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Error: Fitting failed. Unable to retrieve the metadata #163

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pandaqiuqiu opened this issue Nov 26, 2024 · 5 comments
Open

Error: Fitting failed. Unable to retrieve the metadata #163

pandaqiuqiu opened this issue Nov 26, 2024 · 5 comments

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@pandaqiuqiu
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pandaqiuqiu commented Nov 26, 2024 •
edited by stemangiola
Loading

When I used the example data, the following error occurred:

data("counts_obj")
> View(counts_obj)
> sccomp_result = 
+   counts_obj |>
+   sccomp_estimate( 
+     formula_composition = ~ type, 
+     .sample = sample,
+     .cell_group = cell_group,
+     .abundance = count, 
+     cores = 1, verbose = FALSE
+   ) |> 
+   sccomp_remove_outliers(cores = 1, verbose = FALSE) |> # Optional
+   sccomp_test()
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Loading model from cache...
Error: Fitting failed. Unable to retrieve the metadata.

I have installed the latest version of sccomp (2.1.0). Could you check what the issue might be? Thank you!
@stemangiola
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Hello,

it works for me.

Please try to clean the model cache

sccomp:::clear_stan_model_cache()

@pandaqiuqiu
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Author

Thanks you your rapid reply.
But after running sccomp:::clear_stan_model_cache(), rerun the code, this error happed again:

sccomp_result =

  • counts_obj |>
  • sccomp_estimate(
  • formula_composition = ~ type, 

  • .sample = sample,

  • .cell_group = cell_group,

  • .abundance = count, 

  • cores = 1, verbose = FALSE
  • ) |>
  • sccomp_remove_outliers(cores = 1, verbose = FALSE) |> # Optional
  • sccomp_test()

sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Precompiled model not found. Compiling the model...
Compiling Stan program...

Model executable is up to date!
Model compiled and saved to cache successfully.
Error: Fitting failed. Unable to retrieve the metadata.

@stemangiola
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Collaborator

Very strange

> library(sccomp)
> data("counts_obj")
> sccomp_result = 
+       counts_obj |>
+       sccomp_estimate( 
+            formula_composition = ~ type, 
+             .sample = sample,
+             .cell_group = cell_group,
+          .abundance = count, 
+             cores = 1, verbose = FALSE
+           )
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Precompiled model not found. Compiling the model...
Compiling Stan program...
Running make /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b "STAN_THREADS=TRUE" \
  "STANCFLAGS +=  --name='glm_multi_beta_binomial_model'"

--- Translating Stan model to C++ code ---
bin/stanc --name='glm_multi_beta_binomial_model' --o=/var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.hpp /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.stan

--- Compiling C++ code ---
arch -arch arm64e clang++ -Wno-deprecated-declarations -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -ffp-contract=off -Wno-ignored-attributes     -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header.hpp.gch/model_header_threads_15_0.hpp.gch -x c++ -o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.hpp

--- Linking model ---
arch -arch arm64e clang++ -Wno-deprecated-declarations -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -ffp-contract=off -Wno-ignored-attributes     -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS               -Wl,-L,"/Users/a1234450/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb"   -Wl,-rpath,"/Users/a1234450/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb"      /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.o src/cmdstan/main_threads.o       -ltbb   stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b
rm /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c3e41439b.hpp
Model executable is up to date!
Model compiled and saved to cache successfully.
sccomp says: to do hypothesis testing run `sccomp_test()`,
  the `test_composition_above_logit_fold_change` = 0.1 equates to a change of ~10%, and
  0.7 equates to ~100% increase, if the baseline is ~0.1 proportion.
  Use `sccomp_proportional_fold_change` to convert c_effect (linear) to proportion difference (non-linear).
> clear_stan_model_cache() 
Error in clear_stan_model_cache() : 
  could not find function "clear_stan_model_cache"
> sccomp:::clear_stan_model_cache() 
Cache deleted: /Users/a1234450/.sccomp_models/2.1.0
> sccomp_result = 
+       counts_obj |>
+       sccomp_estimate( 
+            formula_composition = ~ type, 
+             .sample = sample,
+             .cell_group = cell_group,
+          .abundance = count, 
+             cores = 1, verbose = FALSE
+           )
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Precompiled model not found. Compiling the model...
Compiling Stan program...
Running make /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b "STAN_THREADS=TRUE" \
  "STANCFLAGS +=  --name='glm_multi_beta_binomial_model'"

