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R wrapper for the RACES package

License: GNU General Public License v3.0

R 20.25% C++ 78.84% Makefile 0.23% Shell 0.26% TeX 0.42%

rraces's Introduction

rRACES

rRACES is the R wrapper for RACES, a C++ tumour evolution simulator.

Help and support

Installation

In order to install the development version of rRACES, you need:

R and Rtools
the R package devtools
git

When the requirements have been satisfied, issue the R command:

devtools::install_github("caravagnalab/rRACES")

Tissue plotting requires the R package hexbin under GNU/Linux and Windows.

Copyright and contacts

Giulio Caravagna, Alberto Casagrande. Cancer Data Science (CDS) Laboratory.

rraces's People

Contributors

Stargazers

Watchers

Forkers

nicola-calonaci

rraces's Issues

Extract lineages information

Provide a getter get_lineage_evolution that returns a data.frame

from | to
---------
A      | B
B      | C

Bug in `update_rates`

On a rather complex example I see

> sim$get_species()
  genotype epistate growth_rate death_rate switch_rate
1        A        -        0.08       0.01        0.01
2        A        +        0.10       0.10        0.01
3        B        -        0.30       0.05        0.10
4        B        +        0.50       0.05        0.05
5        C        -        0.50       0.05        0.10
6        C        +        0.70       0.05        0.05
> sim$update_rates("B-", death=1)
> sim$get_species()
  genotype epistate growth_rate death_rate switch_rate
1        A        -        0.08       0.01        0.01
2        A        +        0.10       0.10        0.01
3        B        -        0.30       0.05        0.10
4        B        +        0.50       0.05        0.05
5        C        -        0.50       0.05        0.10
6        C        +        0.70       0.05        0.05

Problem with x = run(x, what = list(genotype = "A", epistate = "+", size = Ap_count + 1000))

I am running the tutorial and the command x = run(x, what = list(genotype = "A", epistate = "+", size = Ap_count + 1000)) gives:

Errore in !epistate : tipo argomento non valido

is it syntax error?

monoclonal tumour, with epigenetics (for @riccardobergamin and @claracanavese);

monoclonal tumour, shrinking to small numbers, and restarting, for multiple cycles (for @jovoni);

x <- new(Simulation)

x$update_tissue("Liver", 2000, 2000)
x$history_delta = 1
x$add_genotype(name = "A",
                 epigenetic_rates = c("+-" = 0, "-+" = 0),
                 growth_rates = c("+" = 0.2, "-" = 0.08),
                 death_rates = c("+" = 0.1, "-" = 0.01))

x$add_cell("A+", 1000, 1000)
x$get_cells()

# plot_tissue(x) + xlim(999, 1010) + ylim(990, 1010)

x$run_up_to_size("A+", 1500)

plot_tissue(x)

# Add genotype
x$add_genotype(name = "B",
               epigenetic_rates = c("+-" = 0, "-+" = 0),
               growth_rates = c("+" = 0.2, "-" = 0.08),
               death_rates = c("+" = 0.1, "-" = 0.01))

x$mutate_progeny(x$choose_cell_in("A"), "B")

# Simulation
x$run_up_to_size("B+", 200)

plot_tissue(x)

x$update_rates("A+", c(death=0.25))

x$run_up_to_time(x$get_clock() + 80)

plot_timeseries(x) + scale_y_log10()

x$update_rates("B+", c(death=0.5))
x$update_rates("A+", c(death=0.2))

x$run_up_to_time(x$get_clock() + 20)

plot_timeseries(x) + scale_y_log10()

Example case studies: simulated trajectories

Examples of interest (even without simulations)

Wrapper specifications

To begin with @albertocasagrande , let's start with some functions. For every R function I report the equivalent Python code from the wrapper.

init: this probably has not to be changes, we just use it to wrap everything inside an S3 object

#   sim = RACES.Simulation()

create_tissue: this will have to create a tissue. We could argue if we want this to be part of the above init function and remove create_tissue

#   sim.set_tissue("Liver", [100, 100])

add_species: this will have to create a species based on some parameters. It will implement these steps

#   A = RACES.Genotype("A", [[0.01, 0.01]])
#   A.set_rates("-", {RACES.CellEventType.DIE: 0.1,
#     RACES.CellEventType.DUPLICATE: 0.2})
#   A.set_rates("+", {RACES.CellEventType.DIE: 0.01,
#     RACES.CellEventType.DUPLICATE: 0.02})
#   sim.add_species(A)

Let us start with these and then we follow with those to define lineages and sample the data.

