airemlf90' had status 123

[JanKowalczyk]

After upgrading to the new breedR version from 0.10-17 to 0.10-19 the error message appearing as follows:

res.ar1 <- remlf90(fixed = phe_X ~ poch,
                 # random = ~ block,
                   genetic = list(model = 'add_animal',
                                  pedigree = data[, c('self','dad','mum')],
                                  id = 'self'),
                   spatial = list(model = 'AR',
                                  coord = data[, c('x','y')] ,
                                  rho = c(.8,.8)), data = data,  method='em')

No specification of initial variances.
    Using default value of 1 for all variance components.
    See ?breedR.getOption.

Error: zmienna is.null(attr(reml.out, "status")) nie ma wartości TRUE
In addition: Warning message:
running command '"C:/Users/Lenovo/Documents/R/win-library/3.2/breedR/bin/airemlf90"' had status 123 

Below is the session info

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Polish_Poland.1250  LC_CTYPE=Polish_Poland.1250   
[3] LC_MONETARY=Polish_Poland.1250 LC_NUMERIC=C                  
[5] LC_TIME=Polish_Poland.1250    

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

other attached packages:
[1] ggplot2_1.0.1  breedR_0.10-19 sp_1.2-1       Matrix_1.2-2  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2      knitr_1.11       magrittr_1.5     splines_3.2.2   
 [5] MASS_7.3-43      munsell_0.4.2    colorspace_1.2-6 pedigreemm_0.3-3
 [9] lattice_0.20-33  minqa_1.2.4      stringr_1.0.0    highr_0.5.1     
[13] plyr_1.8.3       tools_3.2.2      grid_3.2.2       gtable_0.1.2    
[17] nlme_3.1-122     lme4_1.1-10      digest_0.6.8     nloptr_1.0.4    
[21] reshape2_1.4.1   stringi_1.0-1    scales_0.3.0     proto_0.3-10 

[famuvie]

Jan

Thanks for the report, it's the second today. It seems that my new repository is a bit problematic. I have not yet identified the source of the problem: I'm unable to reproduce the problem here. I test from a 64bit windows machine and works well.

If you have RTools installed, try `install.packages('breedR', type = 'source') please. And tell me if it works.

Otherwise, you can always install with devtools::install_github().

ƒacu.-

El 27/11/2015 a las 15:21, JanKowalczyk escribió:

After upgrading to the new breedR version from 0.10-17 to 0.10-19 the error message appearing as follows:

res.ar1 <- remlf90(fixed = phe_X ~ poch,

random = ~ block,

               genetic = list(model = 'add_animal',
                              pedigree = data[, c('self','dad','mum')],
                              id = 'self'),
               spatial = list(model = 'AR',
                              coord = data[, c('x','y')] ,
                              rho = c(.8,.8)), data = data,  method='em')

No specification of initial variances. Using default value of 1 for all variance components. See ?breedR.getOption.

Error: zmienna is.null(attr(reml.out, "status")) nie ma wartości TRUE In addition: Warning message: running command '"C:/Users/Lenovo/Documents/R/win-library/3.2/breedR/bin/airemlf90"' had status 123

Below is the session info

sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200)

locale: [1] LC_COLLATE=Polish_Poland.1250 LC_CTYPE=Polish_Poland.1250
[3] LC_MONETARY=Polish_Poland.1250 LC_NUMERIC=C
[5] LC_TIME=Polish_Poland.1250

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

other attached packages: [1] ggplot2_1.0.1 breedR_0.10-19 sp_1.2-1 Matrix_1.2-2

loaded via a namespace (and not attached): [1] Rcpp_0.12.2 knitr_1.11 magrittr_1.5 splines_3.2.2
[5] MASS_7.3-43 munsell_0.4.2 colorspace_1.2-6 pedigreemm_0.3-3 [9] lattice_0.20-33 minqa_1.2.4 stringr_1.0.0 highr_0.5.1
[13] plyr_1.8.3 tools_3.2.2 grid_3.2.2 gtable_0.1.2
[17] nlme_3.1-122 lme4_1.1-10 digest_0.6.8 nloptr_1.0.4
[21] reshape2_1.4.1 stringi_1.0-1 scales_0.3.0 proto_0.3-10

— Reply to this email directly or view it on GitHub https://github.com/famuvie/breedR/issues/58.

[famuvie]

Jan, please give me the output of Sys.getenv('R_ARCH')

Also, please try this:

unlink(list.files(system.file('bin', package='breedR'), full.names = T))
remlf90(y~x, data = data.frame(x=1,y=1))

This removes the fortran programs. When you run remlf90() again, it will ask you to download them again. Say yes, and tell me the result.

Thanks ƒacu.-

El 27/11/2015 a las 15:21, JanKowalczyk escribió:

After upgrading to the new breedR version from 0.10-17 to 0.10-19 the error message appearing as follows:

res.ar1 <- remlf90(fixed = phe_X ~ poch,

random = ~ block,

               genetic = list(model = 'add_animal',
                              pedigree = data[, c('self','dad','mum')],
                              id = 'self'),
               spatial = list(model = 'AR',
                              coord = data[, c('x','y')] ,
                              rho = c(.8,.8)), data = data,  method='em')

No specification of initial variances. Using default value of 1 for all variance components. See ?breedR.getOption.

Error: zmienna is.null(attr(reml.out, "status")) nie ma wartości TRUE In addition: Warning message: running command '"C:/Users/Lenovo/Documents/R/win-library/3.2/breedR/bin/airemlf90"' had status 123

Below is the session info

sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200)

locale: [1] LC_COLLATE=Polish_Poland.1250 LC_CTYPE=Polish_Poland.1250
[3] LC_MONETARY=Polish_Poland.1250 LC_NUMERIC=C
[5] LC_TIME=Polish_Poland.1250

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

other attached packages: [1] ggplot2_1.0.1 breedR_0.10-19 sp_1.2-1 Matrix_1.2-2

loaded via a namespace (and not attached): [1] Rcpp_0.12.2 knitr_1.11 magrittr_1.5 splines_3.2.2
[5] MASS_7.3-43 munsell_0.4.2 colorspace_1.2-6 pedigreemm_0.3-3 [9] lattice_0.20-33 minqa_1.2.4 stringr_1.0.0 highr_0.5.1
[13] plyr_1.8.3 tools_3.2.2 grid_3.2.2 gtable_0.1.2
[17] nlme_3.1-122 lme4_1.1-10 digest_0.6.8 nloptr_1.0.4
[21] reshape2_1.4.1 stringi_1.0-1 scales_0.3.0 proto_0.3-10

— Reply to this email directly or view it on GitHub https://github.com/famuvie/breedR/issues/58.