CRAN Package Check Results for Package taxize

Last updated on 2017-01-20 19:47:27.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.8.0 2.80 65.76 68.56 ERROR
r-devel-linux-x86_64-debian-gcc 0.8.4 3.20 234.57 237.77 ERROR
r-devel-linux-x86_64-fedora-clang 0.8.4 49.80 ERROR --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.8.4 92.09 ERROR --no-stop-on-test-error
r-devel-macos-x86_64-clang 0.8.4 65.41 ERROR --no-stop-on-test-error
r-devel-windows-ix86+x86_64 0.8.0 9.00 8.00 17.00 ERROR
r-patched-linux-x86_64 0.8.0 2.89 62.46 65.35 ERROR
r-patched-solaris-sparc 0.8.4 510.60 OK
r-patched-solaris-x86 0.8.4 117.30 ERROR
r-release-linux-x86_64 0.8.4 3.16 232.86 236.02 ERROR
r-release-osx-x86_64-mavericks 0.8.4 ERROR
r-release-windows-ix86+x86_64 0.8.0 8.00 6.00 14.00 ERROR
r-oldrel-windows-ix86+x86_64 0.8.4 19.00 297.00 316.00 ERROR

Check Details

Version: 0.8.0
Check: examples
Result: ERROR
    Running examples in ‘taxize-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: rankagg
    > ### Title: Aggregate data by given taxonomic rank
    > ### Aliases: rankagg
    >
    > ### ** Examples
    >
    > library("vegan")
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.4-2
    > data(dune.taxon, package='vegan')
    > dat <- dune.taxon
    > set.seed(1234)
    > dat$abundance <- round(rlnorm(n=nrow(dat),meanlog=5,sdlog=2),0)
    > rankagg(data=dat, datacol="abundance", rank="Genus")
     Genus sum
    1 Achillea 13
    2 Agrostis 258
    3 Aira 1298
    4 Alopecurus 1
    5 Anthoxanthum 350
    6 Bellis 408
    7 Brachythecium 144
    8 Bromus 47
    9 Calliergonella 23
    10 Chenopodium 50
    11 Cirsium 48
    12 Comarum 25
    13 Eleocharis 57
    14 Elymus 20
    15 Empetrum 31
    16 Hypochaeris 169
    17 Juncus 1130
    18 Lolium 53
    19 Plantago 24
    20 Poa 18642
    21 Ranunculus 194
    22 Rumex 56
    23 Sagina 61
    24 Salix 372
    25 Scorzoneroides 37
    26 Trifolium 476
    27 Vicia 19
    > rankagg(data=dat, "abundance", rank="Family")
     Family sum
    1 Amaranthaceae 50
    2 Asteraceae 675
    3 Brachytheciaceae 144
    4 Caryophyllaceae 61
    5 Cyperaceae 57
    6 Ericaceae 31
    7 Fabaceae 495
    8 Hypnaceae 23
    9 Juncaceae 1130
    10 Plantaginaceae 24
    11 Poaceae 20669
    12 Polygonaceae 56
    13 Ranunculaceae 194
    14 Rosaceae 25
    15 Salicaceae 372
    > rankagg(data=dat, "abundance", rank="Genus", fxn="mean")
     Genus mean
    1 Achillea 13
    2 Agrostis 258
    3 Aira 1298
    4 Alopecurus 1
    5 Anthoxanthum 350
    6 Bellis 408
    7 Brachythecium 144
    8 Bromus 47
    9 Calliergonella 23
    10 Chenopodium 50
    11 Cirsium 48
    12 Comarum 25
    13 Eleocharis 57
    14 Elymus 20
    15 Empetrum 31
    16 Hypochaeris 169
    17 Juncus 565
    18 Lolium 53
    19 Plantago 24
    20 Poa 9321
    21 Ranunculus 194
    22 Rumex 56
    23 Sagina 61
    24 Salix 372
    25 Scorzoneroides 37
    26 Trifolium 238
    27 Vicia 19
    > rankagg(data=dat, "abundance", rank="Class")
    Error in `[.data.frame`(data, , rank) : undefined columns selected
    Calls: rankagg ... aggregate.default -> aggregate.data.frame -> [ -> [.data.frame
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64

Version: 0.8.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [3s/186s]
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
    
