CRAN Package Check Results for Package treeman

Last updated on 2022-05-23 05:52:54 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.4 7.67 96.82 104.49 OK
r-devel-linux-x86_64-debian-gcc 1.1.4 7.64 71.18 78.82 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.4 121.69 OK
r-devel-linux-x86_64-fedora-gcc 1.1.4 111.34 OK
r-devel-windows-x86_64 1.1.4 68.00 158.00 226.00 OK
r-patched-linux-x86_64 1.1.4 13.92 90.23 104.15 OK
r-release-linux-x86_64 1.1.4 ERROR
r-release-macos-arm64 1.1.4 44.00 OK
r-release-macos-x86_64 1.1.4 53.00 OK
r-release-windows-x86_64 1.1.4 89.00 380.00 469.00 ERROR
r-oldrel-macos-arm64 1.1.4 54.00 OK
r-oldrel-macos-x86_64 1.1.4 74.00 OK
r-oldrel-windows-ix86+x86_64 1.1.4 23.00 196.00 219.00 OK

Check Details

Version: 1.1.4
Check: examples
Result: ERROR
    Running examples in ‘treeman-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: taxaResolve
    > ### Title: Resolve taxonmic names online
    > ### Aliases: taxaResolve
    >
    > ### ** Examples
    >
    > my_lovely_names <- c ('Gallus gallus', 'Pongo pingu', 'Homo sapiens',
    + 'Arabidopsis thaliana', 'Macaca thibetana', 'Bacillus subtilis')
    > res <- taxaResolve (nms=my_lovely_names)
    ---- Connection failed: trying again in [2s]----
    ---- Connection failed: trying again in [4s]----
    ---- Connection failed: trying again in [8s]----
    ---- Connection failed: trying again in [16s]----
    ---- Connection failed: trying again in [32s]----
    Warning in .safeFromJSON(query) :
     Failed to connect, server may be down.
    > length(colnames(res)) # 10 different metadata for returned names including original search name
    [1] 0
    > # let's look at the lineages
    > lineages <- strsplit(as.vector(res$lineage), '\\|')
    Error in strsplit(as.vector(res$lineage), "\\|") : non-character argument
    Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 1.1.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [21s/96s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("treeman")
     Loading required package: treeman
     [4] in treelst is not a TreeMan object
     These nodes are invalid:
     n2, n3
    
     These nodes are invalid:
     n5
    
     Root node `x` not in ndlst
    
     These nodes are invalid:
     n8
    
     These nodes are invalid:
     n5, n8
    
     Formal class 'TreeMan' [package "treeman"] with 17 slots
     ..@ ndlst :List of 19
     ..@ nds : chr [1:9] "n1" "n2" "n3" "n4" ...
     ..@ nnds : int 9
     ..@ tips : chr [1:10] "t1" "t10" "t2" "t3" ...
     ..@ ntips : int 10
     ..@ all : chr [1:19] "n1" "n2" "n3" "n4" ...
     ..@ nall : int 19
     ..@ pd : num 8.99
     ..@ wspn : logi TRUE
     ..@ wtxnyms : logi FALSE
     ..@ ply : logi FALSE
     ..@ updtd : logi TRUE
     ..@ ndmtrx :Formal class 'big.matrix' [package "bigmemory"] with 1 slot
     ..@ tinds : int [1:10] 10 11 12 13 14 15 16 17 18 19
     ..@ prinds : num [1:19] 1 1 1 2 3 3 6 4 6 5 ...
     ..@ root : chr "n1"
     ..@ othr_slt_nms: logi(0)
     [1] "TreeMan Object of [10] tips"
     Tree (TreeMan Object):
     + 10 tips
     + 9 internal nodes
     + With node matrix
     + Binary
     + PD 9.28
     + Root node is "n1"
     Node (internal node):
     + ID: "n9"
     + prid: "n3"
     + ptid: "t3", "t5"
     + nkids: 2
     + spn: 0.83
     + predist: 0.93
     + pd: 1
     Tree (TreeMan Object):
     + 10 tips
     + 9 internal nodes
     + Binary
     + PD 7.99
     + Root node is "n1"
     + With additional node slots:
     [binary_val]
     Tree (TreeMan Object):
     + 10 tips
     + 9 internal nodes
     + Binary
     + PD 10.6
     + Root node is "n1"
     [1] "TreeMen Object of [3] trees"
     TreeMen Object of [3] trees---- Connection failed: trying again in [2s]----
     ---- Connection failed: trying again in [4s]----
     ---- Connection failed: trying again in [8s]----
     ---- Connection failed: trying again in [16s]----
     ---- Connection failed: trying again in [32s]----
     [ FAIL 1 | WARN 1 | SKIP 9 | PASS 245 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • empty test (9)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_server_methods.R:53:3): taxaResolve([basic]) works ──────────────
     Error in `complete.cases(res)`: no input has determined the number of cases
     Backtrace:
     ▆
     1. └─stats::complete.cases(res) at test_server_methods.R:53:2
    
