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timjmiller / wham

State-space, age-structured fish stock assessment model
https://timjmiller.github.io/wham
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multivariate-Tweedie likelihood #65

Closed James-Thorson-NOAA closed 2 years ago

James-Thorson-NOAA commented 2 years ago

After some hijinks, I finally got the devel branch merged with changes to implement the multivariate-Tweedie likelihood. I've run the integrated-tests included and get this output:

== Failed tests ================================================================
-- Error (]8;line=100:col=1;file://C:/Users/James.Thorson/Desktop/Git/wham/tests/testthat/test_ex9_retro_pred.Rtest_ex9_retro_pred.R:100:1]8;;): Ex 9 works -----------------------------
Error in `check_breaks_labels(breaks, labels)`: object 'fancy_scientific' not found
Backtrace:
    x
 1. +-base::suppressWarnings(...) at ]8;line=100:col=0;file://test_ex9_retro_pred.Rtest_ex9_retro_pred.R:100:0]8;;
 2. | \-base::withCallingHandlers(...)
 3. \-plot_retro_pred_R(mods, peels = 3:n.yrs.peel, n.yrs.proj = n.yrs.proj)
 4.   \-ggplot2::scale_y_continuous(...) at ]8;line=87:col=8;file://test_ex9_retro_pred.Rtest_ex9_retro_pred.R:87:8]8;;
 5.     \-ggplot2::continuous_scale(...)
 6.       \-ggplot2:::check_breaks_labels(breaks, labels)

[ FAIL 1 | WARN 3 | SKIP 1 | PASS 159 ]
Error: Test failures

can I ignore this error (which seems to be about plotting) or should I try to track this down?

timjmiller commented 2 years ago

fancy_scientific is a function defined in R/compare_wham_models.R here https://github.com/timjmiller/wham/blob/ee5f3ec09a3b678f81c939ea175bd17c705b5bfc/R/compare_wham_models.R#L251. Is it there in your current version of the repo?

On Mon, Aug 1, 2022 at 6:49 PM Jim Thorson @.***> wrote:

After some hijinks, I finally got the devel branch merged with changes to implement the multivariate-Tweedie likelihood. I've run the integrated-tests included and get this output:

== Failed tests ================================================================ -- Error (�]8;line=100:col=1;file://C:/Users/James.Thorson/Desktop/Git/wham/tests/testthat/test_ex9_retro_pred.Rtest_ex9_retro_pred.R:100:1�]8;;): Ex 9 works ----------------------------- Error in check_breaks_labels(breaks, labels): object 'fancy_scientific' not found Backtrace:

x

  1. +-base::suppressWarnings(...) at �]8;line=100:col=0;file://test_ex9_retro_pred.Rtest_ex9_retro_pred.R:100:0�]8;;

  2. | -base::withCallingHandlers(...)

  3. -plot_retro_pred_R(mods, peels = 3:n.yrs.peel, n.yrs.proj = n.yrs.proj)

  4. -ggplot2::scale_y_continuous(...) at �]8;line=87:col=8;file://test_ex9_retro_pred.Rtest_ex9_retro_pred.R:87:8�]8;;

  5. -ggplot2::continuous_scale(...)

  6. -ggplot2:::check_breaks_labels(breaks, labels)

[ FAIL 1 | WARN 3 | SKIP 1 | PASS 159 ] Error: Test failures

can I ignore this error (which seems to be about plotting) or should I try to track this down?

— Reply to this email directly, view it on GitHub https://github.com/timjmiller/wham/issues/65, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEIGN7D76FWK2N642EUZXX3VXBH55ANCNFSM55JDT6CA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

James-Thorson-NOAA commented 2 years ago

fancy_scientific shows up in both timjmiller/devel and james-thorson-NOAA/mvtweedie branches, although it is not exported so only accessed in local functions or via wham:::fancy_scientific. I confirmed that I get the same error messages using the code below when cloning the timjmiller/devel branch and having it installed.

Is the issue something about how I'm calling the testthat check, can you confirm that it occurs in the devel branch, or do you mind if I skip this and proceed with the PR?

library(testthat)
library(wham)

# Check that test results are available locally
path_to_examples <- system.file("extdata", package="wham")
file.exists(file.path(path_to_examples,"ex1_test_results.rds"))

#testthat::test_check("wham")

# Run from local directory
testthat::test_dir( "C:/Users/James.Thorson/Desktop/Git/wham/tests/testthat/", reporter="check" )
timjmiller commented 2 years ago

Your calls to do the testing may be the issue. Do this (#8 under contributing on the wiki)

from your wham repo directory with the appropriate branch checked out:

library(here)wham.source.dir <- here()

confirm that the .cpp compiles and wham can be

loadeddevtools::load_all(path = wham.source.dir)

run all testsdevtools::test(pkg = wham.source.dir)

Actually I don't think wham.source.dir is needed at all.

