version 0.3.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ibdreg
-Version: 0.3.4
-Date: 2021-8-10
+Version: 0.3.6
+Date: 2021-9-3
 Title: Regression Methods for IBD Linkage with Covariates
 Author: Jason P. Sinnwell and Daniel J. Schaid
 Maintainer: Jason P. Sinnwell <Sinnwell.Jason@mayo.edu>
@@ -12,9 +12,8 @@ License: GPL-2 | file LICENSE
 Depends: R (>= 3.3.1), methods, stats, tools, graphics, utils
 Suggests: R.rsp
 VignetteBuilder: R.rsp
-URL:
-        https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software
+URL: https://analytictools.mayo.edu/research/ibdreg/
 NeedsCompilation: yes
-Packaged: 2021-08-10 16:05:21 UTC; sinnwell
+Packaged: 2021-09-03 14:59:39 UTC; sinnwell
 Repository: CRAN
-Date/Publication: 2021-08-25 13:10:02 UTC
+Date/Publication: 2021-09-05 04:30:14 UTC

MD5

@@ -1,4 +1,4 @@
-9146078a0555eb6e2072252b554a3d7a *DESCRIPTION
+a73a97a1d675ad058184b27911f6daa1 *DESCRIPTION
 27bf59c2a37bff07a78c9730061e532b *LICENSE
 2b6bb93d8b0a6a749787e438983c8c9c *NAMESPACE
 0b39a6da6a13f0d071d97fb8a658a562 *R/Ginv.R
@@ -44,9 +44,9 @@ f9e43bc844bce718e16b3e6e293e7a85 *R/setFounderAlleles.q
 d368405f1c604912f51ba286eed9944a *inst/doc/GPL.txt
 c33dae15f90affda6d4fa5b2d1826e17 *inst/doc/README.ibdreg
 66b775cb01555451bee14ad0f8c316bb *inst/doc/ibdreg.Rnw
-58d884ccbfc1a850bda34f08656c0a40 *inst/doc/ibdreg.pdf
+3ce57127ffe4147b84b781b9b8b55da3 *inst/doc/ibdreg.pdf
 9b988dae227129316fc14ea5cdb67338 *inst/doc/manualIBDReg.pdf.asis
-77e7ddded36ed00a8475b22655318cb9 *inst/doc/manualIBDReg.rnwsave
+6b93a345f0c682d3811bacbe0de50fa4 *inst/doc/manualIBDReg.rnwsave
 8d19e38856d01ad19787c321e8cc5756 *inst/perl/exact.ibd.var.pl
 a31859e2d359ec4aaa7fbbe4958be65c *inst/perl/gws.merlin.ibd.pl
 f3e6a55d104c21d753f1d26f908c099e *inst/perl/merlin.post.ibd.pl
@@ -81,9 +81,9 @@ bd1064ab77455c4db2cc517c0939522d *man/resources.Rd
 cd4a6e156ad0f1de5b9dee18c8af9ee2 *man/sim.ibd.setup.Rd
 3a325f2945486184fb9f883ab8adc5b8 *man/sim.ibd.var.Rd
 d3787f1a945341d6ece9eeb2084c764e *man/sim.mark.prop.Rd
-5aa4ae0ed7d2d8d712403651c9459932 *src/ibdreg_init.c
-aea0e407bb6cc00b412ba99fa952ad12 *src/lsConstrain.c
-859ead8b68f02fcd5528345a44bfc3c8 *src/mcmemory.h
+b3f54b1ca41dcb1a555fb0dea26859fa *src/ibdreg_init.c
+4c952ba4f8096a81a908d1d7a579ea34 *src/lsConstrain.c
+174d441793c4bf686c543b574b5c79ba *src/mcmemory.h
 4e6978e10e4ccc32c2dd7b917fcc3e70 *src/sim.mark.prop.c
 66b775cb01555451bee14ad0f8c316bb *vignettes/ibdreg.Rnw
-226dbbacec45b1c13c69863ac42121fc *vignettes/manualIBDReg.pdf
+813e58d4137006364d90c1f008b240e9 *vignettes/manualIBDReg.pdf

inst/doc/manualIBDReg.rnwsave

@@ -1,13 +1,3 @@
-%$Author: sinnwell $
-%$Date: 2006/11/30 21:52:32 $
-%$Header: /people/biostat3/sinnwell/Projects/IBDReg/Make/RCS/manualIBDReg.Rnw,v 1.2 2006/11/30 21:52:32 sinnwell Exp sinnwell $
-%$Id: manualIBDReg.Rnw,v 1.2 2006/11/30 21:52:32 sinnwell Exp sinnwell $
-%$Locker: sinnwell $
-%$Log: manualIBDReg.Rnw,v $
-%Revision 1.2  2006/11/30 21:52:32  sinnwell
-%for release 0.1.0 in early December
-%
-
 
