Last updated on 2019-10-28 07:52:07 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.3.5 | 19.90 | 150.85 | 170.75 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.3.5 | 15.95 | 114.77 | 130.72 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.3.5 | 200.67 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.3.5 | 202.60 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 2.3.5 | 55.00 | 238.00 | 293.00 | OK | |
| r-patched-linux-x86_64 | 2.3.5 | 16.83 | 144.57 | 161.40 | OK | |
| r-patched-solaris-x86 | 2.3.5 | 299.60 | ERROR | |||
| r-release-linux-x86_64 | 2.3.5 | 17.28 | 143.25 | 160.53 | OK | |
| r-release-windows-ix86+x86_64 | 2.3.5 | 49.00 | 170.00 | 219.00 | OK | |
| r-release-osx-x86_64 | 2.3.5 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 2.3.5 | 17.00 | 208.00 | 225.00 | OK | |
| r-oldrel-osx-x86_64 | 2.3.5 | OK |
Version: 2.3.5
Check: examples
Result: ERROR
Running examples in 'soilDB-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OSDquery
> ### Title: Full text searching of the USDA-NRCS Official Series
> ### Descriptions
> ### Aliases: OSDquery
> ### Keywords: manip
>
> ### ** Examples
>
> # find all series that list Pardee as a geographically associated soil.
> s <- OSDquery(geog_assoc_soils = 'pardee')
Error: lexical error: invalid char in json text.
<html><body><h1>503 Service Una
(right here) ------^
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.3.5
Check: tests
Result: ERROR
Running 'testthat.R' [8s/18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(soilDB)
Loading required package: aqp
This is aqp 1.17
Attaching package: 'aqp'
The following object is masked from 'package:base':
union
>
>
>
>
> test_check("soilDB")
-- 1. Error: (unknown) (@test-OSDquery.R#4) -----------------------------------
lexical error: invalid char in json text.
<html><body><h1>503 Service Una
(right here) ------^
1: OSDquery(geog_assoc_soils = "pardee") at testthat/test-OSDquery.R:4
2: jsonlite::fromJSON(r.content)
3: parse_and_simplify(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame,
simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
4: parseJSON(txt, bigint_as_char)
5: parse_string(txt, bigint_as_char)
-- 2. Error: (unknown) (@test-fetchKSSL.R#5) ----------------------------------
cannot open URL 'https://casoilresource.lawr.ucdavis.edu/soil_web/kssl/query.php?gzip=1&what=site&series=sierra'
1: fetchKSSL(series = "sierra") at testthat/test-fetchKSSL.R:5
2: download.file(url = site.url, destfile = tf.site, mode = "wb", quiet = TRUE)
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
-- 3. Failure: fetchOSD() returns an SPC (@test-fetchOSD.R#19) ----------------
class\(x\) does not match "SoilProfileCollection".
Actual value: "NULL"
-- 4. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
class\(x\.extended\) does not match "list".
Actual value: "NULL"
-- 5. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
class\(x\.extended\$SPC\) does not match "SoilProfileCollection".
Actual value: "NULL"
-- 6. Error: fetchOSD() returns reasonable data (@test-fetchOSD.R#34) ---------
unable to find an inherited method for function 'site' for signature '"NULL"'
1: expect_equal(nrow(site(x)) == 2, TRUE) at testthat/test-fetchOSD.R:34
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: nrow(site(x))
5: site(x)
6: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("NULL"), new("standardGeneric", .Data = function (object, ...)
standardGeneric("site"), generic = structure("site", package = "aqp"), package = "aqp",
group = list(), valueClass = character(0), signature = "object", default = NULL,
skeleton = (function (object, ...)
stop("invalid call in method dispatch to 'site' (no default method)", domain = NA))(object,
...)), <environment>)
7: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
-- 7. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchO
names(x.extended) not equal to c(...).
target is NULL, current is character
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
-- 8. Failure: siblings() returns reasonable data (@test-siblings.R#21) -------
length(x) not equal to 2.
1/1 mismatches
[1] 0 - 2 == -2
-- 9. Failure: siblings() returns reasonable data (@test-siblings.R#23) -------
class(x$sib) not equal to "data.frame".
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
-- 10. Failure: siblings() returns reasonable data (@test-siblings.R#24) ------
class(x$sib.data) not equal to "data.frame".