--- Translating Stan model to C++ code ---
bin/stanc --name='glm_multi_beta_binomial_model' --o=/var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.hpp /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.stan

--- Compiling C++ code ---
arch -arch arm64e clang++ -Wno-deprecated-declarations -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -ffp-contract=off -Wno-ignored-attributes     -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header.hpp.gch/model_header_threads_15_0.hpp.gch -x c++ -o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.hpp

--- Linking model ---
arch -arch arm64e clang++ -Wno-deprecated-declarations -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -ffp-contract=off -Wno-ignored-attributes     -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS               -Wl,-L,"/Users/a1234450/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb"   -Wl,-rpath,"/Users/a1234450/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb"      /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.o src/cmdstan/main_threads.o       -ltbb   stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b
rm /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.hpp /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c34e9cd7b.o
Model executable is up to date!
Model compiled and saved to cache successfully.
sccomp says: to do hypothesis testing run `sccomp_test()`,
  the `test_composition_above_logit_fold_change` = 0.1 equates to a change of ~10%, and
  0.7 equates to ~100% increase, if the baseline is ~0.1 proportion.
  Use `sccomp_proportional_fold_change` to convert c_effect (linear) to proportion difference (non-linear).
> sccomp_result = 
+       counts_obj |>
+       sccomp_estimate( 
+            formula_composition = ~ type, 
+             .sample = sample,
+             .cell_group = cell_group,
+          .abundance = count, 
+             cores = 1, verbose = FALSE
+           ) |> 
+     sccomp_remove_outliers(cores = 1, verbose = FALSE) |> # Optional
+     sccomp_test()
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Loading model from cache...
sccomp says: to do hypothesis testing run `sccomp_test()`,
  the `test_composition_above_logit_fold_change` = 0.1 equates to a change of ~10%, and
  0.7 equates to ~100% increase, if the baseline is ~0.1 proportion.
  Use `sccomp_proportional_fold_change` to convert c_effect (linear) to proportion difference (non-linear).
Precompiled model not found. Compiling the model...
Compiling Stan program...
Running make /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4 "STAN_THREADS=TRUE" \
  "STANCFLAGS +=  --name='glm_multi_beta_binomial_generate_data_model'"

--- Translating Stan model to C++ code ---
bin/stanc --name='glm_multi_beta_binomial_generate_data_model' --o=/var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.hpp /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.stan

--- Compiling C++ code ---
arch -arch arm64e clang++ -Wno-deprecated-declarations -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -ffp-contract=off -Wno-ignored-attributes     -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header.hpp.gch/model_header_threads_15_0.hpp.gch -x c++ -o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.hpp

--- Linking model ---
arch -arch arm64e clang++ -Wno-deprecated-declarations -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -ffp-contract=off -Wno-ignored-attributes     -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS               -Wl,-L,"/Users/a1234450/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb"   -Wl,-rpath,"/Users/a1234450/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb"      /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.o src/cmdstan/main_threads.o       -ltbb   stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4
rm /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.o /var/folders/7w/rg5zrgd17dn9pfwgpbgwdvxc0000gp/T/RtmpM2Mud5/model-c53c543baac4.hpp
Model executable is up to date!
Model compiled and saved to cache successfully.
Running standalone generated quantities after 1 MCMC chain, with 1 thread(s) per chain...

Chain 1 finished in 0.0 seconds.
sccomp says: outlier identification - step 1/2
Loading model from cache...
Running standalone generated quantities after 1 MCMC chain, with 1 thread(s) per chain...

