errors with the current target file

parksw3 commented 2 years ago

Some errors in the middle

* record workspace save_diagnostics_filtered
x error target save_diagnostics_filtered
Error: could not load dependencies of target save_diagnostics_filtered. invalid 'description' argument

* start target save_diagnostics_naive
* record workspace save_diagnostics_naive
x error target save_diagnostics_naive
Error: could not load dependencies of target save_diagnostics_naive. invalid 'description' argument

More

* built branch draws_naive_20e9a8c3 [0.01 seconds]
* start branch draws_naive_d73a1e58
* built branch draws_naive_d73a1e58 [0.01 seconds]
* start branch draws_naive_f1b37128
* built branch draws_naive_f1b37128 [0 seconds]
* start branch draws_naive_089a2806
* record workspace draws_naive_089a2806
x error branch draws_naive_089a2806
Error: could not load dependencies of target draws_naive_089a2806. invalid 'description' argument

* start branch draws_naive_26e1a806
* built branch draws_naive_26e1a806 [0.01 seconds]

And more error messages

* record workspace save_lognormal_draws_filtered
x error target save_lognormal_draws_filtered
Error: could not load dependencies of target save_lognormal_draws_filtered. invalid 'description' argument

* start target summarised_draws_filtered
* record workspace summarised_draws_filtered
x error target summarised_draws_filtered
Error: could not load dependencies of target summarised_draws_filtered. invalid 'description' argument

* start target save_lognormal_draws_naive
* record workspace save_lognormal_draws_naive
x error target save_lognormal_draws_naive
Error: could not load dependencies of target save_lognormal_draws_naive. invalid 'description' argument

* start target summarised_draws_naive
* record workspace summarised_draws_naive
x error target summarised_draws_naive
Error: could not load dependencies of target summarised_draws_naive. invalid 'description' argument

* start target save_summarised_draws_filtered_and_censoring_adjusted
* built target save_summarised_draws_filtered_and_censoring_adjusted [0 seconds]
* start target save_summarised_draws_censoring_adjusted
* built target save_summarised_draws_censoring_adjusted [0 seconds]
* start target save_summarised_draws_truncation_adjusted
* built target save_summarised_draws_truncation_adjusted [0.02 seconds]
* start target save_summarised_draws_latent_variable_truncation_and_censoring_adjusted
* built target save_summarised_draws_latent_variable_truncation_and_censoring_adjusted [0 seconds]
* start target save_summarised_draws_truncation_and_censoring_adjusted
* built target save_summarised_draws_truncation_and_censoring_adjusted [0 seconds]
* start target save_summarised_draws_filtered
* record workspace save_summarised_draws_filtered
x error target save_summarised_draws_filtered
Error: could not load dependencies of target save_summarised_draws_filtered. invalid 'description' argument

* start target save_summarised_draws_naive
* record workspace save_summarised_draws_naive
x error target save_summarised_draws_naive
Error: could not load dependencies of target save_summarised_draws_naive. invalid 'description' argument

* end pipeline [4.469 hours]

parksw3 commented 2 years ago

Running tar_make() saved some files in the posteriors folder (except for naive, though I'm not sure why the naive case would break?) but none in the summarised_posteriors folder.

seabbs commented 2 years ago

hmm very odd. I am just rerunning now so will see if I can reproduce.

parksw3 commented 1 year ago

I just reran everything again, and now it won't save any of the posteriors...

Getting a bunch of errors saying

could not load dependencies of target (file name). invalid 'description' argument

Seems like something to do with file name maybe?

https://statisticsglobe.com/r-error-in-file-invalid-description-argument

parksw3 commented 1 year ago

I was also wondering if I'm getting the error because some packages aren't up to date. using renv::restore() to get all the packages up to date and runnig everything again... and also updating R to 4.2.2

parksw3 commented 1 year ago

well, I broke my Windows while trying to update R and what not... will need to spend more time than I thought trying to fix this.. now I get errors from compiling some models...

parksw3 commented 1 year ago

Hmm, so I managed to fix the issue that I was having before (that I couldn't compile any models and cmdstan was completely broken) but now model compilations take way too long. For example, running the naive_fit takes a few mins of compilation (it probably took me a few seconds before). This might not be a huge problem because we only have to compile the models once for the main target file but pretty annoying still... This is the error I get (not asking you to fix it but mostly trying to document the problem so that I can fix it). Nope, couldn't fix it. I'll probably have to ask mc-stan.org....