     [ FAIL 1 | WARN 1 | SKIP 9 | PASS 245 ]
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64

Version: 1.1.4
Check: examples
Result: ERROR
    Running examples in 'treeman-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: taxaResolve
    > ### Title: Resolve taxonmic names online
    > ### Aliases: taxaResolve
    >
    > ### ** Examples
    >
    > my_lovely_names <- c ('Gallus gallus', 'Pongo pingu', 'Homo sapiens',
    + 'Arabidopsis thaliana', 'Macaca thibetana', 'Bacillus subtilis')
    > res <- taxaResolve (nms=my_lovely_names)
    ---- Connection failed: trying again in [2s]----
    ---- Connection failed: trying again in [4s]----
    ---- Connection failed: trying again in [8s]----
    ---- Connection failed: trying again in [16s]----
    ---- Connection failed: trying again in [32s]----
    Warning in .safeFromJSON(query) :
     Failed to connect, server may be down.
    > length(colnames(res)) # 10 different metadata for returned names including original search name
    [1] 0
    > # let's look at the lineages
    > lineages <- strsplit(as.vector(res$lineage), '\\|')
    Error in strsplit(as.vector(res$lineage), "\\|") : non-character argument
    Execution halted
Flavor: r-release-windows-x86_64

Version: 1.1.4
Check: tests
Result: ERROR
     Running 'test-all.R' [126s]
    Running the tests in 'tests/test-all.R' failed.
    Complete output:
     > library(testthat)
     > test_check("treeman")
     Loading required package: treeman
     [4] in treelst is not a TreeMan object
     These nodes are invalid:
     n1, n3, n5
    
     These nodes are invalid:
     n3
    
     Root node `x` not in ndlst
    
     These nodes are invalid:
     n9
    
     These nodes are invalid:
     n5, n9
    
     Formal class 'TreeMan' [package "treeman"] with 17 slots
     ..@ ndlst :List of 19
     ..@ nds : chr [1:9] "n1" "n2" "n3" "n4" ...
     ..@ nnds : int 9
     ..@ tips : chr [1:10] "t1" "t10" "t2" "t3" ...
     ..@ ntips : int 10
     ..@ all : chr [1:19] "n1" "n2" "n3" "n4" ...
     ..@ nall : int 19
     ..@ pd : num 7.79
     ..@ wspn : logi TRUE
     ..@ wtxnyms : logi FALSE
     ..@ ply : logi FALSE
     ..@ updtd : logi TRUE
     ..@ ndmtrx : NULL
     ..@ tinds : int [1:10] 10 11 12 13 14 15 16 17 18 19
     ..@ prinds : num [1:19] 1 1 1 2 4 3 6 7 2 3 ...
     ..@ root : chr "n1"
     ..@ othr_slt_nms: logi(0)
     [1] "TreeMan Object of [10] tips"
     Tree (TreeMan Object):
     + 10 tips
     + 9 internal nodes
     + Binary
     + PD 7.94
     + Root node is "n1"
     Node (root node):
     + ID: "n1"
     + ptid: "n2", "n7"
     + nkids: 10
     + predist: 0
     + pd: 9.1
     Tree (TreeMan Object):
     + 10 tips
     + 9 internal nodes
     + Binary
     + PD 9.19
     + Root node is "n1"
     + With additional node slots:
     [binary_val]
     Tree (TreeMan Object):
     + 10 tips
     + 9 internal nodes
     + With node matrix
     + Binary
     + PD 10.1
     + Root node is "n1"
     [1] "TreeMen Object of [3] trees"
     TreeMen Object of [3] trees---- Connection failed: trying again in [2s]----
     ---- Connection failed: trying again in [4s]----
     ---- Connection failed: trying again in [8s]----
     ---- Connection failed: trying again in [16s]----
     ---- Connection failed: trying again in [32s]----
     ---- Connection failed: trying again in [2s]----
     ---- Connection failed: trying again in [4s]----
     ---- Connection failed: trying again in [8s]----
     ---- Connection failed: trying again in [16s]----
     [ FAIL 1 | WARN 1 | SKIP 9 | PASS 245 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • empty test (9)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_server_methods.R:53:3): taxaResolve([basic]) works ──────────────
     Error in `complete.cases(res)`: no input has determined the number of cases
     Backtrace:
     ▆
     1. └─stats::complete.cases(res) at test_server_methods.R:53:2
    
     [ FAIL 1 | WARN 1 | SKIP 9 | PASS 245 ]
     Error: Test failures
     Execution halted
Flavor: r-release-windows-x86_64