Open mbatgh opened 8 months ago
Hi @mbatgh
You can install rxode2
from CRAN right now. It works mostly the same, though model piping and nlmixr2
style models also work in solving.
Right now RxODE
needs some bug fixes to get on CRAN.
thanks for the swift reply! ... unfortunately, now i get a different error:
install.packages("rxode2")
...
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/lib/R/site-library/RcppEigen/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/lib/R/site-library/RcppParallel/include' -fopenmp -Disrxode2parse -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -D_REENTRANT -isystem"/usr/local/lib/R/site-library/BH/include" -isystem"/usr/lib/R/site-library/RcppEigen/include" -isystem'/usr/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -DTBB_INTERFACE_NEW -isystem/usr/include -DTBB_INTERFACE_NEW -isystem'/usr/local/lib/R/site-library/StanHeaders/include/src' -isystem"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o
In file included from /usr/include/c++/13/ext/string_conversions.h:43,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/streambuf:43,
from /usr/include/c++/13/bits/streambuf_iterator.h:35,
from /usr/include/c++/13/iterator:66,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:25,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/include/c++/13/cstdlib:79:15: fatal error: stdlib.h: No such file or directory
79 | #include_next ~~~~~
compilation terminated.
is there anywhere a listing of all requirements for rxode2? thanks! michael
I'm unsure if your compiler is setup correctly. <stdlib.h>
is one of the standard includes for C
.
For me, because I like things to install quickly and not worry about dependencies, I use:
https://github.com/eddelbuettel/r2u
However, I don't think that you have a supported ubuntu distribution. I haven't even heard of trixie yet.
It could be because you don't have the required dependency packages installed. I looked again ad your issue and it has a prefix of tbb_
which implies you need RcppParallel
setup.
Hi Matthew The following did work in R 4.3.2 on debian trixie (this is the latest/testing version of debian) ...
install.packages("RcppParallel", dependencies = TRUE) install.packages("rxode2") install.packages("nlmixr2",dependencies = TRUE)
I also managed to successfully run the example on https://github.com/nlmixr2/nlmixr2.
Can you please confirm whether the documentation for nlmixr, e.g. here: https://nlmixrdevelopment.github.io/nlmixr_bookdown/applications.html#posters-presentations-and-publications, also applies to nlmixr2? If there are any a major changes, are they documented somewhere?
Thanks again for your help! regards, Michael
Hi Michael, there are some major changes, but I think that the user visible changes are minimal (mostly a bit more stable).
The changes are discussed here:
Hi,
I just tried to install RxODE on my linux box (debian trixie, R version 4.3.2)
install.packages("RxODE") gives me: package ‘RxODE’ is not available for this version of R
devtools::install_github("nlmixrdevelopment/RxODE") gives: [...] g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/dparser/include' -I'/usr/local/lib/R/site-library/PreciseSums/include' -I'/usr/lib/R/site-library/RcppEigen/include' -I'/usr/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/sitmo/include' -I'/usr/local/lib/R/site-library/StanHeaders/include' -I'/usr/local/lib/R/site-library/BH/include' -fopenmp -DisRxODE -DBOOST_DISABLE_ASSERTS -DBOOST_NO_CXX11_STATIC_ASSERT -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -isystem"/usr/local/lib/R/site-library/BH/include" -isystem"/usr/lib/R/site-library/RcppEigen/include" -isystem'/usr/local/lib/R/site-library/StanHeaders/include/src' -isystem"/usr/local/lib/R/site-library/Rcpp/include" -isystem"/usr/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.3.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c lincmtB.cpp -o lincmtB.o In file included from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/Eigen_NumTraits.hpp:5, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/typedefs.hpp:7, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/chainable_object.hpp:6, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:10, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:19, from lincmtB.cpp:4: /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: tbb/tbb_stddef.h: No such file or directory 9 | #include <tbb/tbb_stddef.h> | ^
~~~~~ compilation terminated.libtbb-dev is installed on my systrem (version (2021.11.0-2)) any help highly appreciated! cheers Michael