Rename `get_genotype_names`

Rename get_genotype_names as get_species_names

`R-CMD-check` and `pkgdown` workflows take more than 3 hours

R-CMD-check and pkgdown workflows do not end in 3 hours. This may be due to the ggraph and tidygraph dependencies which require compilation.

Installation problem with Rccp_simulation class

i am getting an installation problem related to Rccp:

Install the project...
-- Install configuration: "Release"
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/lib/libRACES.a
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/allele.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/archive.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/basic_IO.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/binary_logger.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/cell.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/cell_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/cna.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/context.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/context_index.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/ending_conditions.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/event_wrapper.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/fasta_reader.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/fasta_utils.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/genomic_position.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/genomic_region.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/genotype_id.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/genotype_mutation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/genotype_properties.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/lineage_graph.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/logger.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/mutation_engine.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/mutational_properties.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/palette.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/phyloXML.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/phylogenetic_forest.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/plot_2D.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/position.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/position_set.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/progress_bar.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/rate_update.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/read_simulator.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/sample_specification.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/sampling.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/simulation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/simulation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/simulation_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/snv.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/snv_signature.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/species.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/statistics.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/statistics.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/time.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/timed_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/tissue.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/tissue_plotter.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/tissue_sample.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/variables.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpmoBkzi/R.INSTALL450632fa3d47/rRACES/_install/include/indicators.hpp

mac/linux

cp ../_install/lib/*RACES.a ../_install/lib/libRACES.so
clang++ -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -I../_install/include/ -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
14 warnings generated.
clang++ -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -I../_install/include/ -fPIC -Wall -g -O2 -c drivers.cpp -o drivers.o
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
14 warnings generated.
clang++ -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rRACES.so RcppExports.o drivers.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/lib//libStanServices.a -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/lib/ -lStanHeaders -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -ltbb -L../_install/lib/ -lRACES -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-rRACES/00new/rRACES/libs
** R
** byte-compile and prepare package for lazy loading
nel metodo per ‘show’ con firma ‘"Rcpp_Simulation"’: nessuna definizione per la classe “Rcpp_Simulation”
** help
No man pages found in package ‘rRACES’
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: caricamento pacchetto o namespace fallito per ‘rRACES’ in dyn.load(file, DLLpath = DLLpath, ...):
non è possibile caricare un oggetto condiviso '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-rRACES/00new/rRACES/libs/rRACES.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-rRACES/00new/rRACES/libs/rRACES.so, 0x0006): Library not loaded: @rpath/libtbb.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-rRACES/00new/rRACES/libs/rRACES.so
Reason: tried: '/Library/Frameworks/R.framework/Resources/lib/libtbb.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre/lib/server/libtbb.dylib' (no such file)
Errore: caricamento fallito
Esecuzione interrotta
ERROR: loading failed

removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rRACES’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rRACES’
Messaggio di avvertimento:
In i.p(...) :
l'installazione del pacchetto ‘/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T//RtmpHVA7qF/file5f03312e8fa/rRACES_0.0.1.tar.gz’ ha uno stato di uscita non-zero

I cannot find in particular Rcpp_Simulation

`plot_forest` systematically issues warnings

The function plot_forest systematically issues warnings of the kind

#> Warning: Removed 1 rows containing non-finite values (`stat_edge_link()`).
#> Removed 1 rows containing missing values (`geom_point()`).

#> Warning: Removed 1 rows containing non-finite values
#> (`stat_edge_link()`).
#> Warning: Removed 1 rows containing missing values (`geom_point()`).

Check the package article "Tissue sampling" for examples.

`plot_tissue` issue on the site article "Tissue simulation"

In the "Tissue simulation" article on site, all the plot_tissue calls produce empty plots (see following image as an example).

