error in package install

[Ivy-ops]

Hi developer,
Your package seems very interesting! I wanna to apply this to my data. However, error occurs. May I have your help? Thanks!
`installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-mdine/00new/mdine/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package ‘Rcpp’ was built under R version 3.6.2
Execution halted
ERROR: lazy loading failed for package ‘mdine’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mdine’
  Error: Failed to install 'mdine' from GitHub:
  (converted from warning) installation of package ‘/var/folders/b6/vc89542s77q969mss8tnwy41cvdj14/T//RtmpSuW22G/file133e5385817b5/mdine_1.0.1.tar.gz’ had non-zero exit status`

[Ivy-ops]

This error was solved by reinstall the rstan package.
But I face this error in the demo data and code:

mn.family = mdine(counts.top.fam, covars, covars[,"diagnosisCD"], quant=ci.probs)
starting worker pid=54310 on localhost:11634 at 18:34:44.315
starting worker pid=54324 on localhost:11634 at 18:34:44.574
starting worker pid=54340 on localhost:11634 at 18:34:44.814
starting worker pid=54354 on localhost:11634 at 18:34:45.059

SAMPLING FOR MODEL 'mn_model' NOW (CHAIN 1).

SAMPLING FOR MODEL 'mn_model' NOW (CHAIN 2).

SAMPLING FOR MODEL 'mn_model' NOW (CHAIN 3).

SAMPLING FOR MODEL 'mn_model' NOW (CHAIN 4).
Chain 1:
Chain 1: Gradient evaluation took 0.012358 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 123.58 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
[3] "In addition: Warning messages:"
[4] "1: package ‘rstan’ was built under R version 3.6.2 "
[5] "2: package ‘StanHeaders’ was built under R version 3.6.2 "
error occurred during calling the sampler; sampling not done
Chain 2:
Chain 2: Gradient evaluation took 0.012256 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 122.56 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
[3] "In addition: Warning messages:"
[4] "1: package ‘rstan’ was built under R version 3.6.2 "
[5] "2: package ‘StanHeaders’ was built under R version 3.6.2 "
error occurred during calling the sampler; sampling not done
Chain 3:
Chain 3: Gradient evaluation took 0.012352 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 123.52 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
[3] "In addition: Warning messages:"
[4] "1: package ‘rstan’ was built under R version 3.6.2 "
[5] "2: package ‘StanHeaders’ was built under R version 3.6.2 "
error occurred during calling the sampler; sampling not done
Chain 4:
Chain 4: Gradient evaluation took 0.010889 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 108.89 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
[3] "In addition: Warning messages:"
[4] "1: package ‘rstan’ was built under R version 3.6.2 "
[5] "2: package ‘StanHeaders’ was built under R version 3.6.2 "
error occurred during calling the sampler; sampling not done
here are whatever error messages were returned
[[1]]
Stan model 'mn_model' does not contain samples.

[[2]]
Stan model 'mn_model' does not contain samples.

[[3]]
Stan model 'mn_model' does not contain samples.

[[4]]
Stan model 'mn_model' does not contain samples.

Stan model 'mn_model' does not contain samples.
Error in matrix(rstan::get_posterior_mean(stan.fit, par)[, "mean-all chains"], :
'data' must be of a vector type, was 'NULL'
In addition: Warning message:
In .local(object, ...) :
some chains had errors; consider specifying chains = 1 to debug

[kevinmcgregor]

Hi,

Can you share the output from running the command sessionInfo() ?

Thanks,

Kevin

[morganbale]

@kevinmcgregor I have the same error and this is what I get from sessionInfo():

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] bayesplot_1.7.1 forcats_0.4.0 stringr_1.4.0 dplyr_1.0.1 purrr_0.3.2 readr_1.3.1 tidyr_1.1.0
[8] tibble_2.1.3 tidyverse_1.2.1 rstan_2.21.2 ggplot2_3.2.0 StanHeaders_2.21.0-7 MASS_7.3-51.4

loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.7 haven_2.1.0 lattice_0.20-38 V8_3.4.0 colorspace_1.4-1 vctrs_0.3.2
[8] generics_0.0.2 stats4_3.6.0 loo_2.4.1 rlang_0.4.7 pkgbuild_1.0.5 pillar_1.4.2 glue_1.4.1
[15] withr_2.1.2 readxl_1.3.1 modelr_0.1.4 plyr_1.8.4 matrixStats_0.55.0 lifecycle_0.2.0 cellranger_1.1.0
[22] munsell_0.5.0 gtable_0.3.0 rvest_0.3.4 codetools_0.2-16 inline_0.3.15 knitr_1.23 callr_3.2.0
[29] ps_1.3.0 curl_4.0 parallel_3.6.0 broom_0.5.2 Rcpp_1.0.2 scales_1.0.0 backports_1.1.4
[36] RcppParallel_5.0.3 jsonlite_1.6 gridExtra_2.3 hms_0.4.2 stringi_1.4.3 processx_3.3.1 grid_3.6.0
[43] cli_1.1.0 tools_3.6.0 magrittr_1.5 lazyeval_0.2.2 crayon_1.3.4 pkgconfig_2.0.2 xml2_1.2.2
[50] prettyunits_1.0.2 ggridges_0.5.2 lubridate_1.7.4 assertthat_0.2.1 httr_1.4.1 rstudioapi_0.10 R6_2.4.0
[57] nlme_3.1-139 compiler_3.6.0

[kevinmcgregor]

Hi Morgan,

Thanks for the info. Could I ask you to try updating to the latest version of R and trying the install again? Also after updating R you'll probably need to update the pacakges "rstan", "rstantools", and "Rcpp". Let me know if you still have issues running the example code.

Cheers,

Kevin