CRAN Package Check Results for Package soilDB

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

Check Details

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