[pkgsrc/trunk]: pkgsrc/math math/R-nimble: import R-nimble-0.9.0

[brook <brook%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/48c65115abf6
branches:  trunk
changeset: 436655:48c65115abf6
user:      brook <brook%pkgsrc.org@localhost>
date:      Fri Aug 07 02:59:26 2020 +0000

description:
math/R-nimble: import R-nimble-0.9.0

A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate
models and do basic R-style math, and compiling both models and
nimbleFunctions via custom- generated C++. 'NIMBLE' includes default
methods for MCMC, particle filtering, Monte Carlo Expectation
Maximization, and some other tools. The nimbleFunction system makes it
easy to do things like implement new MCMC samplers from R, customize
the assignment of samplers to different parts of a model from R, and
compile the new samplers automatically via C++ alongside the samplers
'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by
making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people
think of MCMC as the main goal of the 'BUGS'/'JAGS' language for
writing models, one can use 'NIMBLE' for writing arbitrary other kinds
of model-generic algorithms as well. A full User Manual is available
at <https://r-nimble.org>.

diffstat:

 math/Makefile          |   3 ++-
 math/R-nimble/DESCR    |  16 ++++++++++++++++
 math/R-nimble/Makefile |  33 +++++++++++++++++++++++++++++++++
 math/R-nimble/distinfo |   6 ++++++
 4 files changed, 57 insertions(+), 1 deletions(-)

diffs (84 lines):

diff -r e5d27e34ebfa -r 48c65115abf6 math/Makefile
--- a/math/Makefile     Fri Aug 07 02:53:12 2020 +0000
+++ b/math/Makefile     Fri Aug 07 02:59:26 2020 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.473 2020/08/07 02:52:56 brook Exp $
+# $NetBSD: Makefile,v 1.474 2020/08/07 02:59:26 brook Exp $
 
 COMMENT=       Mathematics
 
@@ -81,6 +81,7 @@
 SUBDIR+=       R-mvtnorm
 SUBDIR+=       R-ncdf
 SUBDIR+=       R-nloptr
+SUBDIR+=       R-nimble
 SUBDIR+=       R-nortest
 SUBDIR+=       R-numDeriv
 SUBDIR+=       R-pbkrtest
diff -r e5d27e34ebfa -r 48c65115abf6 math/R-nimble/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/R-nimble/DESCR       Fri Aug 07 02:59:26 2020 +0000
@@ -0,0 +1,16 @@
+A system for writing hierarchical statistical models largely
+compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate
+models and do basic R-style math, and compiling both models and
+nimbleFunctions via custom- generated C++. 'NIMBLE' includes default
+methods for MCMC, particle filtering, Monte Carlo Expectation
+Maximization, and some other tools. The nimbleFunction system makes it
+easy to do things like implement new MCMC samplers from R, customize
+the assignment of samplers to different parts of a model from R, and
+compile the new samplers automatically via C++ alongside the samplers
+'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by
+making it extensible: New distributions and functions can be added,
+including as calls to external compiled code. Although most people
+think of MCMC as the main goal of the 'BUGS'/'JAGS' language for
+writing models, one can use 'NIMBLE' for writing arbitrary other kinds
+of model-generic algorithms as well. A full User Manual is available
+at <https://r-nimble.org>.
diff -r e5d27e34ebfa -r 48c65115abf6 math/R-nimble/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/R-nimble/Makefile    Fri Aug 07 02:59:26 2020 +0000
@@ -0,0 +1,33 @@
+# $NetBSD: Makefile,v 1.1 2020/08/07 02:59:26 brook Exp $
+
+R_PKGNAME=     nimble
+R_PKGVER=      0.9.0
+
+MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
+COMMENT=       MCMC, Particle Filtering, and Programmable Hierarchical Modeling
+LICENSE=       modified-bsd OR gnu-gpl-v2 OR gnu-gpl-v3
+
+DEPENDS+=      R-coda>=0.19.3:../../math/R-coda
+DEPENDS+=      R-igraph>=1.2.4.1:../../math/R-igraph
+
+USE_LANGUAGES= c++ fortran
+
+EIGEN_FILES+=  PardisoSupport
+EIGEN_FILES+=  src/Core/Assign_MKL.h
+EIGEN_FILES+=  src/Core/arch/AltiVec/PacketMath.h
+EIGEN_FILES+=  src/Core/arch/SSE/PacketMath.h
+EIGEN_FILES+=  src/Core/arch/ZVector/PacketMath.h
+EIGEN_FILES+=  src/Core/util/BlasUtil.h
+EIGEN_FILES+=  src/Core/util/DisableStupidWarnings.h
+EIGEN_FILES+=  src/Core/util/MKL_support.h
+EIGEN_FILES+=  src/Core/util/Meta.h
+EIGEN_FILES+=  src/Geometry/Scaling.h
+EIGEN_FILES+=  src/misc/lapacke.h
+
+post-extract:
+.for f in ${EIGEN_FILES}
+       ${CHMOD} a-x ${WRKSRC}/inst/include/Eigen/${f}
+.endfor
+
+.include "../../math/R/Makefile.extension"
+.include "../../mk/bsd.pkg.mk"
diff -r e5d27e34ebfa -r 48c65115abf6 math/R-nimble/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/R-nimble/distinfo    Fri Aug 07 02:59:26 2020 +0000
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2020/08/07 02:59:26 brook Exp $
+
+SHA1 (R/nimble_0.9.0.tar.gz) = 5f6f2cb152d8d065f954d2a4a14886e974744ca1
+RMD160 (R/nimble_0.9.0.tar.gz) = cd1a9df18736370c59c5cddbb305f679f6f89d60
+SHA512 (R/nimble_0.9.0.tar.gz) = a2f3ef100a667bca7d88f2b0410679b18df99c684f89bae3d8a0c71e1a2833c9011a126427404cb9c70d46c6cbb253b72a4ce59d81795f444ea4edded5dbcbab
+Size (R/nimble_0.9.0.tar.gz) = 1949890 bytes