Last updated on 2024-06-11 16:49:52 CEST.
| Package | FAIL | ERROR | NOTE | OK |
|---|---|---|---|---|
| DAISIE | 1 | 6 | 6 | |
| DAMOCLES | 13 | |||
| DDD | 1 | 4 | 8 | |
| PBD | 10 | 3 | ||
| SADISA | 13 | |||
| secsse | 4 | 9 |
Current CRAN status: FAIL: 1, NOTE: 6, OK: 6
Version: 4.4.1
Check: package dependencies
Result: NOTE
Package which this enhances but not available for checking: 'doMC'
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 4.4.1
Check: examples
Result: ERROR
Running examples in 'DAISIE-Ex.R' failed
The error most likely occurred in:
> ### Name: DAISIE_convertprobdist
> ### Title: Converts the joint distribution of endemics and non-endemics
> ### under the DAISIE model to list format
> ### Aliases: DAISIE_convertprobdist
> ### Keywords: models
>
> ### ** Examples
>
>
> ### Compute the probability distribution at t = 4 and t = 8, for a mainland pool
> # size of 250 potential colonists and a vector of 5 parameters (cladogenesis, extinction,
> # clade-level carrying capacity, immigration, anagenesis) starting from an empty
> # island; store in list format
>
> pb <- DAISIE_probdist(
+ pars1 = c(0.3,0.35,Inf,0.75,0.012),
+ pars2 = c(100,250),
+ tvec = c(4,8),
+ initEI = c(0,0),
+ initprobs = NULL
+ )
Error: cannot allocate vector of size 78 Kb
Execution halted
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: for unstated dependencies in ‘tests’
Result: WARN
Error: memory exhausted
Execution halted
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: tests
Result: ERROR
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'demo_optimize.Rmd' using rmarkdown
--- finished re-building 'demo_optimize.Rmd'
--- re-building 'demo_sim.Rmd' using rmarkdown
--- finished re-building 'demo_sim.Rmd'
--- re-building 'stac_key.Rmd' using rmarkdown
SUMMARY: processing the following files failed:
'demo_CSvsIW.Rmd' 'stac_key.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: PDF version of manual
Result: WARN
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: PDF version of manual without index
Result: ERROR
Re-running with no redirection of stdout/stderr.
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: HTML version of manual
Result: FAIL
Flavor: r-devel-windows-x86_64
Version: 4.4.1
Check: installed package size
Result: NOTE
installed size is 37.9Mb
sub-directories of 1Mb or more:
libs 35.9Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 4, OK: 8
Version: 5.2.2
Check: tests
Result: ERROR
Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(DDD)
>
> test_check("DDD")
You are optimizing lambda mu K
You are fixing nothing
Optimizing the likelihood - this may take a while.
The loglikelihood for the initial parameter values is -25.46749
1 0.3 0.05 12 -25.467486125794 initial
2 0.315 0.05 12 -25.3638689853479 reflect
3 0.325193798449612 0.0475118483412322 11.2777777777778 -25.3047077318176 expand
4 0.351383399209486 0.0450354609929078 11.6285714285714 -25.0981457548904 expand
5 0.351383399209486 0.0450354609929078 11.6285714285714 -25.0981457548904 reflect
6 0.371256684491979 0.0433910306845004 10.6315789473684 -25.0954757558664 reflect
7 0.428551532033426 0.0409340659340659 10.6315789473685 -24.8169490746501 expand
8 0.450777934936351 0.0344383775351014 10.9459459459459 -24.6593037961974 expand
9 0.450777934936351 0.0344383775351014 10.9459459459459 -24.6593037961974 contract inside
10 0.472766432673899 0.0350663429017431 11.2024539877301 -24.6225115338754 reflect
11 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 reflect
12 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 reflect
13 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 reflect
14 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 contract inside
15 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 reflect
16 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 contract inside
17 0.524910522548318 0.0313693579514359 10.6885406464251 -24.5587134465095 reflect
18 0.565399993921034 0.0280746101403837 10.7477654197068 -24.5440002509993 reflect
19 0.565399993921034 0.0280746101403837 10.7477654197068 -24.5440002509993 contract inside
20 0.565399993921034 0.0280746101403837 10.7477654197068 -24.5440002509993 contract inside
21 0.565399993921034 0.0280746101403837 10.7477654197068 -24.5440002509993 contract inside
22 0.565399993921034 0.0280746101403837 10.7477654197068 -24.5440002509993 reflect
23 0.540604406976813 0.0292092598068244 10.8378418039422 -24.5427881890143 contract inside
24 0.551591146872811 0.0292142904003292 10.8276441773956 -24.5424890846115 contract outside
25 0.544857705831181 0.0294901486502622 10.7913060026132 -24.5418449975907 contract inside
26 0.544857705831181 0.0294901486502622 10.7913060026132 -24.5418449975907 contract inside
