1. crlmm
  2. src
  3. init.c
Browse code

fix conflict in description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@80947 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/09/2013 14:07:17
Showing 1 changed files
src/init.c
History View file @ ba1a7d7
... ... 
@@ -2,12 +2,17 @@
2 2 
 #include <R_ext/Rdynload.h>
3 3 
 #include "crlmm.h"
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 #include <Rinternals.h>
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-#include <R_ext/Rdynload.h>
6 5
7 6 
 static const R_CallMethodDef CallEntries[] = {
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     {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},
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     {"gtypeCallerPart2", (DL_FUNC)&gtypeCallerPart2, 19},
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     {"normalizeBAF", (DL_FUNC)&normalizeBAF, 2},
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+    {"krlmmComputeM", (DL_FUNC)&krlmmComputeM, 2},
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+    {"krlmmComputeS", (DL_FUNC)&krlmmComputeS, 2},
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+    {"readGenCallOutputCFunc", (DL_FUNC)&readGenCallOutputCFunc, 8},
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+    {"krlmmConfidenceScore", (DL_FUNC)&krlmmConfidenceScore, 2},
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+    {"krlmmHardyweinberg", (DL_FUNC)&krlmmHardyweinberg, 1},
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+    {"countFileLines", (DL_FUNC)&countFileLines, 1},
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     {NULL, NULL, 0}
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 };
13 18
... ... 
@@ -15,7 +20,6 @@ void R_init_crlmm(DllInfo *dll){
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     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
16 21 
 }
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-
19 23 
 SEXP subColSummarizeMedianPP(SEXP RMatrix, SEXP R_rowIndexList){
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   static SEXP(*fun)(SEXP, SEXP) = NULL;
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   if (fun == NULL)
Browse code

merge with collab branch containing fix for dqrls and bug-fix for computeRBaf that can misalign sample index with batch index (when batch is not in alphabetical order)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71295 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/11/2012 15:24:46
Showing 1 changed files
src/init.c
History View file @ a3b625d
... ... 
@@ -1,6 +1,8 @@
1 1 
 #include <R.h>
2 2 
 #include <R_ext/Rdynload.h>
3 3 
 #include "crlmm.h"
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+#include <Rinternals.h>
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+#include <R_ext/Rdynload.h>
4 6
5 7 
 static const R_CallMethodDef CallEntries[] = {
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     {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},
... ... 
@@ -12,3 +14,11 @@ static const R_CallMethodDef CallEntries[] = {
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 void R_init_crlmm(DllInfo *dll){
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     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
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 }
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+
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+
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+SEXP subColSummarizeMedianPP(SEXP RMatrix, SEXP R_rowIndexList){
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+  static SEXP(*fun)(SEXP, SEXP) = NULL;
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+  if (fun == NULL)
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+    fun =  (SEXP(*)(SEXP, SEXP))R_GetCCallable("preprocessCore","R_subColSummarize_median");
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+  return fun(RMatrix, R_rowIndexList);
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+}
Browse code

crlmm on github

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58751 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:11:02
Showing 1 changed files
src/init.c
History View file @ af08b5d
... ... 
@@ -10,5 +10,5 @@ static const R_CallMethodDef CallEntries[] = {
10 10 
 };
11 11
12 12 
 void R_init_crlmm(DllInfo *dll){
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-    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
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+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
14 14 
 }
Browse code

bringing changes from GitHub; from now on, keeping code on BioC servers

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58710 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/10/2011 18:12:55
Showing 1 changed files
src/init.c
History View file @ b6f0c38
... ... 
@@ -5,6 +5,7 @@
5 5 
 static const R_CallMethodDef CallEntries[] = {
6 6 
     {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},
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     {"gtypeCallerPart2", (DL_FUNC)&gtypeCallerPart2, 19},
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+    {"normalizeBAF", (DL_FUNC)&normalizeBAF, 2},
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     {NULL, NULL, 0}
9 10 
 };
10 11
Browse code