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
-- 11. Failure: siblings() returns reasonable data (@test-siblings.R#26) ------
names(x$sib) not equal to c("series", "sibling", "majcompflag", "n").
target is NULL, current is character
== testthat results ===========================================================
[ OK: 117 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 11 ]
1. Error: (unknown) (@test-OSDquery.R#4)
2. Error: (unknown) (@test-fetchKSSL.R#5)
3. Failure: fetchOSD() returns an SPC (@test-fetchOSD.R#19)
4. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#26)
5. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#27)
6. Error: fetchOSD() returns reasonable data (@test-fetchOSD.R#34)
7. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchOSD.R#44)
8. Failure: siblings() returns reasonable data (@test-siblings.R#21)
9. Failure: siblings() returns reasonable data (@test-siblings.R#23)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(soilDB)
Loading required package: aqp
This is aqp 1.17
Attaching package: 'aqp'
The following object is masked from 'package:base':
union
>
>
>
>
> test_check("soilDB")
── 1. Error: (unknown) (@test-OSDquery.R#4) ───────────────────────────────────
lexical error: invalid char in json text.
<html><body><h1>503 Service Una
(right here) ------^
1: OSDquery(geog_assoc_soils = "pardee") at testthat/test-OSDquery.R:4
2: jsonlite::fromJSON(r.content)
3: parse_and_simplify(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame,
simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
4: parseJSON(txt, bigint_as_char)
5: parse_string(txt, bigint_as_char)
── 2. Error: (unknown) (@test-fetchKSSL.R#5) ──────────────────────────────────
cannot open URL 'https://casoilresource.lawr.ucdavis.edu/soil_web/kssl/query.php?gzip=1&what=site&series=sierra'
1: fetchKSSL(series = "sierra") at testthat/test-fetchKSSL.R:5
2: download.file(url = site.url, destfile = tf.site, mode = "wb", quiet = TRUE)
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
── 3. Failure: fetchOSD() returns an SPC (@test-fetchOSD.R#19) ────────────────
class\(x\) does not match "SoilProfileCollection".
Actual value: "NULL"
── 4. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
class\(x\.extended\) does not match "list".
Actual value: "NULL"
── 5. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
class\(x\.extended\$SPC\) does not match "SoilProfileCollection".
Actual value: "NULL"
── 6. Error: fetchOSD() returns reasonable data (@test-fetchOSD.R#34) ─────────
unable to find an inherited method for function 'site' for signature '"NULL"'
1: expect_equal(nrow(site(x)) == 2, TRUE) at testthat/test-fetchOSD.R:34
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: nrow(site(x))
5: site(x)
6: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("NULL"), new("standardGeneric", .Data = function (object, ...)
standardGeneric("site"), generic = structure("site", package = "aqp"), package = "aqp",
group = list(), valueClass = character(0), signature = "object", default = NULL,
skeleton = (function (object, ...)
stop("invalid call in method dispatch to 'site' (no default method)", domain = NA))(object,
...)), <environment>)
7: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
── 7. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchO
names(x.extended) not equal to c(...).
target is NULL, current is character
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
── 8. Failure: siblings() returns reasonable data (@test-siblings.R#21) ───────
length(x) not equal to 2.
1/1 mismatches
[1] 0 - 2 == -2
── 9. Failure: siblings() returns reasonable data (@test-siblings.R#23) ───────
class(x$sib) not equal to "data.frame".
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── 10. Failure: siblings() returns reasonable data (@test-siblings.R#24) ──────
class(x$sib.data) not equal to "data.frame".
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── 11. Failure: siblings() returns reasonable data (@test-siblings.R#26) ──────
names(x$sib) not equal to c("series", "sibling", "majcompflag", "n").
target is NULL, current is character
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 117 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 11 ]
1. Error: (unknown) (@test-OSDquery.R#4)
2. Error: (unknown) (@test-fetchKSSL.R#5)
3. Failure: fetchOSD() returns an SPC (@test-fetchOSD.R#19)
4. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#26)
5. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#27)
6. Error: fetchOSD() returns reasonable data (@test-fetchOSD.R#34)
7. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchOSD.R#44)
8. Failure: siblings() returns reasonable data (@test-siblings.R#21)
9. Failure: siblings() returns reasonable data (@test-siblings.R#23)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.3.5
Check: examples
Result: ERROR
Running examples in ‘soilDB-Ex.R’ failed
The error most likely occurred in:
> ### Name: OSDquery
> ### Title: Full text searching of the USDA-NRCS Official Series
> ### Descriptions
> ### Aliases: OSDquery
> ### Keywords: manip
>
> ### ** Examples
>
> # find all series that list Pardee as a geographically associated soil.
> s <- OSDquery(geog_assoc_soils = 'pardee')
Error: lexical error: invalid char in json text.