    
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 151 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.8.4
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘test-all.R’ [3s/186s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > library("taxize")
     > test_check("taxize")
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 151 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.8.4
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘test-all.R’ [4s/190s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > library("taxize")
     > test_check("taxize")
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 151 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.8.4
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘test-all.R’ [2s/186s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > library("taxize")
     > test_check("taxize")
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 151 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-macos-x86_64-clang

Version: 0.8.0
Check: examples
Result: ERROR
    Running examples in 'taxize-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: rankagg
    > ### Title: Aggregate data by given taxonomic rank
    > ### Aliases: rankagg
    >
    > ### ** Examples
    >
    > library("vegan")
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.4-2
    > data(dune.taxon, package='vegan')
    > dat <- dune.taxon
    > set.seed(1234)
    > dat$abundance <- round(rlnorm(n=nrow(dat),meanlog=5,sdlog=2),0)
    > rankagg(data=dat, datacol="abundance", rank="Genus")
     Genus sum
    1 Achillea 13
    2 Agrostis 258
    3 Aira 1298
    4 Alopecurus 1
    5 Anthoxanthum 350
    6 Bellis 408
    7 Brachythecium 144
    8 Bromus 47
    9 Calliergonella 23
    10 Chenopodium 50
    11 Cirsium 48
    12 Comarum 25
    13 Eleocharis 57
    14 Elymus 20
    15 Empetrum 31
    16 Hypochaeris 169
    17 Juncus 1130
    18 Lolium 53
    19 Plantago 24
    20 Poa 18642
    21 Ranunculus 194
    22 Rumex 56
    23 Sagina 61
    24 Salix 372
    25 Scorzoneroides 37
    26 Trifolium 476
    27 Vicia 19
    > rankagg(data=dat, "abundance", rank="Family")
     Family sum
    1 Amaranthaceae 50
    2 Asteraceae 675
    3 Brachytheciaceae 144
    4 Caryophyllaceae 61
    5 Cyperaceae 57
    6 Ericaceae 31
    7 Fabaceae 495
    8 Hypnaceae 23
    9 Juncaceae 1130
    10 Plantaginaceae 24
    11 Poaceae 20669
    12 Polygonaceae 56
    13 Ranunculaceae 194
    14 Rosaceae 25
    15 Salicaceae 372
    > rankagg(data=dat, "abundance", rank="Genus", fxn="mean")
     Genus mean
    1 Achillea 13
    2 Agrostis 258
    3 Aira 1298
    4 Alopecurus 1
    5 Anthoxanthum 350
    6 Bellis 408
    7 Brachythecium 144
    8 Bromus 47
    9 Calliergonella 23
    10 Chenopodium 50
    11 Cirsium 48
    12 Comarum 25
    13 Eleocharis 57
    14 Elymus 20
    15 Empetrum 31
    16 Hypochaeris 169
    17 Juncus 565
    18 Lolium 53
    19 Plantago 24
    20 Poa 9321
    21 Ranunculus 194
    22 Rumex 56
    23 Sagina 61
    24 Salix 372
    25 Scorzoneroides 37
    26 Trifolium 238
    27 Vicia 19
    > rankagg(data=dat, "abundance", rank="Class")
    Error in `[.data.frame`(data, , rank) : undefined columns selected
    Calls: rankagg ... aggregate.default -> aggregate.data.frame -> [ -> [.data.frame
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.8.0
Check: tests
Result: ERROR
     Running 'test-all.R' [190s]
    Running the tests in 'tests/test-all.R' failed.
    Last 13 lines of output:
    
    
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 138 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 0.8.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [4s/187s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > library("taxize")
     > test_check("taxize")
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 151 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.8.4
Check: tests
Result: ERROR
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
     `warnings` does not match "no hierarchy data found in ITIS".
     Actual value: "Unknown column 'itisTerms'"
    
    
     testthat results ================================================================
     OK: 25 SKIPPED: 151 FAILED: 3
     1. Failure: taxon with no data returned from classification() works (@test-tax_name.R#42)
     2. Failure: taxon with no data returned from classification() works (@test-tax_name.R#48)
     3. Failure: taxon with no data returned from classification() works (@test-tax_name.R#54)
    
     Error: testthat unit tests failed
     Execution halted
Flavors: r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-oldrel-windows-ix86+x86_64