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

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