CRAN Package Check Results for Maintainer ‘Arlina Shen <ahshen24 at berkeley.edu>’

Last updated on 2025-03-23 03:54:05 CET.

Package	ERROR	OK
DEHOGT	1	14

Package DEHOGT

Current CRAN status: ERROR: 1, OK: 14

Version: 0.99.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘DEHOGT.Rmd’ using rmarkdown Quitting from DEHOGT.Rmd:54-75 [exampleWorkflow] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `{ genewise_data <- data[i, ] if (!is.null(covariates)) { adjust <- covariates[i, ] %*% beta } else { adjust <- 0 } genewise_dataframe <- data.frame(count = genewise_data, treatment = treatment, size_factors = size_factors, adjust = rep(adjust, num_samples)) model_formula <- as.formula( "count ~ treatment + offset(log(size_factors)) + offset(adjust)") if (dist == "qpois") { model <- glm(formula = model_formula, family = quasipoisson(), data = genewise_dataframe) coefficients <- coef(summary(model))[2, "Estimate"] p_values <- coef(summary(model))[2, "Pr(>|t|)"] padj_values <- p.adjust(p_values, method = "BH") log2fold <- log(exp(abs(coefficients)), base = 2) } else if (dist == "negbin") { model <- glm.nb(formula = model_formula, data = genewise_dataframe) coefficients <- coef(summary(model))[2, "Estimate"] p_values <- coef(summary(model))[2, "Pr(>|z|)"] padj_values <- p.adjust(p_values, method = "BH") log2fold <- log(exp(abs(coefficients)), base = 2) } c(coefficients, p_values, padj_values, log2fold) }`: ! task 1 failed - "subscript out of bounds" --- Backtrace: ▆ 1. └─DEHOGT::dehogt_func(data, treatment, num_cores = 2) 2. └─... %dopar% ... 3. └─e$fun(obj, substitute(ex), parent.frame(), e$data) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'DEHOGT.Rmd' failed with diagnostics: task 1 failed - "subscript out of bounds" --- failed re-building ‘DEHOGT.Rmd’ SUMMARY: processing the following file failed: ‘DEHOGT.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64