The same article produces the following image when locally built

Better naming of `add_timed_mutation`

I think the terminology add_timed_mutation might be misleading because we do not necessarily have a "mutation" to explain passage from population A to B, but it could be a copy number or any other type of alteration we might include in the future.

I think what we actually do with that function is to "link" - in an evolutionary sense - two genotypes (not even two species, based on our recent renaming) in a linear evolutionary relation.

How about we call it any of:

link_genotype
add_linear_evolution
link_?

`get_firings`: get number of stochastic events (cell division, death) per species.

Proposed format, event has to be some literal encoding of a formula.

event | species | epistate  | firings
growth | A | + | 140
death | A | + | 1440
growth | A | - | 140
death | A | - | 144440
switch+- | A | + | 23432
switch-+ | A | - | 23432

Decide if these have to be relative to the last stop, or cumulative for the overall simulation. I think cumulative makes sense.

Visualisation: plot_firings

Growth model

The models in the vignette gives the same MRCAs, and therefore the vignette/ implementation does not seem very convincing. I do not have an intuition on why this happens.

I added a visualisation to highlight lineages in the tree -- it might help figure out.

Also, the model with the boundary-driven growth (as we usually call it), should be the default. Otherwise all other plots in the vignettes have those unexpected MRCAs.

problem with ape dependence

I am trying to install "ape" and "ggmuller" in R, but i am getting the error from c++

In file included from /orfeo/cephfs/home/cdslab/rbergamin/.conda/envs/stick-breaking/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
from /orfeo/cephfs/home/cdslab/rbergamin/.conda/envs/stick-breaking/x86_64-conda-linux-gnu/include/c++/11.2.0/locale:41,
from /orfeo/cephfs/home/cdslab/rbergamin/.conda/envs/stick-breaking/x86_64-conda-linux-gnu/include/c++/11.2.0/iomanip:43,
from /orfeo/cephfs/home/cdslab/rbergamin/R/R-packages/Rcpp/include/RcppCommon.h:53,
from /orfeo/cephfs/home/cdslab/rbergamin/R/R-packages/Rcpp/include/Rcpp.h:27,
from RcppExports.cpp:4:
/orfeo/cephfs/home/cdslab/rbergamin/.conda/envs/stick-breaking/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::'
80 | using ::timespec_get;
| ^~~~~~~~~~~~

I am not understanding if it is related to my configuration or some missing dependence. If this is the case, should we provide also a list of c++ libraries needed for rRACES?

`get_info`: get current simulation info.

Tibble format

field | value
--------------------
name | "My Simulation"
tissue | "Liver"
tissue_size | 100x100

Visualisation: none, but will be used to augment other visualisations.

Time-varying rates

After I have specified a species etc, I can.

sim$update_rates(
    species = "A+",
    rates = list(switch = 0.01, growth = 0.08, death = 0.23)
)

Suggested function `add_species(sim, species)`

@caravagn wrote in the nobuild/test.R file

# Create a species object with the required parameters
# species <- list(
#   name = "B",
#   epigenetic_rates = c("+-" = 0.01, "-+" = 0.01),
#   growth_rates = c("+" = 0.1, "-" = 0.3),
#   death_rates = c("+" = 0.05, "-" = 0.1)
# )
# 
# # Call the R wrapper function with the simulation object and the prepared species object
# add_species(sim, species)

Should we add a Simulation method that takes a list as a parameter?

`get_clock`: get current simulation clock.

syntax error "x$simulation$get_firings() %>% filter(genotype == "A", epistate == "+", events == "switch") %>% pull(firings)"

it should be

x$simulation$get_firings() %>%
filter(genotype == "A", epistate == "+", event == "switch") %>%
pull(fired)

Both `pkgdown` and `R-CMD-check` actions fail

The "Tissue simulation" article requires the patchwork package to build the site. Because of this, both pkgdown and R-CMD-check actions fail.

This is not a real package requirement because it is exclusively used during the site-building. Can we avoid forcing users to install it?

`run_up_to_size(species, count)`, run until species `species` reaches value `count`;

`Rcpp_Simulation$show` raises errors

The version of Rcpp_Simulation$show introduced by commit dfa2e4b raises errors.

Sample names need to be unique

Avoid to allow the creation of samples with the same name (both across time and space).

