Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

R-CMD-check fails #23

Open
delfarahalireza opened this issue Nov 21, 2023 · 0 comments
Open

R-CMD-check fails #23

delfarahalireza opened this issue Nov 21, 2023 · 0 comments
Assignees
Labels
bug Something isn't working

Comments

@delfarahalireza
Copy link
Contributor

delfarahalireza commented Nov 21, 2023

Error when checking build in R:

Duration: 1m 8.1s

❯ checking examples ... ERROR
  Running examples in ‘claman-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_volcano
  > ### Title: Volcano plot
  > ### Aliases: plot_volcano
  > 
  > ### ** Examples
  > 
  > library(dplyr)
  
  Attaching package: ‘dplyr’
  
  The following objects are masked from ‘package:stats’:
  
      filter, lag
  
  The following objects are masked from ‘package:base’:
  
      intersect, setdiff, setequal, union
  
  > regression_significance <- diffex_mzroll(
  + nplug_mzroll_normalized,
  + "normalized_log2_abundance",
  + "limitation + limitation:DR + 0") %>%
  + dplyr::left_join(
  + nplug_mzroll_normalized$features %>% select(groupId, compoundName),
  + by = "groupId")
  Warning: There was 1 warning in `dplyr::mutate()`.
  ℹ In argument: `fdr_summary = purrr::map(term_data, diffex_fdr)`.
  Caused by warning in `.f()`:
  ! q-value calculation initially failed due to too many small p-values
          but claman was able to recover results
  > 
  > plot_volcano(regression_significance, 10, 0.1, c("Ribose-P", "acetyl-CoA", "ATP"))
  Warning in geom_point(aes(y = p.value.trans, color = is_discovery, name = compoundName)) :
    Ignoring unknown aesthetics: name
  Error in `plot_volcano()`:
  ! Cannot add <ggproto> objects together
  ℹ Did you forget to add this object to a <ggplot> object?
  Backtrace:
      ▆
   1. └─claman::plot_volcano(...)
   2.   └─ggplot2:::`+.gg`(...)
   3.     └─cli::cli_abort(...)
   4.       └─rlang::abort(...)
  Execution halted

There might be other issues.

@delfarahalireza delfarahalireza added the bug Something isn't working label Nov 21, 2023
@delfarahalireza delfarahalireza self-assigned this Nov 21, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant