On 15.05.2019 19:50, Jarrett Phillips wrote:
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.
Right, apparently there is some test that tries to confirm that "probs
must sum to 1" and that is not exactly true on platforms without long
doubles. You can test for that via all.equal(), perhaps you have to
adjust the tolerance.
Best,
Uwe Ligges
-----
* 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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