`R CMD check --as-cran` produces 7 warning and 4 notes

On 75856a3, the command R CMD check --as-cran produces 7 warning and 4 notes (see the file 00check.log). These warnings and nodes make R CMD check failing on github.

polyclonal tumour with epigenetics, 3 species and branched evolution;

`get_counts`: get number of cells per species, at last stop.

Tibble format

species | epistate | counts
 ---------------
A | + | 1000
A | - | 400
B | + | 102
C | - | 455

Visualisation function: https://github.com/caravagnalab/rRACES/blob/main/R/plot_counts.R

Rcpp does not support named arguments

Apparently, Rcpp does not support named arguments. This may be an issue for methods such as Simulation$get_cells(species_filter, epigenetic_filter) because we are forced to specify both arguments, and we do not have a way to distinguish Simulation$get_cells(species_filter) from Simulation$get_cells(epigenetic_filter).

Can we assume that the single-argument Simulation$get_cells(...) always refers to Simulation$get_cells(epigenetic_filter)? Any other ideas?

Deafult seed

Not sure this is a point.

I think that the constructor should, by default, fix a seed (1234) and should leave it random if seed = NULL. This would make it easier for us to code vignettes in a deterministic fashion.

Species vs Genotype

The difference between species and genotype needs to be clarified in the API.

A species is a cell set with the same duplication, death, and epigenetic mutation rates. Thus, the call

sim$add_speces(name="A", 
               epigenetic_rates = c("+-" = 0.01, "-+" = 0.01),
               growth_rates = c("+" = 0.2, "-" = 0.08),
               death_rates = c("+" = 0.1, "-" = 0.01))

defines two species: namely, A+ and A-.

Even though we still don't know their genetic characterization, A+ and A- are identical from the genomic point of view, and they exclusively differ because of their epigenetic state. Thus, A is their genotype name.

Do you agree with this terminology, @caravagn?

`get_cells`: get cells: returns a tibble of alive cells, including the cell id, the species and their tissue position

cell_id | species | epistate | position_x | position_y
0x3423 | A | + | 3354 | 425

polyclonal tumour, with 2 species, one shrinking to small numbers, the other avoiding negative selection (for @AliceAntonello and @riccardobergamin, at a later stage to be used to model HLA loss);

`plot_muller` produces many warnings

Using plot_muller produces warnings for using deprecated functions.

Every time plot_muller is called, it issues

#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.

Once every 8 hours, it produces

#> Warning: `filter_()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `filter()` instead.
#> ℹ See vignette('programming') for more help
#> ℹ The deprecated feature was likely used in the ggmuller package.
#>   Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `summarise_()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `summarise()` instead.
#> ℹ The deprecated feature was likely used in the ggmuller package.
#>   Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `group_by_()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `group_by()` instead.
#> ℹ See vignette('programming') for more help
#> ℹ The deprecated feature was likely used in the ggmuller package.
#>   Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `arrange_()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `arrange()` instead.
#> ℹ See vignette('programming') for more help
#> ℹ The deprecated feature was likely used in the ggmuller package.
#>   Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `select_()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `select()` instead.
#> ℹ The deprecated feature was likely used in the ggmuller package.
#>   Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
#> of ggplot2 3.3.4.
#> ℹ The deprecated feature was likely used in the ggmuller package.
#>   Please report the issue to the authors.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.

See the package article "Tissue sampling" for examples.

Naming convention

Should this be now "genotype" and no species.

https://github.com/caravagnalab/rRACES/blob/534d467d10aebe6f692d0a2609c3845cb18b833b/nobuild/test_Cpp.R#L34C1-L36C37

RCpp/R bad constructor output folder

It seems the R wrapper fails picking up the right Rcpp constructor @albertocasagrande and the output folder is always neglected as output folders have the form races_3242343_345243 etc. disregarding the parameter.

rRACES/R/create_simulation.R

Line 18 in 2dfd55f

output_dir = 'output_races',

Need to export also the seed and use the full constructor (not sure how I spec that).

`run_up_to_time (time)`, run until `t = time`;

Time series stored in `Simulation`

Add a time-series stored in the Simulation object, with a discretisation Delta with default value 1. Make it exportable.

`R CMD build` does not end anymore

The vignette compilation does not end from commit bd5226a.

