version 0.2.5

cran · Apr 16, 2013 · a2fb963 · a2fb963
1 parent e31a53c
commit a2fb963
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ibdreg
-Version: 0.2.2
-Date: 2013-1-4
+Version: 0.2.5
+Date: 2013-4-16
 Title: Regression Methods for IBD Linkage With Covariates
 Author: Jason P. Sinnwell and Daniel J. Schaid
 Maintainer: Jason P. Sinnwell <Sinnwell.Jason@mayo.edu>
@@ -11,6 +11,7 @@ Description: A method to test genetic linkage with covariates by
 License: GPL-2 | file LICENSE
 Depends: R (>= 2.15.0)
 URL: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
-Packaged: 2013-01-04 22:26:31 UTC; sinnwell
+Packaged: 2013-04-19 20:17:37 UTC; sinnwell
+NeedsCompilation: yes
 Repository: CRAN
-Date/Publication: 2013-01-05 08:26:41
+Date/Publication: 2013-04-20 07:47:38
diff --git a/MD5 b/MD5
@@ -1,12 +1,12 @@
-d95247bdaf32ba61a4e6c90096371e7b *DESCRIPTION
+6b1074e1b9b09626bcd5f3383d149644 *DESCRIPTION
 27bf59c2a37bff07a78c9730061e532b *LICENSE
 6a1d7de4f64a74e51469d619b05e30bc *NAMESPACE
 3c3314613f983d73f7a4e47e79fd51ca *R/Ginv.R
 da00d790b86e88df9a7441c2fd0186bd *R/align.ibd.var.q
 3ba56b64c55320241d1bd370716152c7 *R/chibar3.w.q
 9cb27ea687f6acf0cd2db4e1dad8881e *R/create.ibd.dat.q
 7857ef210b764d1f08c96b5494ce3b83 *R/create.pairs.frame.cvec.q
-3d27060f9fb360088bcde3f0b222d312 *R/create.pairs.frame.q
+5263c5bd73393e2b7075bb049c0cadda *R/create.pairs.frame.q
 e4afcf095b0b01fddb493cd8bf084a30 *R/exact.ibd.var.q
 bb31c0158c648095b7134d4244ac7bc7 *R/ibd.df.merlin.q
 15ea877d29d5723e8cffd68ee9520b47 *R/ibd.moments.q
@@ -32,7 +32,7 @@ e55e09fb4e4b5ccb8f2931fbd85fc485 *R/print.ibdreg.q
 8e172c0e2d0ee3d4a8dedea462d1306e *R/print.linkage.all.q
 087ed7433315a6c7000c452697fbc4fe *R/print.linkage.tests.q
 ac041fc616815527ef260c22d8cdd77a *R/printBanner.q
-033dc9145bafbe2d1cf690c04e40ccf8 *R/resources.q
+974a07ed1259765abfcdf0215443f7c4 *R/resources.q
 f9e43bc844bce718e16b3e6e293e7a85 *R/setFounderAlleles.q
 447b635fa0ca8b7066a0f4862cade7a1 *R/sim.ibd.setup.q
 88d503e80aaa027a81f6bcca016953f0 *R/sim.ibd.var.q
@@ -76,5 +76,5 @@ a31859e2d359ec4aaa7fbbe4958be65c *perl/gws.merlin.ibd.pl
 f3e6a55d104c21d753f1d26f908c099e *perl/merlin.post.ibd.pl
 1b2fd16a99e3a0bcf0ced3b6b8ef9809 *perl/merlin.prior.ibd.pl
 253cdd482b07d5e640b59364a304b9c0 *src/lsConstrain.c
-ed1cacad8ae54f70022e0bb89386b8cb *src/mcmemory.h
-e9fcdae4746f5aa441276588921aa17c *src/sim.mark.prop.c
+46b60d79a180c4b8a31b21d5ab3cba8c *src/mcmemory.h
+c37ce6b54c404bbe74391ba6d2ec5ca3 *src/sim.mark.prop.c
diff --git a/R/create.pairs.frame.q b/R/create.pairs.frame.q
@@ -99,8 +99,9 @@ create.pairs.frame <- function(ibd.dat,
   if(length(formula.terms)) {
     for(term in formula.terms) {
 
