Hello
I am trying to run the tutorial example: M1 <- solarPolygenic(trait1 ~ age + sex, data = dat30)

And I recieve the below error - do you know what might be causing this?
Program ibdprep failed to run
Error in df2solar(df, dir, ...) :
file.exists(file.path(dir, "phi2.gz")) is not TRUE

Hi, I'm having trouble sending an e-mail to ask for a Solar Key. The delivery has failed to these recipients or groups:

[email protected]

Thanks in advance for any help!

Hello Solarius Team;

Sorry for disturbing you guys. In have issues using solarius
after a succesful install in R on my MACbook. Firstly, I tried running
the examples on the vignette, but failed at certain point,
but do not seem to figure out why?

nature of problem

load data and check out ID names

library(solarius)
data(dat30)
matchIdNames(names(dat30))
id famid mo fa sex
"ID" "FAMID" "MO" "FA" "SEX"

basic (univariate) polygenic model

mod <- solarPolygenic(trait1 ~ age + sex, dat30,)
sh: solar: command not found
Error in system("solar", input = cmd, intern = result, ignore.stdout = ignore.stdout, :
error in running command
Error in df2solar(data, dir) :
file.exists(file.path(dir, "phi2.gz")) is not TRUE

Please could you help me out? I will be greatful.

Best Regards

There is an attempt to load kinship2 namespace in examples datasets.R#L47, code below is the results from examples.
As kinship2 is suggested dependency, it should not be required to run examples according to R-exts. This can be conditionally escaped with requireNamespace.
It is possible there are other cases of that issue in other examples, this one was to first that fails.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dat30
> ### Title: dat30 data set adapted from multic R package
> ### Aliases: dat30 genocovdat30 mapdat30
> 
> ### ** Examples
> 
> data(dat30)
> 
> str(dat30)
'data.frame':   174 obs. of  10 variables:
 $ famid : int  1 1 1 1 1 1 2 2 2 2 ...
 $ id    : int  11 12 13 14 15 16 21 22 23 24 ...
 $ fa    : int  0 0 11 11 11 11 0 0 21 21 ...
 $ mo    : int  0 0 12 12 12 12 0 0 22 22 ...
 $ sex   : int  1 2 1 2 1 1 1 2 2 1 ...
 $ affect: int  2 2 2 2 2 2 2 2 2 2 ...
 $ class : logi  NA NA NA NA NA NA ...
 $ trait1: num  11.96 7.1 10.32 9.76 9.46 ...
 $ trait2: num  13.58 5.37 6.4 8.98 9.21 ...
 $ age   : int  50 25 35 49 51 45 37 29 39 41 ...
> 
> plotPed(dat30, 2) # plot the pedigree tree for family #2
Error: requireNamespace("kinship2", quietly = TRUE) is not TRUE
Execution halted

Hi,

With R version 4.0 matrix objects now also inherit from class "array", so e.g., class(matrix(1:9)) is c("matrix", "array"). This is problematic if you want to use de function solarPolygenic with the parameter "kinship" because the function checks if this input is a matrix... but it's not only a matrix anymore. So, you cannot use this function with a predefined kinship matrix.

It returns this error: <Error in kmat2kf(kmat) : class(kmat) == "matrix" are not all TRUE>.

Could you fix this bug, please?