On Tue, Aug 2, 2022 at 11:33 AM Jim Thorson @.***> wrote:

fancy_scientific shows up in both timjmiller/devel and james-thorson-NOAA/mvtweedie branches, although it is not exported so only accessed in local functions or via wham:::fancy_scientific. I confirmed that I get the same error messages using the code below when cloning the timjmiller/devel branch and having it installed.

Is the issue something about how I'm calling the testthat check, can you confirm that it occurs in the devel branch, or do you mind if I skip this and proceed with the PR?

library(testthat) library(wham)

Check that test results are available locallypath_to_examples <- system.file("extdata", package="wham")

file.exists(file.path(path_to_examples,"ex1_test_results.rds"))

testthat::test_check("wham")

Run from local directorytestthat::test_dir( "C:/Users/James.Thorson/Desktop/Git/wham/tests/testthat/", reporter="check" )

— Reply to this email directly, view it on GitHub https://github.com/timjmiller/wham/issues/65#issuecomment-1202836481, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEIGN7DIBSRDXQXUN6BWJO3VXE5UJANCNFSM55JDT6CA . You are receiving this because you commented.Message ID: @.***>

-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

James-Thorson-NOAA commented 2 years ago

OK, using this code, I get a really long error on devtools::load_all(path = wham.source.dir), which I think also occurs when I tried devtools::document(). But I can confirm that the CPP does in fact compile during installation. Any thoughts?

I'll work on an integrated-test for mvtweedie in parallel.

   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__vector(2) double'} [-Wignored-attributes]
      enum {
           ^

   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator<Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >':
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:99:8:   required from 'struct Eigen::internal::evaluator<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:681:51:   required from 'struct Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:665:8:   required from 'struct Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >'
C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39:   required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eige

   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39:   required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:416:17:   required from 'typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >; typename Eigen::internal::traits<T>::Scalar = double]'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:453:73:   [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:796:41:   required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing<Src>::value, void*>::type = void*]'
C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18:   required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<c

   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18:   required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>]'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Assign.h:66:28:   required from 'Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Derived = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >]'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1:   required from 'void atomic::matmul(const CppAD::vector<Type>&, CppAD::vector<Type>&) [with Double = double]'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1:   required from 'bool atomic::atomicmatmul<Type>::forward(size_t, size_t, const CppAD::vector<bool>&, CppAD::vector<bool>&, const CppAD::vector<Type>&, CppAD::vector<Type>&) [with Type = double; size_t = long long unsigned int]'
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1:   required from here
   C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__vector(2) double'} [-Wignored-attributes]

   C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564)

   C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Assembler messages:
   C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't write 308 bytes to section .text of wham_v0.o: 'file too big'
   C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564)

   C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't close wham_v0.o: file too big

   make: *** [C:/Users/James.Thorson/Work/R/R-4.1.0/etc/x64/Makeconf:245: wham_v0.o] Error 1

   ERROR: compilation failed for package 'wham'

-  removing 'C:/Users/JAMES~1.THO/AppData/Local/Temp/RtmpglStWx/devtools_install_18282b667307/wham'

Error in `(function (command = NULL, args = character(), error_on_status = TRUE, ...`:
! System command 'Rcmd.exe' failed
---
Exit status: 1
stdout & stderr: <printed>
---
Type .Last.error to see the more details.

and then 

> .Last.error
<system_command_status_error/rlib_error_3_0/rlib_error/error>
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, ...`:
! System command 'Rcmd.exe' failed
---
Exit status: 1
stdout & stderr: <printed>
---
Backtrace:
 1. devtools::load_all(path = wham.source.dir)
 2. pkgload::load_all(path = path, reset = reset, recompile = recompile, ...
 3. pkgbuild::compile_dll(path, quiet = quiet)
 4. withr::with_makevars(compiler_flags(debug), assignment = "+=", ...
 5. withr::with_envvar(c(R_MAKEVARS_USER = makevars_file), { ...
 6. base::force(code)
 7. base::force(code)
 8. pkgbuild:::install_min(path, dest = install_dir, components = "libs", args = if (needs_clean(path)) "--preclean", ...
 9. pkgbuild::rcmd_build_tools("INSTALL", c(path, paste("--library=", dest, ...
10. pkgbuild::with_build_tools({ ...
11. withr::with_path(rtools_path(), code)
12. base::force(code)
13. base::withCallingHandlers(callr::rcmd_safe(..., env = env, spinner = FALSE, ...
14. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, ...
15. callr:::run_r(options)
16. base::with(options, with_envvar(env, do.call(processx::run, c(list(bin, ...
17. base::with.default(options, with_envvar(env, do.call(processx::run, ...
18. base::eval(substitute(expr), data, enclos = parent.frame())
19. base::eval(substitute(expr), data, enclos = parent.frame())
20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...
21. base::force(code)
22. base::do.call(processx::run, c(list(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), ...
23. (function (command = NULL, args = character(), error_on_status = TRUE, ...
24. base::throw(new_process_error(res, call = sys.call(), echo = echo, ...
25. | base::signalCondition(cond)
26. (function (e) ...
27. asNamespace("callr")$err$throw(e)
timjmiller commented 2 years ago

