bayes.glmm giving an error Error in prep_call_sampler(object)

[vinod1981]

Hello, I am running bayes.glmm r package but it is giving an error:

data("sample", package = "bayes.glmm") pheno = data$pheno geno = data$geno cov = data$cov L <- t(chol(data$K)) mymodel = stan_models(model = "glm", auto_write = TRUE) y2 = myGWAS_fit(model = mymodel, method = "sampling", type = "categorical", cov = cov, geno = geno[c(1, 3), ], pheno = pheno)

Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons:

compiled with save_dso=FALSE;
compiled on a different platform;
does not exist (created from reading csv files).

I couldn't find any solution on google. How can I get rid of this error. I've installed and uninstalled rstan and bayes.glmm packages many times which couldn't solve the problem. Thanks, Vinod

[xulong82]

Hi Vinod:

Thank you for your email.

Looks to me the compiled object is not working anymore because the package was not updated regularly, so it does not keep up with other required packages.

If rstan was already installed successfully, I suggest you take the code under the R folder and start the analysis from there. Basically, take the code of the GWAS_fit function. This won't be as convenient, but you will also have better flexibility to change the rstan parameters.

Would like to help in that regard, if needed.

Xulong

On Tue, Nov 3, 2020 at 10:02 AM vinod1981 notifications@github.com wrote:

Hello, I am running bayes.glmm r package but it is giving an error:

data("sample", package = "bayes.glmm") pheno = data$pheno geno = data$geno cov = data$cov L <- t(chol(data$K)) mymodel = stan_models(model = "glm", auto_write = TRUE) y2 = myGWAS_fit(model = mymodel, method = "sampling", type = "categorical", cov = cov, geno = geno[c(1, 3), ], pheno = pheno)

Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons:

compiled with save_dso=FALSE; compiled on a different platform; does not exist (created from reading csv files).

I couldn't find any solution on google. How can I get rid of this error. I've installed and uninstalled rstan and bayes.glmm packages many times which couldn't solve the problem. Thanks, Vinod

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/xulong82/bayes.glmm/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZUW27TPLDQDX6SVBF3RALSOALPFANCNFSM4TI3IUZA .

-- Xulong

[vinod1981]

Hi Xulong, Thank you very much for the answer. Sorry I don't have very deep knowledge of R. You are suggesting me to save these codes ( https://github.com/xulong82/bayes.glmm/commit/ab06967845002a3224b4cbffc73fa5d3d41bc472) in a .txt file and upload them as a source and then I can use this program. Or you are suggesting something more complex which I am not understanding. Thanks,

Best wishes,

Vinod,

On Tue, Nov 3, 2020 at 8:42 PM Xulong notifications@github.com wrote:

Hi Vinod:

Thank you for your email.

Looks to me the compiled object is not working anymore because the package was not updated regularly, so it does not keep up with other required packages.

If rstan was already installed successfully, I suggest you take the code under the R folder and start the analysis from there. Basically, take the code of the GWAS_fit function. This won't be as convenient, but you will also have better flexibility to change the rstan parameters.

Would like to help in that regard, if needed.

Xulong

On Tue, Nov 3, 2020 at 10:02 AM vinod1981 notifications@github.com wrote:

Hello, I am running bayes.glmm r package but it is giving an error:

data("sample", package = "bayes.glmm") pheno = data$pheno geno = data$geno cov = data$cov L <- t(chol(data$K)) mymodel = stan_models(model = "glm", auto_write = TRUE) y2 = myGWAS_fit(model = mymodel, method = "sampling", type = "categorical", cov = cov, geno = geno[c(1, 3), ], pheno = pheno)

Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons:

compiled with save_dso=FALSE; compiled on a different platform; does not exist (created from reading csv files).

I couldn't find any solution on google. How can I get rid of this error. I've installed and uninstalled rstan and bayes.glmm packages many times which couldn't solve the problem. Thanks, Vinod

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/xulong82/bayes.glmm/issues/3, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAZUW27TPLDQDX6SVBF3RALSOALPFANCNFSM4TI3IUZA

.

-- Xulong

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-- Vinod Kumar, Postdoc,

Department of Molecular Genetics and Physiology of PlantsRuhr-University BochumUniversitätsstraße 15044801 BochumGermany