Hello, I am trying to run an analysis with the package LEA, but when using the function lfmm() I am getting the following message:

Error in lfmm("Genidentity.geno", "variables.env", K = 3, rep = 10, iterations = 1e+05, : internal error in trio library

I believe my .geno and my .env files are formatted correctly, and I am using an updated R version. I also tried to install again the trio library, but apparently none of this helped.

This is the command I am using, with the related output:

obj.lfmm = lfmm("Genidentity.geno", "variables.env", K = 3, rep = 10, iterations =100000, burnin=50000, project="new")


[1] "*********************************************************"
[1] " Conversion from the geno format to the lfmm format"
[1] "*********************************************************"
The project is saved into :
 Genidentity_variables.lfmmProject 

To load the project, use:
 project = load.lfmmProject("Genidentity_variables.lfmmProject")

To remove the project, use:
 remove.lfmmProject("Genidentity_variables.lfmmProject")

[1] "********************************"
[1] "* K = 3  repetition 1  d = 1   *"
[1] "********************************"
Summary of the options:

        -n (number of individuals)      206
        -L (number of loci)             454
        -K (number of latent factors)   3
        -o (output file)                Genidentity_variables.lfmm/K3/run1/Genidentity_r1
        -i (number of iterations)       100000
        -b (burnin)                     50000
        -s (seed random init)           1657784617
        -p (number of processes (CPU))  1
        -x (genotype file)              Genidentity.lfmm
        -v (variable file)              variables.env
        -D (number of covariables)      18
        -d (the dth covariable)         1

SNP 1 is constant among individuals.

Error in lfmm("Genidentity.geno", "variables.env", K = 3, rep = 10, iterations = 1e+05,  : 
  internal error in trio library


sessionInfo( )

R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] LEA_3.2.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          raster_3.4-10       magrittr_2.0.1      usethis_2.0.1       devtools_2.4.1     
 [6] pkgload_1.2.1       lattice_0.20-41     R6_2.5.0            rlang_0.4.11        fastmap_1.1.0      
[11] tools_4.0.5         pkgbuild_1.2.0      rgdal_1.5-23        grid_4.0.5          sessioninfo_1.1.1  
[16] cli_2.5.0           withr_2.4.2         remotes_2.3.0       ellipsis_0.3.2      rprojroot_2.0.2    
[21] lifecycle_1.0.0     crayon_1.4.1        processx_3.5.2      purrr_0.3.4         BiocManager_1.30.15
[26] callr_3.7.0         fs_1.5.0            ps_1.6.0            codetools_0.2-18    testthat_3.0.2     
[31] glue_1.4.2          memoise_2.0.0       cachem_1.0.4        sp_1.4-5            compiler_4.0.5     
[36] desc_1.3.0          prettyunits_1.1.1

I would really appreciate if you could give me any tip to fix this error. Thanks, Valentina

Recently,I had the same problem.Running the sample file found no problems. I think there's something wrong with my file.So I reformatted it.

#Convert the .lfmm file again. LFMM format before conversion, but error: internal error in trio library.
library("LEA")

r <- read.lfmm("H:/LEA/plink3_recode12.lfmm")
r1 <- write.lfmm(r, "plink3_recode.lfmm")

#Create an .env file.

f <- matrix(1:33, )   #This number should be equal to your number of individuals. I have 33.
f[1:33, ] <- c(rep(1, 33))  #I found that the values of this data are not all the same. An error that SNP 1 is constant among individuals is reported when all values are the same.
f <- write.env(f, "f.env")

#lfmm analysis

project <- lfmm("plink3_recode.lfmm", 'f.env', K = 3 , repetitions = 2,
               project = "new")

I hope my experience is useful to you.