On windows, I've found I have to silence warnings to get the devtools::load_all to work in Rstudio.

I have a Makevars.win file in C:.R with this in it CFLAGS+= -w

which silences all warnings (but not errors) when compiling, if I recall correctly. If you already have a Makevars.win just add that line to it. I'd be interested to know if doing that fixes your compilation error.

On Tue, Aug 2, 2022 at 11:53 AM Jim Thorson @.***> wrote:

OK, using this code, I get a really long error on devtools::load_all(path = wham.source.dir), which I think also occurs when I tried devtools::document(). But I can confirm that the CPP does in fact compile during installation. Any thoughts?

I'll work on an integrated-test for mvtweedie in parallel.

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes] enum { ^

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator<Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >': C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:99:8: required from 'struct Eigen::internal::evaluator<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:681:51: required from 'struct Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:665:8: required from 'struct Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >'C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39: required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eige C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39: required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:416:17: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >; typename Eigen::internal::traits::Scalar = double]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:453:73: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:796:41: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing::value, void>::type) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing::value, void>::type = void*]'C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<c

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Assign.h:66:28: required from 'Derived& Eigen::MatrixBase::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Derived = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from 'void atomic::matmul(const CppAD::vector&, CppAD::vector&) [with Double = double]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from 'bool atomic::atomicmatmul::forward(size_t, size_t, const CppAD::vector&, CppAD::vector&, const CppAD::vector&, CppAD::vector&) [with Type = double; size_t = long long unsigned int]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from here C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes]

C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564)

C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Assembler messages: C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't write 308 bytes to section .text of wham_v0.o: 'file too big' C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564) C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't close wham_v0.o: file too big

make: *** [C:/Users/James.Thorson/Work/R/R-4.1.0/etc/x64/Makeconf:245: wham_v0.o] Error 1

ERROR: compilation failed for package 'wham'

  • removing 'C:/Users/JAMES~1.THO/AppData/Local/Temp/RtmpglStWx/devtools_install_18282b667307/wham' Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:! System command 'Rcmd.exe' failed---Exit status: 1stdout & stderr: ---Type .Last.error to see the more details.

and then

.Last.error<system_command_status_error/rlib_error_3_0/rlib_error/error>Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:! System command 'Rcmd.exe' failed---Exit status: 1stdout & stderr: ---Backtrace:

  1. devtools::load_all(path = wham.source.dir)
  2. pkgload::load_all(path = path, reset = reset, recompile = recompile, ...
  3. pkgbuild::compile_dll(path, quiet = quiet)
  4. withr::with_makevars(compiler_flags(debug), assignment = "+=", ...
  5. withr::with_envvar(c(R_MAKEVARS_USER = makevars_file), { ...
  6. base::force(code)
  7. base::force(code)
  8. pkgbuild:::install_min(path, dest = install_dir, components = "libs", args = if (needs_clean(path)) "--preclean", ...
  9. pkgbuild::rcmd_build_tools("INSTALL", c(path, paste("--library=", dest, ...10. pkgbuild::with_build_tools({ ...11. withr::with_path(rtools_path(), code)12. base::force(code)13. base::withCallingHandlers(callr::rcmd_safe(..., env = env, spinner = FALSE, ...14. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, ...15. callr:::run_r(options)16. base::with(options, with_envvar(env, do.call(processx::run, c(list(bin, ...17. base::with.default(options, with_envvar(env, do.call(processx::run, ...18. base::eval(substitute(expr), data, enclos = parent.frame())19. base::eval(substitute(expr), data, enclos = parent.frame())20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...21. base::force(code)22. base::do.call(processx::run, c(list(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), ...23. (function (command = NULL, args = character(), error_on_status = TRUE, ...24. base::throw(new_process_error(res, call = sys.call(), echo = echo, ...25. | base::signalCondition(cond)26. (function (e) ...27. asNamespace("callr")$err$throw(e)

