[R-pkg-devel] noLD error in CRAN checks in package 'HACSim'

[Jarrett Phillips]

Hello,

My package has recently been posted to CRAN, however, there is an
additional issue of noLD on tests on x86_64 Linux with R-devel.

I haven't yet received an email from CRAN maintainers on resolving the
issue.

However, I would like to submit an updated package version with improved
documentation and thought that I could fix this error as well.

Any ideas on how to solve the below problem?

I suspect it has something to do with numerical precision of estimates.

-----

* checking examples ... ERROR
Running examples in ‘HACSim-Ex.R’ failed
The error most likely occurred in:

> ### Name: HAC.simrep
> ### Title: Run a simulation of haplotype accumulation curves for
> ###   hypothetical or real species
> ### Aliases: HAC.simrep
>
> ### ** Examples
>
>
>   ## Simulate hypothetical species ##
>
>   N <- 100 # total number of sampled individuals
>   Hstar <- 10 # total number of haplotypes
>   probs <- rep(1/Hstar, Hstar) # equal haplotype frequency distribution
>
>   HACSObj <- HACHypothetical(N = N, Hstar = Hstar , probs = probs,
+   filename = "output") # outputs a CSV file called "output.csv"
>
>   ## Simulate hypothetical species - subsampling ##
>   HACSObj <- HACHypothetical(N = N, Hstar = Hstar, probs = probs,
+   perms = 1000, p = 0.95, subsample = TRUE, prop = 0.25,
+   conf.level = 0.95, filename = "output")
>
>   ## Simulate hypothetical species and all paramaters changed - subsampling ##
>   HACSObj <- HACHypothetical(N = N, Hstar = Hstar, probs = probs,
+   perms = 10000, p = 0.90, subsample = TRUE, prop = 0.15, conf.level = 0.95,
+   filename = "output")
>
>   HAC.simrep(HACSObj) # runs a simulation

 Simulating haplotype accumulation...


  |
  |
  |   0%Error in HAC.sim(N = envr$N, Hstar = envr$Hstar, probs =
envr$probs, perms = envr$perms,  :
  probs must sum to 1
Calls: HAC.simrep -> HAC.sim
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/HACSim.Rcheck/00check.log’
for details.


Thanks.


Cheers,

Jarrett

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