 %\VignetteIndexEntry{ibdreg}
 %\VignetteKeywords{ibd, linkage, heterogeneity}
@@ -31,9 +21,8 @@
 \newenvironment{Schunk}{}{}
 
 \documentclass[11pt]{article}
-\def\version{version 0.1.2}
-\def\Rversion{version 2.7.1}
-\def\Sversion{version 8.0.1}
+\def\version{version 0.3.6}
+\def\Rversion{version 4.0.3}
 \def\pack{{\sf ibdreg}}
 \def\func{{\sl ibdreg()}}
 \def\Explain{\paragraph{\large {\bf Explanation of Results \vspace{.1in}} \\}}
@@ -92,25 +81,14 @@ excess allele sharing in the direction expected under linkage.
 
 
 \section{Operating System and Installation}
-The \pack\ package \version\ is written for both S-PLUS (\Sversion) and 
-R (\Rversion) for Unix and Windows.  It has been placed on the Comprehensive R 
-Archive Network (CRAN), and is made available on other systems through
-CRAN. Installation procedures for S-PLUS and R systems will vary; the 
-Unix installations are explained in the {\sl README.ibdreg} text file,
-located at the top level of the \pack\ directory.
-
-It is assumed that users have a general working knowledge of the S
-language.  Some of the basic steps in using \pack\ will be confusing
-without a general knowledge of the S language.  Users who are new to S-PLUS 
-or R, please refer to Venebles and Ripley\cite{Venebles Ripley}, and
-introductory guides on the Insightful\cite{Insightful} and 
-R Project\cite{Rhome} home pages.
-
-The procedures for running analyses in \pack\ are the same for S-PLUS and R,
-following instructions in this document.
-
-\section{Installing and Loading the Library}
-To install \pack\ for S-PLUS or R, refer to
+The \pack\ package \version\ is written for R 
+R (\Rversion) and has been placed on the Comprehensive R 
+Archive Network (CRAN), where it is made available on other systems.
+It is assumed that users have a general working knowledge of the R
+language.  
+
+\section{Installing and Loading the Packae}
+To install \pack\, refer to
 instructions given in {\sl README.ibdreg}.  The package may be
 installed for global or local use on your system.  After installing the 
 \pack\ library, the routines are available by starting a session and 
@@ -127,8 +105,8 @@ if(any(objects()=="pairDiff")) rm(pairDiff)
 @
 <<echo=TRUE>>=
 # load the library, load and preview at demo dataset
-library(ibdreg)
-
+library(ibdreg, lib="~/Rlib403")
+sessionInfo()
 @
 
 \section{Data Setup }

src/ibdreg_init.c

@@ -20,7 +20,7 @@ Then add the .registration=TRUE string as second argument to useDynLib() in NAME
 /* .C calls */
 extern void lsConstrain(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 extern void sim_mark_prop_free_mem();
-extern void sim_mark_prop_gen_ped(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern void sim_mark_prop_gen_ped(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 extern void simulate_marker_propagation(void *, void *, void *, void *);
 
 static const R_CMethodDef CEntries[] = {

src/lsConstrain.c

@@ -23,7 +23,7 @@
 #include <math.h>
 #include <string.h>
 #include <R.h> 
-
+#include <R_ext/Error.h>
 #define ulong unsigned
 
 static double **double_vec_to_mat(double *Yvec, ulong nrow, ulong ncol);
@@ -298,6 +298,10 @@ static void errmsg(char *string){
   /* Function to emulate "stop" of S+ - see page 134, S Programing, by
      Venables and Ripley */
 
-   PROBLEM "%s", string RECOVER(NULL_ENTRY);
+  /* PROBLEM "%s", string RECOVER(NULL_ENTRY); 
+     For R 4.1.x and later, use Rf_error from R_ext/Error.h 
+  */
+  Rf_error(string);
+
 }
 

src/mcmemory.h

@@ -2,7 +2,10 @@
 
 #define Salloc(l,s) mc_calloc((l),sizeof(s))
 #define Calloc(l,s) mc_calloc((l),(s))
-#define Free(p) mc_free(p)
+/*
+ #define Free(p) mc_free(p)  
+rename mc_free to just Free so this line not needed, so this not needed  JPS 9/2021
+*/
 
 struct mcMemory
 { void *firstMemory;
@@ -72,9 +75,9 @@ static void *mc_calloc(size_t num, size_t size)
 /*                                                                          */
 /****************************************************************************/
 /****************************************************************************/
-/****************************************************************************/
+/**********9/2021 replace mc_free with just "Free" **************************/
 
-static void mc_free(void *memory2free)
+static void Free(void *memory2free)
 {
   struct mcMemory *previousMemory = NULL;
   struct mcMemory *currentMemory, *oldMemoryEnd;