@caravagn, can you check the package by issuing R CMD check --as-cran before committing the new code?

Simulate up to (more complex predicates)

We have run_up_to but we might want to define

#18
#19
run_up_to_events (event, species, epistate, count), run until the stochastic event event, in species species with epigenetic state epistate happens at least count times. Refer to events names syntax as in #11 .

Note that run_up_to_size and run_up_to_events might not be determinable a priori.

In the future, we might want to use CTL.

Installation issue?

Installation issue

> devtools::install_github("caravagnalab/rRACES")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo caravagnalab/rRACES@HEAD
✔  checking for file ‘/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpIwp3pQ/remotes109f54a35960/caravagnalab-rRACES-534d467/DESCRIPTION’ ...
─  preparing ‘rRACES’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘rRACES_0.0.1.tar.gz’
   
* installing *source* package ‘rRACES’ ...
** using staged installation
++ set -e
++ which cmake
/usr/local/bin/cmake
++ rm -rf _builds _include RACES
++ git clone https://github.com/albertocasagrande/RACES.git
Cloning into 'RACES'...
++ cd RACES
++ git checkout 4d45d78c0af
Note: switching to '4d45d78c0af'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 4d45d78 Fixed missing  method in `TissueStatistics` - implemented missing `contains_data_for(const Species&) const`
++ cmake -H./RACES/ -B_builds -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=_install -DCMAKE_SHARED_LIBRARY_PREFIX_CXX= -DONLY_LIBRARIES=1 -DAVOID_OPTIONAL_LIBS=1
-- The CXX compiler identification is AppleClang 12.0.0.12000032
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Avoiding optional libraries
Downloading "p-ranav/indicators" library...
done
Using "p-ranav/indicators"
Building exclusively RACES libraries
-- Configuring done (0.7s)
-- Generating done (0.0s)
-- Build files have been written to: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_builds
++ cmake --build _builds --target install --config Release
[  2%] Building CXX object CMakeFiles/objlib.dir/src/basic_IO.cpp.o
[  4%] Building CXX object CMakeFiles/objlib.dir/src/archive.cpp.o
[  7%] Building CXX object CMakeFiles/objlib.dir/src/driver_genotype.cpp.o
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/driver_genotype.cpp:225:22: warning: loop variable 'b_value' is always a copy because the range of type 'const Races::Drivers::MethylationSignature' (aka 'const vector<bool>') does not return a reference [-Wrange-loop-analysis]
    for (const bool& b_value: methylation_signature) {
                     ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/driver_genotype.cpp:225:10: note: use non-reference type 'bool'
    for (const bool& b_value: methylation_signature) {
         ^~~~~~~~~~~~~~~~~~~~
1 warning generated.
[  9%] Building CXX object CMakeFiles/objlib.dir/src/species.cpp.o
[ 11%] Building CXX object CMakeFiles/objlib.dir/src/position.cpp.o
[ 14%] Building CXX object CMakeFiles/objlib.dir/src/ending_conditions.cpp.o
[ 16%] Building CXX object CMakeFiles/objlib.dir/src/simulation.cpp.o
[ 19%] Building CXX object CMakeFiles/objlib.dir/src/tissue.cpp.o
[ 21%] Building CXX object CMakeFiles/objlib.dir/src/cell.cpp.o
[ 23%] Building CXX object CMakeFiles/objlib.dir/src/cell_event.cpp.o
[ 26%] Building CXX object CMakeFiles/objlib.dir/src/simulation_event.cpp.o
[ 28%] Building CXX object CMakeFiles/objlib.dir/src/driver_mutation.cpp.o
[ 30%] Building CXX object CMakeFiles/objlib.dir/src/rate_update.cpp.o
[ 33%] Building CXX object CMakeFiles/objlib.dir/src/tissue_sample.cpp.o
[ 35%] Building CXX object CMakeFiles/objlib.dir/src/sample_specification.cpp.o
[ 38%] Building CXX object CMakeFiles/objlib.dir/src/sampling.cpp.o
[ 40%] Building CXX object CMakeFiles/objlib.dir/src/event_wrapper.cpp.o
[ 42%] Building CXX object CMakeFiles/objlib.dir/src/timed_event.cpp.o
[ 45%] Building CXX object CMakeFiles/objlib.dir/src/logger.cpp.o
[ 47%] Building CXX object CMakeFiles/objlib.dir/src/binary_logger.cpp.o
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/binary_logger.cpp:36:
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/binary_logger.hpp:38:
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/logger.hpp:37:
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/cell.hpp:36:
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1093:19: warning: loop variable 'value' is always a copy because the range of type 'const vector<bool, std::__1::allocator<bool> >' does not return a reference [-Wrange-loop-analysis]
    for (const T& value : container) {
                  ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/driver_genotype.hpp:274:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, vector, bool, std::__1::allocator<bool>, true>' requested here
                & methylation_signature 
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::EpigeneticGenotype::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/species.hpp:415:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::EpigeneticGenotype, true>' requested here
        archive & static_cast<const EpigeneticGenotype &>(*this);
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::Simulation::Species::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1094:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::Simulation::Species, true>' requested here
        archive & value;
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/tissue.hpp:781:17: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                & species
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::Simulation::Tissue::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1094:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::Simulation::Tissue, true>' requested here
        archive & value;
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/simulation.hpp:731:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, vector, Races::Drivers::Simulation::Tissue, std::__1::allocator<Races::Drivers::Simulation::Tissue>, true>' requested here
        archive & tissues
