[Seqinr-commits] r2027 - in pkg: . src

[noreply at r-forge.r-project.org]

Author: simonpenel
Date: 2017-04-03 09:40:18 +0200 (Mon, 03 Apr 2017)
New Revision: 2027

Added:
   pkg/src/packagename_init.c
Modified:
   pkg/DESCRIPTION
   pkg/NAMESPACE
Log:
Addition of packagename_init.c and modifications for registered routines

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2016-10-14 16:34:27 UTC (rev 2026)
+++ pkg/DESCRIPTION	2017-04-03 07:40:18 UTC (rev 2027)
@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Package: seqinr
 Version: 3.3-4
-Date: 2016-10-14
+Date: 2017-03-31
 Title: Biological Sequences Retrieval and Analysis
 Authors at R: c(person("Delphine", "Charif", role = "aut"),
              person("Olivier", "Clerc", role = "ctb"),
@@ -23,3 +23,9 @@
 SystemRequirements: zlib headers and library.
 URL: http://seqinr.r-forge.r-project.org/
 NeedsCompilation: yes
+Repository: CRAN
+Repository/R-Forge/Project: seqinr
+Repository/R-Forge/Revision: 2020
+Repository/R-Forge/DateTimeStamp: 2016-10-12 17:32:34
+Date/Publication: 2016-10-13 20:37:21
+Packaged: 2016-10-12 17:45:23 UTC; rforge

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2016-10-14 16:34:27 UTC (rev 2026)
+++ pkg/NAMESPACE	2017-04-03 07:40:18 UTC (rev 2027)
@@ -1,6 +1,6 @@
 # Export all names
-useDynLib(seqinr, .registration = TRUE)
-exportPattern(".")
+useDynLib(seqinr, .registration = TRUE,.fixes = "C_")
+exportPattern("^[^C_]")
 importFrom("ade4", "dudi.coa")
 importFrom("grDevices", "col2rgb", "grey", "rainbow", "rgb")
 importFrom("graphics", "abline", "axis", "box", "dotchart", "hist",

Added: pkg/src/packagename_init.c
===================================================================
--- pkg/src/packagename_init.c	                        (rev 0)
+++ pkg/src/packagename_init.c	2017-04-03 07:40:18 UTC (rev 2027)
@@ -0,0 +1,43 @@
+#include <R.h>
+#include <Rinternals.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* FIXME: 
+   Check these declarations against the C/Fortran source code.
+*/
+
+/* .Call calls */
+extern SEXP distance(SEXP, SEXP, SEXP, SEXP, SEXP);
+extern SEXP fastacc(SEXP, SEXP, SEXP, SEXP, SEXP);
+extern SEXP getzlibsock(SEXP, SEXP, SEXP);
+extern SEXP is_a_protein_seq(SEXP);
+extern SEXP kaks(SEXP, SEXP, SEXP);
+extern SEXP read_clustal_align(SEXP);
+extern SEXP read_fasta_align(SEXP);
+extern SEXP read_mase(SEXP);
+extern SEXP read_msf_align(SEXP);
+extern SEXP read_phylip_align(SEXP);
+extern SEXP s2c(SEXP);
+
+static const R_CallMethodDef CallEntries[] = {
+    {"distance",           (DL_FUNC) &distance,           5},
+    {"fastacc",            (DL_FUNC) &fastacc,            5},
+    {"getzlibsock",        (DL_FUNC) &getzlibsock,        3},
+    {"is_a_protein_seq",   (DL_FUNC) &is_a_protein_seq,   1},
+    {"kaks",               (DL_FUNC) &kaks,               3},
+    {"read_clustal_align", (DL_FUNC) &read_clustal_align, 1},
+    {"read_fasta_align",   (DL_FUNC) &read_fasta_align,   1},
+    {"read_mase",          (DL_FUNC) &read_mase,          1},
+    {"read_msf_align",     (DL_FUNC) &read_msf_align,     1},
+    {"read_phylip_align",  (DL_FUNC) &read_phylip_align,  1},
+    {"s2c",                (DL_FUNC) &s2c,                1},
+    {NULL, NULL, 0}
+};
+
+void R_init_seqinr(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}
+