CVS commit: pkgsrc/math

["Brook Milligan" <brook%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   brook
Date:           Fri Aug  7 02:59:26 UTC 2020

Modified Files:
        pkgsrc/math: Makefile
Added Files:
        pkgsrc/math/R-nimble: DESCR Makefile distinfo

Log Message:
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>.


To generate a diff of this commit:
cvs rdiff -u -r1.473 -r1.474 pkgsrc/math/Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/math/R-nimble/DESCR \
    pkgsrc/math/R-nimble/Makefile pkgsrc/math/R-nimble/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/Makefile
diff -u pkgsrc/math/Makefile:1.473 pkgsrc/math/Makefile:1.474
--- pkgsrc/math/Makefile:1.473  Fri Aug  7 02:52:56 2020
+++ pkgsrc/math/Makefile        Fri Aug  7 02:59:26 2020
@@ -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-moonsun
 SUBDIR+=       R-mvtnorm
 SUBDIR+=       R-ncdf
 SUBDIR+=       R-nloptr
+SUBDIR+=       R-nimble
 SUBDIR+=       R-nortest
 SUBDIR+=       R-numDeriv
 SUBDIR+=       R-pbkrtest

Added files:

Index: pkgsrc/math/R-nimble/DESCR
diff -u /dev/null pkgsrc/math/R-nimble/DESCR:1.1
--- /dev/null   Fri Aug  7 02:59:26 2020
+++ pkgsrc/math/R-nimble/DESCR  Fri Aug  7 02:59:26 2020
@@ -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>.
Index: pkgsrc/math/R-nimble/Makefile
diff -u /dev/null pkgsrc/math/R-nimble/Makefile:1.1
--- /dev/null   Fri Aug  7 02:59:26 2020
+++ pkgsrc/math/R-nimble/Makefile       Fri Aug  7 02:59:26 2020
@@ -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"
Index: pkgsrc/math/R-nimble/distinfo
diff -u /dev/null pkgsrc/math/R-nimble/distinfo:1.1
--- /dev/null   Fri Aug  7 02:59:26 2020
+++ pkgsrc/math/R-nimble/distinfo       Fri Aug  7 02:59:26 2020
@@ -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