Chain 1 finished in 0.0 seconds.
sccomp says: outlier-free model fitting - step 2/2
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Loading model from cache...
> 
> sccomp_result 
# A tibble: 72 × 14
   cell_group parameter   factor c_lower c_effect c_upper    c_pH0     c_FDR v_lower v_effect v_upper v_pH0 v_FDR count_data        
   <chr>      <chr>       <chr>    <dbl>    <dbl>   <dbl>    <dbl>     <dbl>   <dbl>    <dbl>   <dbl> <dbl> <dbl> <list>            
 1 B1         (Intercept) NA      0.975     1.13   1.28   0        0           -6.36    -5.95   -5.53     0     0 <tibble [20 × 12]>
 2 B1         typecancer  type   -1.15     -0.898 -0.644  0        0           NA       NA      NA       NA    NA <tibble [20 × 12]>
 3 B2         (Intercept) NA      0.476     0.773  1.07   0        0           -5.63    -5.27   -4.93     0     0 <tibble [20 × 12]>
 4 B2         typecancer  type   -1.19     -0.776 -0.359  0.000500 0.0000909   NA       NA      NA       NA    NA <tibble [20 × 12]>
 5 B3         (Intercept) NA     -0.625    -0.332 -0.0431 0.0583   0.00410     -6.83    -6.47   -6.11     0     0 <tibble [20 × 12]>
 6 B3         typecancer  type   -0.625    -0.210  0.183  0.291    0.0826      NA       NA      NA       NA    NA <tibble [20 × 12]>
 7 BM         (Intercept) NA     -1.25     -0.953 -0.660  0        0           -7.48    -7.00   -6.53     0     0 <tibble [20 × 12]>
 8 BM         typecancer  type   -0.752    -0.333  0.109  0.144    0.0369      NA       NA      NA       NA    NA <tibble [20 × 12]>
 9 CD4 1      (Intercept) NA      0.200     0.380  0.564  0.00225  0.000163    -6.74    -6.36   -6.00     0     0 <tibble [20 × 12]>
10 CD4 1      typecancer  type   -0.0779    0.155  0.391  0.326    0.106       NA       NA      NA       NA    NA <tibble [20 × 12]>
# ℹ 62 more rows
# ℹ Use `print(n = ...)` to see more rows

Please

  • reinstall from github,
  • update all outdated packages upon request
  • retry the code on multiple machines
  • print your sessionInfo()

Thanks

@pandaqiuqiu
Copy link
Author

Very very strange.

I reinstall from github and then update all outdated packages upon request, this error return:

data("counts_obj")
sccomp_result =

  • counts_obj |>
  • sccomp_estimate(
  • formula_composition = ~ type, 

  • .sample = sample,

  • .cell_group = cell_group,

  • .abundance = count, 

  • cores = 1, verbose = FALSE
  • ) |>
  • sccomp_remove_outliers(cores = 1, verbose = FALSE) |> # Optional
  • sccomp_test()

sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
Precompiled model not found. Compiling the model...
Compiling Stan program...
Running mingw32-make.exe "C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.exe"
"STAN_THREADS=TRUE" "STANCFLAGS += --name='glm_multi_beta_binomial_model'"

--- Translating Stan model to C++ code ---
bin/stanc.exe --name='glm_multi_beta_binomial_model' --o=C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.hpp C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.stan

--- Compiling C++ code ---
g++ -Wno-nonnull -D_UCRT -Wno-deprecated-declarations -std=c++17 -m64 -D_UCRT -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -Wno-class-memaccess -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -D_USE_MATH_DEFINES -D_GLIBCXX11_USE_C99_COMPLEX -DBOOST_DISABLE_ASSERTS -c -Wno-ignored-attributes -x c++ -o C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.o C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.hpp

