Package: CoDaLoMic
Check: examples
New result: ERROR
  Running examples in ‘CoDaLoMic-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ZeroData
  > ### Title: Zero replacement
  > ### Aliases: ZeroData
  > 
  > ### ** Examples
  > 
  > 
  > set.seed(2)
  > dat=gtools::rdirichlet(6,c(1,2,3,1,2,3))
  > dat2=dat
  > dat2[2,1]=0
  > dat2[2,2]=dat[2,1]+dat[2,2]
  > dat2[4,3]=0
  > dat2[4,4]=dat[4,3]+dat[4,4]
  > 
  > X <- cbind( c(1:6) ,dat2)
  > 
  > Final=ZeroData(X,"multKM",1)
  Error in zCompositions::multKM(Y, label = 0, dl = rep(1, ncol(Y))) : 
    The 'NADA' package is required by multLN but it has been archived by CRAN.
             Please download and install an archived version of 'NADA' manually to use this function.
  Calls: ZeroData -> <Anonymous>
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
  TauAndParameters_EstParmFunc_FBM 5.697  0.035   5.734

Package: CoDaLoMic
Check: tests
New result: ERROR
    Running ‘testthat.R’ [58s/101s]
  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/testing-design.html#sec-tests-files-overview
    > # * https://testthat.r-lib.org/articles/special-files.html
    > 
    > library(testthat)
    > library(CoDaLoMic)
    > 
    > test_check("CoDaLoMic")
    % latex table generated in R 4.6.0 by xtable 1.8-4 package
    % Sun Jun 29 17:28:45 2025
    \begin{table}[ht]
    \centering
    \begin{tabular}{lllll}
      \toprule
     SPBal  & NUM/DEM & Bacteria & SPBal mean & Genera most \\ 
      (\% of variance) &  & in & (Relation between & influenced by \\ 
       &  & NUM/DEM & NUM/DEM) & the SPBal \\ 
       \midrule
    SPBal1 & NUM & 3,4 & -0.301 &  \\ 
      (41.37\%) & DEM & 1 & (Similar) &  \\ 
       \midrule
    SPBal2 & NUM & 3 & -0.398 &  \\ 
      (21.08\%) & DEM & 5 & (Similar) &  \\ 
       \midrule
    SPBal3 & NUM & 2 & 0.085 &  \\ 
      (19.17\%) & DEM & 4 & (Similar) &  \\ 
       \bottomrule
    \end{tabular}
    \caption{We rename each bacteria with a number so 1  is  Bact1, 2  is  Bact2, 3  is  Bact3, 4  is  Bact4, 5  is  Bact5} 
    \end{table}
    % latex table generated in R 4.6.0 by xtable 1.8-4 package
    % Sun Jun 29 17:28:45 2025
    \begin{table}[ht]
    \centering
    \begin{tabular}{llll}
      \toprule
     Name & Intercept  & Weight & Weight \\ 
       &  & of the bacteria & of the rest \\ 
       &  & in defining herself  & of the community  \\ 
       &  & in the next & in defining the \\ 
       &  & time point & bacteria in the \\ 
       &  &  & next time point \\ 
       \midrule
    Bact1 & 1 & 2 & 3 \\ 
      Bact2 & 1 & 2 & 3 \\ 
       \bottomrule
    \end{tabular}
    \end{table}
    % latex table generated in R 4.6.0 by xtable 1.8-4 package
    % Sun Jun 29 17:28:45 2025
    \begin{table}[ht]
    \centering
    \begin{tabular}{llll}
      \toprule
     Names & Weight that & Weight that &  \\ 
       & the bacteria has & the interaction of &  \\ 
       & in defining & both bacteria &  \\ 
       & herself in the & has in defining &  \\ 
       & next time point & the bacteria in &  \\ 
       &  & in the row in the &  \\ 
       &  & next time point &  \\ 
       \midrule
     &  & a & b \\ 
       \midrule
    a & 0.1 & 0.2 & 0.3 \\ 
      b & 0.4 & 0.5 & 0.6 \\ 
       \bottomrule
    \end{tabular}
    \end{table}
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 69 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('testZeroData.R:11:1'): (code run outside of `test_that()`) ──────────
    Error in `zCompositions::multKM(Y, label = 0, dl = rep(1, ncol(Y)))`: The 'NADA' package is required by multLN but it has been archived by CRAN.
               Please download and install an archived version of 'NADA' manually to use this function.
    Backtrace:
        ▆
     1. └─CoDaLoMic::ZeroData(X, "multKM", 1) at testZeroData.R:11:1
     2.   └─zCompositions::multKM(Y, label = 0, dl = rep(1, ncol(Y)))
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 69 ]
    Error: Test failures
    Execution halted