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::Simulation::Simulation::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/binary_logger.cpp:232:13: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::Simulation::Simulation, true>' requested here
    archive & simulation;
            ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1093:10: note: use non-reference type 'bool'
    for (const T& value : container) {
         ^~~~~~~~~~~~~~~~
1 warning generated.
[ 50%] Building CXX object CMakeFiles/objlib.dir/src/statistics.cpp.o
[ 52%] Building CXX object CMakeFiles/objlib.dir/src/palette.cpp.o
[ 54%] Building CXX object CMakeFiles/objlib.dir/src/plot_2D.cpp.o
[ 57%] Building CXX object CMakeFiles/objlib.dir/src/progress_bar.cpp.o
[ 59%] Building CXX object CMakeFiles/objlib.dir/src/context.cpp.o
[ 61%] Building CXX object CMakeFiles/objlib.dir/src/snv_signature.cpp.o
[ 64%] Building CXX object CMakeFiles/objlib.dir/src/snv.cpp.o
[ 66%] Building CXX object CMakeFiles/objlib.dir/src/allele.cpp.o
[ 69%] Building CXX object CMakeFiles/objlib.dir/src/genomic_region.cpp.o
[ 71%] Building CXX object CMakeFiles/objlib.dir/src/genomic_position.cpp.o
[ 73%] Building CXX object CMakeFiles/objlib.dir/src/fasta_reader.cpp.o
[ 76%] Building CXX object CMakeFiles/objlib.dir/src/fasta_utils.cpp.o
[ 78%] Building CXX object CMakeFiles/objlib.dir/src/genome_mutations.cpp.o
[ 80%] Building CXX object CMakeFiles/objlib.dir/src/cna.cpp.o
[ 83%] Building CXX object CMakeFiles/objlib.dir/src/mutation_engine.cpp.o
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/mutation_engine.cpp:31:
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/mutation_engine.hpp:494:29: warning: loop variable 'child' of type 'const Races::Drivers::PhylogeneticForest::const_node' creates a copy from type 'const Races::Drivers::PhylogeneticForest::const_node' [-Wrange-loop-analysis]
            for (const auto child: node.children()) {
                            ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/mutation_engine.hpp:494:18: note: use reference type 'const Races::Drivers::PhylogeneticForest::const_node &' to prevent copying
            for (const auto child: node.children()) {
                 ^~~~~~~~~~~~~~~~~
                            &
1 warning generated.
[ 85%] Building CXX object CMakeFiles/objlib.dir/src/mutational_properties.cpp.o
[ 88%] Building CXX object CMakeFiles/objlib.dir/src/read_simulator.cpp.o
[ 90%] Building CXX object CMakeFiles/objlib.dir/src/position_set.cpp.o
[ 92%] Building CXX object CMakeFiles/objlib.dir/src/phyloXML.cpp.o
[ 95%] Building CXX object CMakeFiles/objlib.dir/src/phylogenetic_forest.cpp.o
[ 95%] Built target objlib
[ 97%] Linking CXX shared library RACES.dylib
[ 97%] Built target libRACES
[100%] Linking CXX static library libRACES.a
[100%] Built target libRACES_static
Install the project...
-- Install configuration: "Release"
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/lib/RACES.0.1.0.dylib
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/lib/RACES.dylib
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/variables.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/basic_IO.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/archive.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype_id.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/species.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_mutation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/rate_update.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_sample.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sample_specification.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sampling.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/event_wrapper.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/timed_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/logger.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/binary_logger.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/plot_2D.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/progress_bar.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_plotter.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/time.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/ending_conditions.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context_index.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv_signature.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/allele.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_region.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_position.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_reader.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_utils.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cna.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutation_engine.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutational_properties.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/read_simulator.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position_set.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/indicators.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/lib/libRACES.a
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/variables.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/basic_IO.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/archive.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype_id.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/species.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell_event.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation_event.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_mutation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/rate_update.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_sample.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sample_specification.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sampling.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/event_wrapper.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/timed_event.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/logger.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/binary_logger.