--- Linking model ---
g++ -Wno-nonnull -D_UCRT -Wno-deprecated-declarations -std=c++17 -m64 -D_UCRT -D_REENTRANT -Wall -Wno-unused-function -Wno-uninitialized -Wno-unused-but-set-variable -Wno-unused-variable -Wno-sign-compare -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-attributes -Wno-ignored-attributes -Wno-class-memaccess -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -D_USE_MATH_DEFINES -D_GLIBCXX11_USE_C99_COMPLEX -DBOOST_DISABLE_ASSERTS -Wl,-L,"C:/Users/erzac/.cmdstan/cmdstan-2.35.0/stan/lib/stan_math/lib/tbb" C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.o src/cmdstan/main_threads.o -static-libgcc -static-libstdc++ -ltbb stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a stan/lib/stan_math/lib/tbb/tbb.dll -o C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.exe
rm C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.o C:/Users/erzac/AppData/Local/Temp/RtmpC2i0LZ/model-262033d943a4.hpp
Model executable is up to date!
Model compiled and saved to cache successfully.
Error: Fitting failed. Unable to retrieve the metadata.

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=English_American Samoa.utf8 LC_CTYPE=English_American Samoa.utf8
[3] LC_MONETARY=English_American Samoa.utf8 LC_NUMERIC=C
[5] LC_TIME=English_American Samoa.utf8