-      # split up the term by an open paren '(', use S::unpaste R::strsplit
-      split.term <- strsplit(term, split='(')
+      ## split up the term by an open paren '(', use S::unpaste R::strsplit
+      ## fixed=TRUE suggested 3/2013 by Claire Simpson
+      split.term <- strsplit(term, split='(',fixed=TRUE)
 
       # extract the function name to apply to the covariate pair
       fname <- split.term[[1]][1]

diff --git a/R/resources.q b/R/resources.q
@@ -29,21 +29,22 @@ resources <- function(expr, doPrint=TRUE) {
 #   systemtimech - System elapsed times in child processes.
 #   mem - maximum memory allocated by the process
 
-  loc <- sys.parent(1)
-  if(loc == 1) loc <- FALSE
+
+
+  #loc <- sys.parent(1)
+  #if(loc == 1) loc <- FALSE
   on.exit(cat("Timing stopped at:", proc.time() - time, "\n"))
   expr <- substitute(expr)
   stime <- proc.time()
-
+  
   mem1 <- gc(reset=TRUE)
-  w <- eval(expr, envir=loc)
- 
+  w <- eval(expr)#, envir=loc) 
+
   etime <- proc.time()
 
   mem2=gc(reset=TRUE)
   mem <- data.frame(mem2[2,1]-mem1[2,1])
   names(mem) <- "Vcells"
-
 
   on.exit()
 
@@ -62,3 +63,5 @@ resources <- function(expr, doPrint=TRUE) {
   invisible(df)
 
 }
+
+
diff --git a/src/mcmemory.h b/src/mcmemory.h
@@ -5,7 +5,7 @@
 #define Calloc(l,s) mc_calloc((l),(s))
 #define Free(p) mc_free(p)
 
-static struct mcMemory
+struct mcMemory
 { void *firstMemory;
   struct mcMemory  *nextMemory;
 };
@@ -348,7 +348,7 @@ static void *mc_malloc_local(size_t size,
     }
 }
 
-static long mc_free_local(void *memory2free,
+static void mc_free_local(void *memory2free,
                           struct mcMemory **memoryStart, 
                           struct mcMemory **memoryEnd)
 {

diff --git a/src/sim.mark.prop.c b/src/sim.mark.prop.c
@@ -41,7 +41,7 @@ struct pedigreeData *pedData = NULL;
 
 /* Represents a person in a generated pedigree                                */
 
-static struct person
+struct person
 { struct marriage  *parents;              /* Parents' marriage node           */
   struct marriage  *nuclearFamily;        /* Person's first marriage node     */
   long              sex;		  /* M or F depending on sex          */
@@ -54,7 +54,7 @@ static struct person
 
 /* Represents a marriage in a generated pedigree                              */
 
-static struct marriage
+struct marriage
 { struct person    *husband;	          /* Husband in this marriage         */
   struct person    *wife;                 /* Wife in this marriage	      */
   struct children  *child;                /* Children from this marriage      */
@@ -64,14 +64,14 @@ static struct marriage
 
 /* Represents a linked list of children in a marriage                         */
 
-static struct children
+struct children
 { struct person    *firstChild;		  /* First child		      */
   struct children  *nextChild;		  /* Next child			      */
 };
 
 /* Represents a pedigree                                                      */
 
-static struct pedigree
+struct pedigree
 { struct person    *proband;              /* Proband of the pedigree          */
   long              n;                    /* Number of people in the pedigree */
   struct person   **personNodes;          /* People in the pedigree           */
@@ -80,7 +80,7 @@ static struct pedigree
 /* Represents a conglomeration of all the data required/generated for a       */
 /* pedigree                                                                   */
 
-static struct pedigreeData
+struct pedigreeData
 { long     *father;                  /* Father ID's                           */
   long     *mother;		     /* Mother ID's                           */
   long     *person;                  /* Person ID's                           */