CRAN Package Check Results for Package corncob

Last updated on 2022-09-24 21:50:59 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-fedora-gcc 0.3.0 621.14 OK
r-devel-windows-x86_64 0.2.0 53.00 301.00 354.00 ERROR
r-release-macos-arm64 0.2.0 149.00 NOTE
r-release-macos-x86_64 0.2.0 295.00 NOTE
r-oldrel-macos-arm64 0.3.0 142.00 OK
r-oldrel-macos-x86_64 0.2.0 303.00 NOTE

Check Details

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in 'corncob-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: HDIbetabinom
    > ### Title: Get highest density interval of beta-binomial
    > ### Aliases: HDIbetabinom
    >
    > ### ** Examples
    >
    > data(soil_phylum_small)
    > mod <- bbdml(formula = OTU.1 ~ DayAmdmt,
    + phi.formula = ~ DayAmdmt,
    + data = soil_phylum_small)
    Error in if (detectseparation::detect_separation(y = cbind(W, M - W), :
     argument is of length zero
    Calls: bbdml
    Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'testthat.R' [17s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(corncob)
     >
     > test_check("corncob")
     [ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_bbdml.R:32:0
     ── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
     Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
     DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
     boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
     inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
    
     If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
    
     Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
    
     To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
     Backtrace:
     ▆
     1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
     ── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
     ── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_lrtest.R:19:0
     ── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_pb.R:14:0
     ── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_s3.R:12:0
     ── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_sandwich.R:12:0
     ── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
     ── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_simulate.R:12:0
     ── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
     Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
     x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
     warning(paste("Separation detected in abundance model!",
     "Likely, one of your covariates/experimental conditions is such that",
     "there are all zero counts within a group. Consider identifying and removing",
     "this covariate from your model. The results of this model are not to be",
     "trusted because there is not enough data. \n", sep = "\n"),
     immediate. = TRUE)
     sep_da <- TRUE
     }`: argument is of length zero
     Backtrace:
     ▆
     1. └─corncob::bbdml(...) at test_waldtest.R:18:0
    
     [ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64

Version: 0.2.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘Matrix’ ‘rmutil’
     All declared Imports should be used.
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64