time zone: America/Toronto
tzcode source: internal

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

other attached packages:
[1] dplyr_1.1.3 sccomp_2.1.0

loaded via a namespace (and not attached):
[1] fs_1.6.3 matrixStats_1.0.0 spatstat.sparse_3.0-2
[4] bitops_1.0-7 enrichplot_1.22.0 devtools_2.4.5
[7] HDO.db_0.99.1 httr_1.4.7 RColorBrewer_1.1-3
[10] doParallel_1.0.17 profvis_0.3.8 tools_4.3.1
[13] sctransform_0.4.1 backports_1.4.1 utf8_1.2.3
[16] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[19] GetoptLong_1.0.5 urlchecker_1.0.1 withr_2.5.2
[22] sp_2.0-0 prettyunits_1.2.0 gridExtra_2.3
[25] progressr_0.14.0 cli_3.6.1 Biobase_2.62.0
[28] spatstat.explore_3.2-3 fastDummies_1.7.3 scatterpie_0.2.1
[31] Seurat_5.1.0 spatstat.data_3.0-1 readr_2.1.4
[34] ggridges_0.5.4 pbapply_1.7-2 QuickJSR_1.0.7
[37] yulab.utils_0.1.3 StanHeaders_2.32.2 gson_0.1.0
[40] DOSE_3.28.2 R.utils_2.12.2 parallelly_1.36.0
[43] sessioninfo_1.2.2 limma_3.58.1 rstudioapi_0.15.0
[46] RSQLite_2.3.1 shape_1.4.6 generics_0.1.3
[49] gridGraphics_0.5-1 ica_1.0-3 spatstat.random_3.1-6
[52] car_3.1-2 distributional_0.3.2 inline_0.3.19
[55] GO.db_3.17.0 loo_2.6.0 Matrix_1.6-5
[58] fansi_1.0.4 S4Vectors_0.40.2 abind_1.4-5
[61] R.methodsS3_1.8.2 lifecycle_1.0.4 edgeR_4.0.12
[64] carData_3.0-5 SummarizedExperiment_1.32.0 SparseArray_1.2.2
[67] qvalue_2.34.0 Rtsne_0.16 grid_4.3.1
[70] blob_1.2.4 promises_1.2.1 crayon_1.5.2
[73] miniUI_0.1.1.1 lattice_0.21-8 msigdbr_7.5.1
[76] cowplot_1.1.1 KEGGREST_1.40.0 pillar_1.9.0
[79] knitr_1.45 ComplexHeatmap_2.18.0 GenomicRanges_1.54.1
[82] fgsea_1.28.0 rjson_0.2.21 future.apply_1.11.0
[85] codetools_0.2-19 fastmatch_1.1-4 leiden_0.4.3
[88] glue_1.6.2 ggfunnel_0.1.0 ggfun_0.1.4
[91] data.table_1.14.8 remotes_2.4.2.1 vctrs_0.6.3
[94] png_0.1-8 treeio_1.26.0 spam_2.9-1
[97] gtable_0.3.4 cachem_1.0.8 xfun_0.40
[100] S4Arrays_1.2.0 mime_0.12 tidygraph_1.3.0
[103] survival_3.5-5 SingleCellExperiment_1.24.0 iterators_1.0.14
[106] statmod_1.5.0 ellipsis_0.3.2 fitdistrplus_1.1-11
[109] ROCR_1.0-11 nlme_3.1-162 ggtree_3.10.0
[112] usethis_2.2.2 bit64_4.0.5 RcppAnnoy_0.0.21
[115] rprojroot_2.0.4 rstan_2.32.3 GenomeInfoDb_1.38.8
[118] tensorA_0.36.2.1 irlba_2.3.5.1 KernSmooth_2.23-21
[121] colorspace_2.1-0 BiocGenerics_0.48.1 DBI_1.1.3
[124] tidyselect_1.2.0 processx_3.8.2 curl_5.0.2
[127] bit_4.0.5 compiler_4.3.1 DelayedArray_0.28.0
[130] desc_1.4.2 plotly_4.10.2 posterior_1.6.0
[133] shadowtext_0.1.3 checkmate_2.3.0 scales_1.3.0
[136] lmtest_0.9-40 callr_3.7.3 stringr_1.5.0
[139] digest_0.6.33 goftest_1.2-3 spatstat.utils_3.0-3
[142] XVector_0.42.0 htmltools_0.5.6 pkgconfig_2.0.3
[145] MatrixGenerics_1.14.0 fastmap_1.1.1 GlobalOptions_0.1.2
[148] rlang_1.1.1 htmlwidgets_1.6.2 shiny_1.7.5
[151] farver_2.1.1 zoo_1.8-12 jsonlite_1.8.7
[154] BiocParallel_1.34.2 GOSemSim_2.28.1 R.oo_1.25.0
[157] RCurl_1.98-1.13 magrittr_2.0.3 GenomeInfoDbData_1.2.11
[160] ggplotify_0.1.2 dotCall64_1.0-2 sceasy_0.0.7
[163] patchwork_1.2.0 munsell_0.5.0 Rcpp_1.0.11
[166] babelgene_22.9 ape_5.7-1 viridis_0.6.4
[169] reticulate_1.34.0 stringi_1.7.12 ggraph_2.1.0
[172] zlibbioc_1.48.0 MASS_7.3-60 plyr_1.8.8
[175] pkgbuild_1.4.2 parallel_4.3.1 listenv_0.9.0
[178] ggrepel_0.9.3 forcats_1.0.0 deldir_1.0-9
[181] Biostrings_2.68.1 graphlayouts_1.1.0 splines_4.3.1
[184] tensor_1.5 hms_1.1.3 circlize_0.4.15
[187] locfit_1.5-9.8 ps_1.7.5 ggpubr_0.6.0
[190] igraph_1.5.1 spatstat.geom_3.2-5 ggsignif_0.6.4
[193] RcppHNSW_0.5.0 reshape2_1.4.4 stats4_4.3.1
[196] pkgload_1.3.3 SeuratObject_5.0.2 RcppParallel_5.1.7
[199] BiocManager_1.30.22 tzdb_0.4.0 foreach_1.5.2
[202] tweenr_2.0.2 httpuv_1.6.11 RANN_2.6.1
[205] tidyr_1.3.0 purrr_1.0.2 polyclip_1.10-6
[208] clue_0.3-65 future_1.33.0 scattermore_1.2
[211] ggplot2_3.5.1 ggforce_0.4.1 broom_1.0.5
[214] xtable_1.8-4 RSpectra_0.16-1 tidytree_0.4.6
[217] rstatix_0.7.2 later_1.3.1 viridisLite_0.4.2
[220] instantiate_0.2.3.9000 tibble_3.2.1 clusterProfiler_4.13.0
[223] aplot_0.2.2 memoise_2.0.1 AnnotationDbi_1.66.0
[226] IRanges_2.36.0 cluster_2.1.4 globals_0.16.2
[229] cmdstanr_0.8.1

@stemangiola
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stemangiola commented Nov 26, 2024 •
edited
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I suggest to update R. 4.3 is very outdated.

Please try after updating if you can.

I will also try to ask to some windows users to reproduce the code.

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