— Reply to this email directly, view it on GitHub https://github.com/timjmiller/wham/issues/65#issuecomment-1202883672, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEIGN7BC7Q25R3VHYJOWJUTVXE77DANCNFSM55JDT6CA . You are receiving this because you commented.Message ID: @.***>

-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

timjmiller commented 2 years ago

I also can confirm I get all existing tests to pass on your mvtweedie branch

On Tue, Aug 2, 2022 at 11:53 AM Jim Thorson @.***> wrote:

OK, using this code, I get a really long error on devtools::load_all(path = wham.source.dir), which I think also occurs when I tried devtools::document(). But I can confirm that the CPP does in fact compile during installation. Any thoughts?

I'll work on an integrated-test for mvtweedie in parallel.

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes] enum { ^

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator<Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >': C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:99:8: required from 'struct Eigen::internal::evaluator<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:681:51: required from 'struct Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:665:8: required from 'struct Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >'C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39: required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eige C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39: required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:416:17: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >; typename Eigen::internal::traits::Scalar = double]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:453:73: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:796:41: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing::value, void>::type) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing::value, void>::type = void*]'C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<c

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Assign.h:66:28: required from 'Derived& Eigen::MatrixBase::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Derived = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from 'void atomic::matmul(const CppAD::vector&, CppAD::vector&) [with Double = double]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from 'bool atomic::atomicmatmul::forward(size_t, size_t, const CppAD::vector&, CppAD::vector&, const CppAD::vector&, CppAD::vector&) [with Type = double; size_t = long long unsigned int]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from here C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes]

C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564)

C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Assembler messages: C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't write 308 bytes to section .text of wham_v0.o: 'file too big' C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564) C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't close wham_v0.o: file too big

make: *** [C:/Users/James.Thorson/Work/R/R-4.1.0/etc/x64/Makeconf:245: wham_v0.o] Error 1

ERROR: compilation failed for package 'wham'

  • removing 'C:/Users/JAMES~1.THO/AppData/Local/Temp/RtmpglStWx/devtools_install_18282b667307/wham' Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:! System command 'Rcmd.exe' failed---Exit status: 1stdout & stderr: ---Type .Last.error to see the more details.

and then

.Last.error<system_command_status_error/rlib_error_3_0/rlib_error/error>Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:! System command 'Rcmd.exe' failed---Exit status: 1stdout & stderr: ---Backtrace:

  1. devtools::load_all(path = wham.source.dir)
  2. pkgload::load_all(path = path, reset = reset, recompile = recompile, ...
  3. pkgbuild::compile_dll(path, quiet = quiet)
  4. withr::with_makevars(compiler_flags(debug), assignment = "+=", ...
  5. withr::with_envvar(c(R_MAKEVARS_USER = makevars_file), { ...
  6. base::force(code)
  7. base::force(code)
  8. pkgbuild:::install_min(path, dest = install_dir, components = "libs", args = if (needs_clean(path)) "--preclean", ...
  9. pkgbuild::rcmd_build_tools("INSTALL", c(path, paste("--library=", dest, ...10. pkgbuild::with_build_tools({ ...11. withr::with_path(rtools_path(), code)12. base::force(code)13. base::withCallingHandlers(callr::rcmd_safe(..., env = env, spinner = FALSE, ...14. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, ...15. callr:::run_r(options)16. base::with(options, with_envvar(env, do.call(processx::run, c(list(bin, ...17. base::with.default(options, with_envvar(env, do.call(processx::run, ...18. base::eval(substitute(expr), data, enclos = parent.frame())19. base::eval(substitute(expr), data, enclos = parent.frame())20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...21. base::force(code)22. base::do.call(processx::run, c(list(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), ...23. (function (command = NULL, args = character(), error_on_status = TRUE, ...24. base::throw(new_process_error(res, call = sys.call(), echo = echo, ...25. | base::signalCondition(cond)26. (function (e) ...27. asNamespace("callr")$err$throw(e)

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-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

James-Thorson-NOAA commented 2 years ago

Thanks for running it locally on your machine, and sorry for whatever is causing this trouble :0

I get the same error after adding the Makevars.win file containing "CFLAGS+= -w", and adding it to the R program file (in case located at C:\Users\James.Thorson\Work\R). But I'll skip this discussion for now (given that it passes locally for you) and will go ahead with adding an integrated-test, getting that to pass testthat locally, and then do a PR.