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/plot_2D.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/progress_bar.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_plotter.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/time.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/ending_conditions.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context_index.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv_signature.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/allele.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_region.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_position.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_reader.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_utils.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cna.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutation_engine.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutational_properties.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/read_simulator.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position_set.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/indicators.hpp
++ cp _install/lib/libRACES.so src/
cp: _install/lib/libRACES.so: No such file or directory
++ echo 'Failed: libRACES.so -> src'
Failed: libRACES.so -> src
++ cp _install/lib/RACES.dylib src/libRACES.so
++ cp _install/lib/libRACES.a src/libRACES.so
++ /Library/Frameworks/R.framework/Resources/bin/R --vanilla --silent -e 'Rcpp::compileAttributes()'
> Rcpp::compileAttributes()
> 
> 
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I../_install/include/ -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I../_install/include/ -fPIC  -Wall -g -O2  -c drivers.cpp -o drivers.o
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:143:28: error: 'path' is unavailable: introduced in macOS 10.15
    Basic(std::filesystem::path filename, std::ios_base::openmode mode);
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:151:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:153:12: error: 'open' is unavailable: introduced in macOS 10.15
        fs.open(filename, mode);
           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/fstream:1610:10: note: 'open' has been explicitly marked unavailable here
    void open(const filesystem::path& __p, ios_base::openmode __mode = ios_base::in|ios_base::out)
         ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:219:35: error: 'path' is unavailable: introduced in macOS 10.15
    explicit Out(std::filesystem::path filename);
                                  ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:230:26: error: 'path' is unavailable: introduced in macOS 10.15
    Out(std::filesystem::path filename, std::ios_base::openmode mode);
                         ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:240:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:242:21: error: 'path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::out);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:763:29: note: 'path' has been explicitly marked unavailable here
  _LIBCPP_INLINE_VISIBILITY path(const path& __p) : __pn_(__p.__pn_) {}
                            ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:242:21: error: '~path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::out);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:790:3: note: '~path' has been explicitly marked unavailable here
  ~path() = default;
  ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:269:34: error: 'path' is unavailable: introduced in macOS 10.15
    explicit In(std::filesystem::path filename);
                                 ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:280:25: error: 'path' is unavailable: introduced in macOS 10.15
    In(std::filesystem::path filename, std::ios_base::openmode mode);
                        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:290:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:292:21: error: 'path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::in);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:763:29: note: 'path' has been explicitly marked unavailable here
  _LIBCPP_INLINE_VISIBILITY path(const path& __p) : __pn_(__p.__pn_) {}
                            ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:292:21: error: '~path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::in);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:790:3: note: '~path' has been explicitly marked unavailable here
  ~path() = default;
  ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:416:35: error: 'path' is unavailable: introduced in macOS 10.15
    explicit Out(std::filesystem::path filename);
                                  ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:427:26: error: 'path' is unavailable: introduced in macOS 10.15
    Out(std::filesystem::path filename, std::ios_base::openmode mode);
                         ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:436:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:449:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:438:14: error: 'path' is unavailable: introduced in macOS 10.15
        open(filename, std::fstream::binary);
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:763:29: note: 'path' has been explicitly marked unavailable here
  _LIBCPP_INLINE_VISIBILITY path(const path& __p) : __pn_(__p.__pn_) {}
                            ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:438:14: error: '~path' is unavailable: introduced in macOS 10.15
        open(filename, std::fstream::binary);
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:790:3: note: '~path' has been explicitly marked unavailable here
  ~path() = default;
  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [drivers.o] Error 1
ERROR: compilation failed for package ‘rRACES’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rRACES’
Messaggio di avvertimento:
In i.p(...) :
  l'installazione del pacchetto ‘/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T//RtmpIwp3pQ/file109f7168f69e/rRACES_0.0.1.tar.gz’ ha uno stato di uscita non-zero

