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 |
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