Fixes on C code and dependencies on oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43012 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/11/2009 12:54:26
Showing 1 changed files
src/init.c
History View file @ 8bbb1b1
... ... 
@@ -3,20 +3,11 @@
3 3 
 #include "crlmm.h"
4 4
5 5 
 static const R_CallMethodDef CallEntries[] = {
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-    {"test", (DL_FUNC)&test, 1},
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-    {"gtypeCallerPart1nm", (DL_FUNC)&gtypeCallerPart1nm, 17},
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-    {"gtypeCallerPart2nm", (DL_FUNC)&gtypeCallerPart2nm, 19},
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-    {"gtypeCallerPart1NormalNoN", (DL_FUNC)&gtypeCallerPart1NormalNoN, 17},
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     {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},
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     {"gtypeCallerPart2", (DL_FUNC)&gtypeCallerPart2, 19},
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-    {"gtypeCallerPart1TNoN", (DL_FUNC)&gtypeCallerPart1TNoN, 17},
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-    {"gtypeCallerPart2TNoN", (DL_FUNC)&gtypeCallerPart2TNoN, 19},
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     {NULL, NULL, 0}
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 };
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17 11 
 void R_init_crlmm(DllInfo *dll){
18 12 
     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
19 13 
 }
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-
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-
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-
Browse code

Fixing registration of C functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@36711 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/01/2009 12:52:10
Showing 1 changed files
src/init.c
History View file @ a0b9555
... ... 
@@ -14,8 +14,7 @@ static const R_CallMethodDef CallEntries[] = {
14 14 
     {NULL, NULL, 0}
15 15 
 };
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-void R_init_crlmm(DllInfo *dll)
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-{
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+void R_init_crlmm(DllInfo *dll){
19 18 
     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
20 19 
 }
21 20
Browse code

edited the registration fucntion

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@36699 bc3139a8-67e5-0310-9ffc-ced21a209358

Nishant Gopalakrishnan authored on 16/01/2009 01:00:38
Showing 1 changed files
src/init.c
History View file @ 250a167
... ... 
@@ -14,7 +14,7 @@ static const R_CallMethodDef CallEntries[] = {
14 14 
     {NULL, NULL, 0}
15 15 
 };
16 16
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-void R_init_flowCore(DllInfo *dll)
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+void R_init_crlmm(DllInfo *dll)
18 18 
 {
19 19 
     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
20 20 
 }
Browse code

Added registration for C functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@36696 bc3139a8-67e5-0310-9ffc-ced21a209358

Nishant Gopalakrishnan authored on 16/01/2009 00:50:49
Showing 1 changed files
src/init.c
History View file @ 0710eb7
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,23 @@
1 
+#include <R.h>
2 
+#include <R_ext/Rdynload.h>
3 
+#include "crlmm.h"
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+
5 
+static const R_CallMethodDef CallEntries[] = {
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+    {"test", (DL_FUNC)&test, 1},
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+    {"gtypeCallerPart1nm", (DL_FUNC)&gtypeCallerPart1nm, 17},
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+    {"gtypeCallerPart2nm", (DL_FUNC)&gtypeCallerPart2nm, 19},
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+    {"gtypeCallerPart1NormalNoN", (DL_FUNC)&gtypeCallerPart1NormalNoN, 17},
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+    {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},
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+    {"gtypeCallerPart2", (DL_FUNC)&gtypeCallerPart2, 19},
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+    {"gtypeCallerPart1TNoN", (DL_FUNC)&gtypeCallerPart1TNoN, 17},
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+    {"gtypeCallerPart2TNoN", (DL_FUNC)&gtypeCallerPart2TNoN, 19},
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+    {NULL, NULL, 0}
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+};
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+
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+void R_init_flowCore(DllInfo *dll)
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+{
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+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
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+}
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+
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+
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+