Installation with usual remote procedures

This is the default installation way, but it does not work for me

# install.packages("devtools")
devtools::install_github("caravagnalab/rRACES")

Getters post-simulation, pre data generation

cell_id | species | epi-state | position_x | position_y
0x3423 | A | + | 3354 | 425

evaluate if we want to add extra parameters (eg, what portion of tissue to look at, or which species), or if we want actually leave this as a low-lever wrapper and export something higher-level (in R).

Garbage committed to the repository

The commit 75b7df7 contains directories and files that are not supposed to be submitted to the repository.

In particular,

./_builds and its content
./_install and its content
./output_dir and its content
./src/RACES.so
./src/libRACES.so
./src/drivers.o
./rRACES.Rproj

are not part of the wrapper source and must be removed from the repository.

Resurrection of a simulation

Since the final state of a simulation is always dumped to disk, should we allow and R function

x = resume_from_disk(dir)

that returns an object of class Simulation as if I had just simulated and obtained what is in dir?

`R CMD check` ends with an error on Ubuntu

R CMD check on commit 621f286 ends with an error on GitHub Ubuntu containers. The command on the same commit succeeds on macOS (see here and here for the complete logs).

This may be a bug exposed by the different compilers or by how the two OS handle memory.

The error message on Ubuntu is

  checking examples ... ERROR
  Running examples in ‘rRACES-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
Error: Error: R CMD check found ERRORs
  > ### Name: Simulation$get_cells
  > ### Title: Gets the tissue cells
  > ### Aliases: Simulation$get_cells
  > 
  > ### ** Examples
  > 
  > sim <- new(Simulation)
  > sim$add_species(genotype = "A",
  +                 epigenetic_rates = c("+-" = 0.01, "-+" = 0.01),
  +                 growth_rates = c("+" = 0.2, "-" = 0.08),
  +                 death_rates = c("+" = 0.1, "-" = 0.01))
  > sim$add_species(genotype = "B",
  +                 epigenetic_rates = c("+-" = 0.02, "-+" = 0.01),
  +                 growth_rates = c("+" = 0.3, "-" = 0.1),
  +                 death_rates = c("+" = 0.1, "-" = 0.01))
  > sim$add_timed_mutation(src = "A", dst = "B", time = 50)
  > sim$add_cell("A+", 500, 500)
  > sim$run_up_to_time(70)
  25l
   [██████████------------------------------] 23% [00m:00s] Cells: 13
   [██████████------------------------------] 23% [00m:00s] Cells: 13
  25hError: The position does not belong to the tissue
  Execution halted

`plot_muller` produces discontinuous plots

plot_muller produces discontinuous plots like the ones below.

(between time 87 and time 89)

(at the bottom of the plot around time 67)

As far as I know, Muller plots should be continuous. Am I wrong?

Actions run locally, but fail online

I am not understanding why runs do work on my machine, like pkgdown, and file with actions... need some help from the expert @luca-dex

GitHub Actions: website and CMD check

We have https://github.com/caravagnalab/rRACES/actions

one to build pkgdown website
one for R CMD check

but all give errors for required libraries, or general package configuration.

Generated files in the repository

Some of the files in the directories man and docs of commit 2d2ff08 are automatically generated by roxygen2 and pkgdown, respectively.

These files should not be stored in the repository, but instead produced at building time. Maintaining them in the repository is a waste of space, may lead to bugs, and affects the cleanliness of the repository.