Compiling Stan program...
In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array/multi_array_ref.hpp:32,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array.hpp:34,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:63,
                 from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9,
                 from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from stan/lib/stan_math/stan/math/prim/functor.hpp:14,
                 from stan/lib/stan_math/stan/math/prim.hpp:15,
                 from stan/src/stan/io/dump.hpp:7,
                 from src/cmdstan/command.hpp:30,
                 from src/cmdstan/main.cpp:1:
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:180:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  180 |         : public boost::functional::detail::unary_function<typename unary_traits<Predicate>::argument_type,bool>
      |                                             ^~~~~~~~~~~~~~

In file included from C:/rtools42/ucrt64/include/c++/12.2.0/string:48,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/bits/locale_classes.h:40,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/bits/ios_base.h:41,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/streambuf:41,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/bits/streambuf_iterator.h:35,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/iterator:66,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/iterator/iterator_traits.hpp:10,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/range/iterator_range_core.hpp:26,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/lexical_cast.hpp:30,
                 from stan/src/stan/callbacks/writer.hpp:4,
                 from src/cmdstan/arguments/argument.hpp:4,
                 from src/cmdstan/arguments/categorical_argument.hpp:4,
                 from src/cmdstan/arguments/arg_data.hpp:4,
                 from src/cmdstan/command.hpp:4:
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:214:45: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  214 |         : public boost::functional::detail::binary_function<
      |                                             ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:252:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  252 |         : public boost::functional::detail::unary_function<
      |                                             ^
~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:299:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  299 |         : public boost::functional::detail::unary_function<
      |                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:345:57: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  345 |     class mem_fun_t : public boost::functional::detail::unary_function<T*, S>
      |                                                         ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:361:58: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  361 |     class mem_fun1_t : public boost::functional::detail::binary_function<T*, A, S>
      |                                                          ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:377:63: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  377 |     class const_mem_fun_t : public boost::functional::detail::unary_function<const T*, S>
      |                                                    
           ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:393:64: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  393 |     class const_mem_fun1_t : public boost::functional::detail::binary_function<const T*, A, S>
      |                                                                ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:438:61: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  438 |     class mem_fun_ref_t : public boost::functional::detail::unary_function<T&, S>
      |                                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:454:62: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  454 |     class mem_fun1_ref_t : public boost::functional::detail::binary_function<T&, A, S>
      |                                                              ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:470:67: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  470 |     class const_mem_fun_ref_t : public boost::fun
ctional::detail::unary_function<const T&, S>
      |                                                                   ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:487:68: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  487 |     class const_mem_fun1_ref_t : public boost::functional::detail::binary_function<const T&, A, S>
      |                                                                    ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:533:73: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  533 |     class pointer_to_unary_function : public boost::functional::detail::unary_function<Arg,Result>
      |                                                                         ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:557:74: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  557 |     class pointer_to_binary_function : public boost::functional::detail::binary_function<Arg1,Arg2,Result>
      |                                                                          ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~

In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array/multi_array_ref.hpp:32,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array.hpp:34,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22,
                 from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:63,
                 from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9,
                 from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from stan/lib/stan_math/stan/math/prim/functor.hpp:14,
                 from stan/lib/stan_math/stan/math/rev/fun.hpp:196,
                 from stan/lib/stan_math/stan/math/rev.hpp:10,
                 from stan/lib/stan_math/stan/math.hpp:19,
                 from stan/src/stan/model/model_header.hpp:4,
                 from C:/Users/sangw/AppData/Local/Temp/Rtmpc7w67W/model-2a8412bc315f.hpp:3:
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:180:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  180 |         : public boost::functional::detail::unary_function<typename unary_traits<Predicate>::argument_type,bool>
      |                                             ^~~~~~~~~~~~~~

In file included from C:/rtools42/ucrt64/include/c++/12.2.0/string:48,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/bits/locale_classes.h:40,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/bits/ios_base.h:41,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/ios:42,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/istream:38,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/sstream:38,
                 from C:/rtools42/ucrt64/include/c++/12.2.0/complex:45,
                 from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:96,
                 from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1,
                 from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22,
                 from stan/lib/stan_math/stan/math/rev.hpp:4:
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:214:45: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  214 |         : public boost::functional::detail::binary_function<
      |                                             ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:252:45: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  252 |         : public boost::functional::detail::unary_function<
      |                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:299:45: warning: 'template<cl
ass _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  299 |         : public boost::functional::detail::unary_function<
      |                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:345:57: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  345 |     class mem_fun_t : public boost::functional::detail::unary_function<T*, S>
      |                                                         ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:361:58: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  361 |     class mem_fun1_t : public boost::functional::detail::binary_function<T*, A, S>
      |                                                          ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:377:63: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  377 |     class const_mem_fun_t : public boost::functional::detail::unary_function<const T*, S>
      |                                                               ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:393:64: warning: 
'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  393 |     class const_mem_fun1_t : public boost::functional::detail::binary_function<const T*, A, S>
      |                                                                ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:438:61: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  438 |     class mem_fun_ref_t : public boost::functional::detail::unary_function<T&, S>
      |                                                             ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:454:62: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  454 |     class mem_fun1_ref_t : public boost::functional::detail::binary_function<T&, A, S>
      |                                                              ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:470:67: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  470 |     class const_mem_fun_ref_t : public boost::functional::detail::unary_function<const T&, S>
      |                                                                   ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function

      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:487:68: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  487 |     class const_mem_fun1_ref_t : public boost::functional::detail::binary_function<const T&, A, S>
      |                                                                    ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:533:73: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  533 |     class pointer_to_unary_function : public boost::functional::detail::unary_function<Arg,Result>
      |                                                                         ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:557:74: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  557 |     class pointer_to_binary_function : public boost::functional::detail::binary_function<Arg1,Arg2,Result>
      |                                                                          ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~

seabbs commented 1 year ago

I can't reproduce this (tested on a windows system and everything was fine). Going to close but feel free to reopen if its still an issue.

parksw3 / epidist-paper

errors with the current target file #28