4, 1.3, 1.5, 1.4, 1.7 ]),
ShortDoubleVector->new([ 0.2, 0.2, 0.2, 0.2, 0.2, 0.4 ]),
Statistics::R::REXP::Integer->new(
elements => [ 1, 1, 1, 1, 1, 1 ],
attributes => {
levels => Statistics::R::REXP::Character->new([
'setosa', 'versicolor', 'virginica']),
class => Statistics::R::REXP::Character->new(['factor'])
} ),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'Sepal.Length', 'Sepal.Width', 'Petal.Length',
'Petal.Width', 'Species']),
class => Statistics::R::REXP::Character->new(['data.frame']),
'row.names' => Statistics::R::REXP::Integer->new([
1, 2, 3, 4, 5, 6
]),
}),
'the iris data frame');
};
## Call lm(mpg ~ wt, data = head(mtcars))
check_qap('t/data/lang-lm-mpgwt',
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('lm'),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('head'),
Statistics::R::REXP::Symbol->new('mtcars'),
]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'', 'formula', 'data' ])
}),
'language lm(mpg~wt, head(mtcars))');
## serialize lm(mpg ~ wt, data = head(mtcars))
check_qap('t/data/mtcars-lm-mpgwt',
Statistics::R::REXP::List->new(
elements => [
# coefficients
ShortDoubleVector->new(
elements => [ 30.3002034730204, -3.27948805566774 ],
attributes => {
names => Statistics::R::REXP::Character->new(['(Intercept)', 'wt'])
}),
# residuals
ShortDoubleVector->new(
elements => [ -0.707944767170941, 0.128324687024322, 0.108208816128727,
1.64335062595135, -0.318764561523408, -0.853174800410051 ],
attributes => {
names => Statistics::R::REXP::Character->new([
"Mazda RX4", "Mazda RX4 Wag",
"Datsun 710", "Hornet 4 Drive",
"Hornet Sportabout", "Valiant" ])
}),
# effects
ShortDoubleVector->new(
elements => [ -50.2145397270552, -3.39713386075597, 0.13375416348722,
1.95527848390874, 0.0651588996571721, -0.462851730054076 ],
attributes => {
names => Statistics::R::REXP::Character->new([
'(Intercept)', 'wt', '',
'', '', '' ])
}),
# rank
Statistics::R::REXP::Integer->new([2]),
# fitted.values
ShortDoubleVector->new(
elements => [ 21.7079447671709, 20.8716753129757, 22.6917911838713,
19.7566493740486, 19.0187645615234, 18.9531748004101 ],
attributes => {
names => Statistics::R::REXP::Character->new([
"Mazda RX4", "Mazda RX4 Wag",
"Datsun 710", "Hornet 4 Drive",
"Hornet Sportabout", "Valiant" ])
}),
# assign
Statistics::R::REXP::Integer->new([0, 1]),
# qr
Statistics::R::REXP::List->new(
elements => [
# qr
ShortDoubleVector->new(
elements => [ -2.44948974278318, 0.408248290463863,
0.408248290463863, 0.408248290463863,
0.408248290463863, 0.408248290463863,
-7.31989184801706, 1.03587322261623,
0.542107126002057, -0.321898217952644,
-0.539106265315558, -0.558413647303373 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([ 6, 2 ]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new([
"Mazda RX4", "Mazda RX4 Wag",
"Datsun 710", "Hornet 4 Drive",
"Hornet Sportabout", "Valiant" ]),
Statistics::R::REXP::Character->new([
'(Intercept)', 'wt' ])
]),
assign => Statistics::R::REXP::Integer->new([
0, 1
]),
}),
# qraux
ShortDoubleVector->new(
[ 1.40824829046386, 1.0063272758402 ]),
# pivot
Statistics::R::REXP::Integer->new([1, 2]),
# tol
ShortDoubleVector->new([1E-7]),
# rank
Statistics::R::REXP::Integer->new([2]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
"qr", "qraux", "pivot",
"tol", "rank" ]),
class => Statistics::R::REXP::Character->new(['qr'])
}),
# df.residual
Statistics::R::REXP::Integer->new([4]),
# xlevels
Statistics::R::REXP::List->new(
elements => [],
attributes => {
names => Statistics::R::REXP::Character->new([])
}),
# call
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('lm'),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('head'),
Statistics::R::REXP::Symbol->new('mtcars'),
]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'', 'formula', 'data' ])
}),
# terms
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
],
attributes => {
variables => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
factors => Statistics::R::REXP::Integer->new(
elements => [ 0, 1 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([ 2, 1 ]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new([
'mpg', 'wt' ]),
Statistics::R::REXP::Character->new([ 'wt' ]),
]),
}),
'term.labels' => Statistics::R::REXP::Character->new(['wt']),
order => Statistics::R::REXP::Integer->new([1]),
intercept => Statistics::R::REXP::Integer->new([1]),
response => Statistics::R::REXP::Integer->new([1]),
class => Statistics::R::REXP::Character->new([
'terms', 'formula'
]),
'.Environment' => Statistics::R::REXP::Unknown->new(sexptype=>4),
predvars => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
dataClasses => Statistics::R::REXP::Character->new(
elements => ['numeric', 'numeric'],
attributes => {
names => Statistics::R::REXP::Character->new(['mpg', 'wt'])
}),
}),
# model
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 21.0, 21.0, 22.8, 21.4, 18.7, 18.1 ]),
ShortDoubleVector->new([ 2.62, 2.875, 2.32, 3.215, 3.44, 3.46 ]),
],
attributes => {
names => Statistics::R::REXP::Character->new(['mpg', 'wt']),
'row.names' => Statistics::R::REXP::Character->new([
'Mazda RX4', 'Mazda RX4 Wag', 'Datsun 710',
'Hornet 4 Drive', 'Hornet Sportabout', 'Valiant']),
class => Statistics::R::REXP::Character->new(['data.frame']),
terms => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
],
attributes => {
variables => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
factors => Statistics::R::REXP::Integer->new(
elements => [ 0, 1 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([ 2, 1 ]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new([
'mpg', 'wt' ]),
Statistics::R::REXP::Character->new([ 'wt' ]),
]),
}),
'term.labels' => Statistics::R::REXP::Character->new(['wt']),
order => Statistics::R::REXP::Integer->new([1]),
intercept => Statistics::R::REXP::Integer->new([1]),
response => Statistics::R::REXP::Integer->new([1]),
class => Statistics::R::REXP::Character->new([
'terms', 'formula'
]),
'.Environment' => Statistics::R::REXP::Unknown->new(sexptype=>4),
predvars => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
dataClasses => Statistics::R::REXP::Character->new(
elements => ['numeric', 'numeric'],
attributes => {
names => Statistics::R::REXP::Character->new(['mpg', 'wt'])
}),
}),
}),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'coefficients', 'residuals', 'effects', 'rank',
'fitted.values', 'assign', 'qr', 'df.residual',
'xlevels', 'call', 'terms', 'model',
]),
class => Statistics::R::REXP::Character->new(['lm']) }),
'lm mpg~wt, head(mtcars)');
while ( my ($name, $value) = each %{TEST_CASES()} ) {
SKIP: {
skip "not yet supported", 1 if ($value->{skip} || '' =~ 'rserve');
check_qap('t/data/' . $name,
$value->{value},
$value->{desc});
}
}
|