27 0.544857705831181 0.0294901486502622 10.7913060026132 -24.5418449975907 reflect
28 0.544857705831181 0.0294901486502622 10.7913060026132 -24.5418449975907 reflect
29 0.547669258302531 0.0290332446813533 10.7710866248936 -24.5416107774359 contract outside
30 0.552537137556962 0.0290055908700993 10.7566772849364 -24.5415697146764 contract inside
31 0.551902444365116 0.0289326885146061 10.7781127709133 -24.5415001310085 contract inside
32 0.551902444365116 0.0289326885146061 10.7781127709133 -24.5415001310085 contract inside
33 0.551902444365116 0.0289326885146061 10.7781127709133 -24.5415001310085 reflect
34 0.551847573936345 0.0290459044173069 10.7666829208567 -24.5414809794301 contract inside
35 0.550143155218703 0.0291308442256673 10.7761154213649 -24.5414592890655 contract inside
36 0.550143155218703 0.0291308442256673 10.7761154213649 -24.5414592890655 contract inside
37 0.550143155218703 0.0291308442256673 10.7761154213649 -24.5414592890655 reflect
38 0.550700338936786 0.0292326915435412 10.7763939113835 -24.5414383262945 reflect
39 0.550700338936786 0.0292326915435412 10.7763939113835 -24.5414383262945 contract inside
40 0.550700338936786 0.0292326915435412 10.7763939113835 -24.5414383262945 contract inside
41 0.552992740444887 0.0292948248046123 10.7673211951811 -24.5414315859038 expand
42 0.552992740444887 0.0292948248046123 10.7673211951811 -24.5414315859038 reflect
43 0.553043423472515 0.0295125379906136 10.7721036710523 -24.5413870369674 expand
44 0.553043423472515 0.0295125379906136 10.7721036710523 -24.5413870369674 contract outside
45 0.553043423472515 0.0295125379906136 10.7721036710523 -24.5413870369674 reflect
46 0.555107541766785 0.029899847340529 10.7706134553579 -24.5413431208549 expand
47 0.554346632745662 0.0301636511747847 10.7703854722913 -24.5412938046044 expand
48 0.554346632745662 0.0301636511747847 10.7703854722913 -24.5412938046044 reflect
49 0.557609045923729 0.0311894310185791 10.7742048001697 -24.5412286888155 expand
50 0.557609045923729 0.0311894310185791 10.7742048001697 -24.5412286888155 reflect
51 0.559178452816876 0.0321585360421564 10.7671538543792 -24.5411410320459 expand
52 0.559178452816876 0.0321585360421564 10.7671538543792 -24.5411410320459 reflect
53 0.566110181020457 0.0339539514936558 10.7620321531169 -24.5410877155385 expand
54 0.561271377420958 0.0320597842022417 10.7601539273727 -24.5410813728105 reflect
55 0.566780436867999 0.0342618535525845 10.7520412152507 -24.5409992525452 reflect
56 0.570294655835273 0.0346931292167706 10.7490084795055 -24.5409762780952 reflect
57 0.566103176320321 0.0333868069861459 10.7454448664923 -24.5409555337576 reflect
58 0.566103176320321 0.0333868069861459 10.7454448664923 -24.5409555337576 reflect
59 0.573639108100867 0.0352398542168362 10.7359545529905 -24.5409108654377 reflect
60 0.572337449156562 0.0351726229290054 10.7302895597922 -24.5408860152716 reflect
61 0.572337449156562 0.0351726229290054 10.7302895597922 -24.5408860152716 contract inside
62 0.572337449156562 0.0351726229290054 10.7302895597922 -24.5408860152716 contract outside
63 0.572337449156562 0.0351726229290054 10.7302895597922 -24.5408860152716 reflect
64 0.572337449156562 0.0351726229290054 10.7302895597922 -24.5408860152716 reflect
65 0.57380514206983 0.0354005327322286 10.7242391979914 -24.5408844704547 contract outside
66 0.574869242408817 0.0357827800059855 10.7240017852585 -24.5408830811722 contract inside
67 0.574660440840576 0.0355727826486203 10.726180681152 -24.5408815805989 contract inside
68 0.574660440840576 0.0355727826486203 10.726180681152 -24.5408815805989 contract inside
69 0.574660440840576 0.0355727826486203 10.726180681152 -24.5408815805989 contract outside
70 0.574535788240467 0.0356611509003949 10.7254130068384 -24.5408815719029 contract inside
71 0.573987221142279 0.0355062710817476 10.7268303118148 -24.540881346539 contract inside
72 0.573987221142279 0.0355062710817476 10.7268303118148 -24.540881346539 reflect
73 0.574455962308996 0.0355631544650995 10.726053754282 -24.5408810635454 contract inside
74 0.574455962308996 0.0355631544650995 10.726053754282 -24.5408810635454 contract inside
75 0.574455962308996 0.0355631544650995 10.726053754282 -24.5408810635454 contract inside
76 0.574455962308996 0.0355631544650995 10.726053754282 -24.5408810635454 contract outside
77 0.574400202165416 0.0355741819494762 10.7257836830008 -24.5408810620575 contract inside
78 0.574361088755513 0.0355488183671071 10.725818860841 -24.540881056554 contract inside
79 0.574260377202649 0.0355384977562783 10.7263313961958 -24.5408810523275 reflect
80 0.574398255958295 0.0355584934485082 10.7260158643531 -24.5408810317905 contract inside