James-Thorson-NOAA commented 2 years ago

OK, I got the integrated test to work, and confirm that it shows up as a new test relative to the devel branch. I'm doing a PR now and will close this for now ... we can do any further discussion on the PR thread.

timjmiller commented 2 years ago

There is more information on where files for testing go here https://github.com/timjmiller/wham/wiki/Release-checklist-(for-maintainers)

On Tue, Aug 2, 2022 at 11:53 AM Jim Thorson @.***> wrote:

OK, using this code, I get a really long error on devtools::load_all(path = wham.source.dir), which I think also occurs when I tried devtools::document(). But I can confirm that the CPP does in fact compile during installation. Any thoughts?

I'll work on an integrated-test for mvtweedie in parallel.

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes] enum { ^

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator<Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >': C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:99:8: required from 'struct Eigen::internal::evaluator<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:681:51: required from 'struct Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:665:8: required from 'struct Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >'C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39: required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eige C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:349:39: required from 'class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> > >' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:416:17: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 1, -1, false> >, const Eigen::Block<const Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, -1, 1, true> >; typename Eigen::internal::traits::Scalar = double]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Redux.h:453:73: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:796:41: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing::value, void>::type) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<Eigen::internal::evaluator_assume_aliasing::value, void>::type = void*]'C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<c

C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/Assign.h:66:28: required from 'Derived& Eigen::MatrixBase::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 0>; Derived = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from 'void atomic::matmul(const CppAD::vector&, CppAD::vector&) [with Double = double]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from 'bool atomic::atomicmatmul::forward(size_t, size_t, const CppAD::vector&, CppAD::vector&, const CppAD::vector&, CppAD::vector&) [with Type = double; size_t = long long unsigned int]' C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/TMB/include/atomic_math.hpp:435:1: required from here C:/Users/James.Thorson/Desktop/Work files/Software/MRAN/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes]

C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564)

C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Assembler messages: C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't write 308 bytes to section .text of wham_v0.o: 'file too big' C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/as.exe: wham_v0.o: too many sections (109564) C:\Users\JAMES~1.THO\AppData\Local\Temp\ccql26Nv.s: Fatal error: can't close wham_v0.o: file too big

make: *** [C:/Users/James.Thorson/Work/R/R-4.1.0/etc/x64/Makeconf:245: wham_v0.o] Error 1

ERROR: compilation failed for package 'wham'

  • removing 'C:/Users/JAMES~1.THO/AppData/Local/Temp/RtmpglStWx/devtools_install_18282b667307/wham' Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:! System command 'Rcmd.exe' failed---Exit status: 1stdout & stderr: ---Type .Last.error to see the more details.

and then

.Last.error<system_command_status_error/rlib_error_3_0/rlib_error/error>Error in (function (command = NULL, args = character(), error_on_status = TRUE, ...:! System command 'Rcmd.exe' failed---Exit status: 1stdout & stderr: ---Backtrace:

  1. devtools::load_all(path = wham.source.dir)
  2. pkgload::load_all(path = path, reset = reset, recompile = recompile, ...
  3. pkgbuild::compile_dll(path, quiet = quiet)
  4. withr::with_makevars(compiler_flags(debug), assignment = "+=", ...
  5. withr::with_envvar(c(R_MAKEVARS_USER = makevars_file), { ...
  6. base::force(code)
  7. base::force(code)
  8. pkgbuild:::install_min(path, dest = install_dir, components = "libs", args = if (needs_clean(path)) "--preclean", ...
  9. pkgbuild::rcmd_build_tools("INSTALL", c(path, paste("--library=", dest, ...10. pkgbuild::with_build_tools({ ...11. withr::with_path(rtools_path(), code)12. base::force(code)13. base::withCallingHandlers(callr::rcmd_safe(..., env = env, spinner = FALSE, ...14. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, ...15. callr:::run_r(options)16. base::with(options, with_envvar(env, do.call(processx::run, c(list(bin, ...17. base::with.default(options, with_envvar(env, do.call(processx::run, ...18. base::eval(substitute(expr), data, enclos = parent.frame())19. base::eval(substitute(expr), data, enclos = parent.frame())20. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...21. base::force(code)22. base::do.call(processx::run, c(list(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), ...23. (function (command = NULL, args = character(), error_on_status = TRUE, ...24. base::throw(new_process_error(res, call = sys.call(), echo = echo, ...25. | base::signalCondition(cond)26. (function (e) ...27. asNamespace("callr")$err$throw(e)

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-- Timothy J. Miller, PhD (he, him, his) Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365