<html><body><h1>503 Service Una
(right here) ------^
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.3.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(soilDB)
Loading required package: aqp
This is aqp 1.17
Attaching package: 'aqp'
The following object is masked from 'package:base':
union
>
>
>
>
> test_check("soilDB")
── 1. Error: (unknown) (@test-OSDquery.R#4) ───────────────────────────────────
lexical error: invalid char in json text.
<html><body><h1>503 Service Una
(right here) ------^
1: OSDquery(geog_assoc_soils = "pardee") at testthat/test-OSDquery.R:4
2: jsonlite::fromJSON(r.content)
3: parse_and_simplify(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame,
simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
4: parseJSON(txt, bigint_as_char)
5: parse_string(txt, bigint_as_char)
── 2. Error: (unknown) (@test-fetchKSSL.R#5) ──────────────────────────────────
cannot open URL 'https://casoilresource.lawr.ucdavis.edu/soil_web/kssl/query.php?gzip=1&what=site&series=sierra'
1: fetchKSSL(series = "sierra") at testthat/test-fetchKSSL.R:5
2: download.file(url = site.url, destfile = tf.site, mode = "wb", quiet = TRUE)
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
── 3. Failure: fetchOSD() returns an SPC (@test-fetchOSD.R#19) ────────────────
class\(x\) does not match "SoilProfileCollection".
Actual value: "NULL"
── 4. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
class\(x\.extended\) does not match "list".
Actual value: "NULL"
── 5. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
class\(x\.extended\$SPC\) does not match "SoilProfileCollection".
Actual value: "NULL"
── 6. Error: fetchOSD() returns reasonable data (@test-fetchOSD.R#34) ─────────
unable to find an inherited method for function 'site' for signature '"NULL"'
1: expect_equal(nrow(site(x)) == 2, TRUE) at testthat/test-fetchOSD.R:34
2: quasi_label(enquo(object), label, arg = "object")
3: eval_bare(get_expr(quo), get_env(quo))
4: nrow(site(x))
5: site(x)
6: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("NULL"), new("standardGeneric", .Data = function (object, ...)
standardGeneric("site"), generic = structure("site", package = "aqp"), package = "aqp",
group = list(), valueClass = character(0), signature = "object", default = NULL,
skeleton = (function (object, ...)
stop("invalid call in method dispatch to 'site' (no default method)", domain = NA))(object,
...)), <environment>)
7: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
── 7. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchO
names(x.extended) not equal to c(...).
target is NULL, current is character
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
Error in open.connection(con, "rb") : HTTP error 503.
── 8. Failure: siblings() returns reasonable data (@test-siblings.R#21) ───────
length(x) not equal to 2.
1/1 mismatches
[1] 0 - 2 == -2
── 9. Failure: siblings() returns reasonable data (@test-siblings.R#23) ───────
class(x$sib) not equal to "data.frame".
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── 10. Failure: siblings() returns reasonable data (@test-siblings.R#24) ──────
class(x$sib.data) not equal to "data.frame".
1/1 mismatches
x[1]: "NULL"
y[1]: "data.frame"
── 11. Failure: siblings() returns reasonable data (@test-siblings.R#26) ──────
names(x$sib) not equal to c("series", "sibling", "majcompflag", "n").
target is NULL, current is character
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 117 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 11 ]
1. Error: (unknown) (@test-OSDquery.R#4)
2. Error: (unknown) (@test-fetchKSSL.R#5)
3. Failure: fetchOSD() returns an SPC (@test-fetchOSD.R#19)
4. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#26)
5. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#27)
6. Error: fetchOSD() returns reasonable data (@test-fetchOSD.R#34)
7. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchOSD.R#44)
8. Failure: siblings() returns reasonable data (@test-siblings.R#21)
9. Failure: siblings() returns reasonable data (@test-siblings.R#23)
1. ...
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.3.5
Check: examples
Result: ERROR
Running examples in ‘soilDB-Ex.R’ failed
The error most likely occurred in:
> ### Name: OSDquery
> ### Title: Full text searching of the USDA-NRCS Official Series
> ### Descriptions
> ### Aliases: OSDquery
> ### Keywords: manip
>
> ### ** Examples
>
> # find all series that list Pardee as a geographically associated soil.
> s <- OSDquery(geog_assoc_soils = 'pardee')
> # get data for these series
> x <- fetchOSD(s$series, extended = TRUE, colorState = 'dry')
Error in open.connection(con, "rb") :
Timeout was reached: [casoilresource.lawr.ucdavis.edu] Resolving timed out after 10000 milliseconds
error
> # simple figure
> par(mar=c(0,0,1,1))
> plot(x$SPC)
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot -> plot -> plot.default -> localWindow -> plot.window
Execution halted
Flavor: r-patched-solaris-x86