81 0.574398255958295 0.0355584934485082 10.7260158643531 -24.5408810317905 contract outside
82 0.574398255958295 0.0355584934485082 10.7260158643531 -24.5408810317905 contract inside
83 0.574398255958295 0.0355584934485082 10.7260158643531 -24.5408810317905 contract inside
84 0.574398255958295 0.0355584934485082 10.7260158643531 -24.5408810317905 reflect
85 0.574398255958295 0.0355584934485082 10.7260158643531 -24.5408810317905 reflect
86 0.57434767797101 0.035552014765064 10.7261135291981 -24.5408810312512 contract inside
87 0.574381408935999 0.0355602321114336 10.7260700515206 -24.5408810301407 contract inside
88 0.574381470227534 0.0355598033419026 10.7260093352529 -24.540881030112 contract inside
89 0.574384220629339 0.0355579217534517 10.7260400847106 -24.540881029942 contract inside
90 0.574399711482537 0.0355629712580445 10.7260029714119 -24.5408810298061 contract outside
91 0.574384938162847 0.0355602321125204 10.726043757586 -24.5408810297044 contract inside
92 0.574384938162847 0.0355602321125204 10.726043757586 -24.5408810297044 contract inside
93 0.574387143035261 0.0355595096334502 10.7260310199285 -24.5408810296954 contract inside
94 0.574392793710196 0.0355614574493382 10.7260171380295 -24.5408810296741 contract inside
95 0.574386919213117 0.035560244460292 10.7260248875271 -24.5408810296449 contract inside
96 0.574386919213117 0.035560244460292 10.7260248875271 -24.5408810296449 contract inside
97 0.574386919213117 0.035560244460292 10.7260248875271 -24.5408810296449 contract inside
98 0.574384542557207 0.0355595982287137 10.7260349961347 -24.5408810296429 contract outside
99 0.574387075062465 0.0355600725103244 10.7260297509775 -24.54088102964 contract inside
100 0.574386562006419 0.0355601448563842 10.726031965621 -24.5408810296392 contract inside
Optimization has terminated successfully.
Maximum likelihood parameter estimates: lambda: 0.574387, mu: 0.035560, K: 10.726032
Maximum loglikelihood: -24.540881
You are optimizing lambda mu K
You are fixing nothing
Optimizing the likelihood - this may take a while.
The loglikelihood for the initial parameter values is -25.46749
Maximum likelihood parameter estimates: lambda: 0.570837, mu: 0.034500, K: 10.735662
Maximum loglikelihood: -24.540902
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 30 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• Run only on CI (1): 'test_DDD.R:269:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_DDD.R:360:3'): DDD_MS works ────────────────────────────────────
Error in `.M2C(r)`: 'R_Calloc' could not allocate memory (49798 of 8 bytes)
Backtrace:
▆
1. └─DDD::dd_MS_loglik(pars1, pars2, brtsM, brtsS, missnumspec, methode = "analytical") at test_DDD.R:360:3
2. └─DDD:::dd_loglik_M3(...)
3. └─DDD:::dd_loglik_M3_aux(pars, lx, ddep, kM, kS)
4. └─Matrix::sparseMatrix(...)
5. └─Matrix::.M2C(r)
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 30 ]
Error in sub("([^.]+)\\.[[:alnum:]]+$", "\\1", x) :
invalid regular expression '([^.]+)\.[[:alnum:]]+$', reason 'Out of memory'
Calls: test_check ... snapshot_outdated -> snapshot_expected -> paste0 -> <Anonymous> -> sub
In addition: Warning message:
In sub("([^.]+)\\.[[:alnum:]]+$", "\\1", x) :
TRE pattern compilation error 'Out of memory'
Execution halted
Flavor: r-devel-windows-x86_64
Version: 5.2.2
Check: PDF version of manual
Result: WARN
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Flavor: r-devel-windows-x86_64
Version: 5.2.2
Check: installed package size
Result: NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
libs 7.3Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: NOTE: 10, OK: 3
Version: 1.4
Check: Rd files
Result: NOTE
checkRd: (-1) pbd_loglik.Rd:31: Lost braces
31 | \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
| ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
32 | \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
| ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
33 | \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
| ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
34 | \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
| ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
35 | \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
| ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
36 | \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
| ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
37 | \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.4
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘ade4’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: NOTE: 4, OK: 9
Version: 3.1.0
Check: installed package size
Result: NOTE
installed size is 9.8Mb
sub-directories of 1Mb or more:
doc 1.1Mb
libs 8.4Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64