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applied patch to allow msa to work with the new Windows UCRT toolchain; version number bumped to 1.27.2

UBod authored on 21/03/2022 12:58:40
Showing4 changed files

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@@ -1,8 +1,8 @@
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 Package: msa
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 Type: Package
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 Title: Multiple Sequence Alignment
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-Version: 1.27.1
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-Date: 2022-02-17
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+Version: 1.27.2
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+Date: 2022-03-21
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 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
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 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
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 Description: The 'msa' package provides a unified R/Bioconductor interface to
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@@ -1,6 +1,9 @@
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 Change history of package msa:
2 2
 ==============================
3 3
 
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+Version 1.27.2:
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+- applied patch to allow msa to work with the new Windows UCRT toolchain
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+
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 Version 1.27.1:
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 - workaround for problems running texi2dvi() on R 4.2.0; those occurred 
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   during package checks when running some examples and the vignette code
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@@ -32,7 +32,7 @@ USA.
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 #include <limits.h>
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 /* local error codes */
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-enum {EMINCOUNT=1,EMAXCOUNT,EBADINT,EOVERFLOW};
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+enum {EMINCOUNT=1,EMAXCOUNT,EBADINT,CO_EOVERFLOW};
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 static void resetfn(struct arg_int *parent)
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     {
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@@ -187,28 +187,28 @@ static int scanfn(struct arg_int *parent, const char *argval)
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         /* Safety check for integer overflow. WARNING: this check    */
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         /* achieves nothing on machines where size(int)==size(long). */
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         if ( val>INT_MAX || val<INT_MIN )
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-            errorcode = EOVERFLOW;
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+            errorcode = CO_EOVERFLOW;
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         /* Detect any suffixes (KB,MB,GB) and multiply argument value appropriately. */
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         /* We need to be mindful of integer overflows when using such big numbers.   */
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         if (detectsuffix(end,"KB"))             /* kilobytes */
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             {
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             if ( val>(INT_MAX/1024) || val<(INT_MIN/1024) )
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-                errorcode = EOVERFLOW;          /* Overflow would occur if we proceed */
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+                errorcode = CO_EOVERFLOW;          /* Overflow would occur if we proceed */
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             else
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                 val*=1024;                      /* 1KB = 1024 */
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             }
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         else if (detectsuffix(end,"MB"))        /* megabytes */
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             {
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             if ( val>(INT_MAX/1048576) || val<(INT_MIN/1048576) )
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-                errorcode = EOVERFLOW;          /* Overflow would occur if we proceed */
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+                errorcode = CO_EOVERFLOW;          /* Overflow would occur if we proceed */
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             else
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                 val*=1048576;                   /* 1MB = 1024*1024 */
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             }
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         else if (detectsuffix(end,"GB"))        /* gigabytes */
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             {
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             if ( val>(INT_MAX/1073741824) || val<(INT_MIN/1073741824) )
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-                errorcode = EOVERFLOW;          /* Overflow would occur if we proceed */
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+                errorcode = CO_EOVERFLOW;          /* Overflow would occur if we proceed */
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             else
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                 val*=1073741824;                /* 1GB = 1024*1024*1024 */
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             }
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@@ -258,7 +258,7 @@ static void errorfn(struct arg_int *parent, FILE *fp, int errorcode, const char
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             arg_print_option(fp,shortopts,longopts,datatype,"\n");
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             break;
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-        case EOVERFLOW:
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+        case CO_EOVERFLOW:
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             fputs("integer overflow at option ",fp);
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             arg_print_option(fp,shortopts,longopts,datatype," ");
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             fprintf(fp,"(%s is too large)\n",argval);
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@@ -9,8 +9,8 @@ all: gc72
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 gc72:
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 	export PKG_LIBS="$(PKG_LIBS) -I$(AO_INCLUDE_DIR) -I$(INCLUDE_DIR) -I$(PRIVATE_INCLUDE_DIR)"; \
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-	export PKG_CFLAGS="$(PKG_CFLAGS) -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I$(AO_INCLUDE_DIR) -I$(INCLUDE_DIR) -I$(PRIVATE_INCLUDE_DIR)"; \
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I$(AO_INCLUDE_DIR) -I$(INCLUDE_DIR) -I$(PRIVATE_INCLUDE_DIR)"; \
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+	export PKG_CFLAGS="-fcommon $(PKG_CFLAGS) -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I$(AO_INCLUDE_DIR) -I$(INCLUDE_DIR) -I$(PRIVATE_INCLUDE_DIR)"; \
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+	export PKG_CXXFLAGS="-fcommon $(PKG_CXXFLAGS) -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I$(AO_INCLUDE_DIR) -I$(INCLUDE_DIR) -I$(PRIVATE_INCLUDE_DIR)"; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o gc7612.dll *.c; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o gccpp7612.dll -L. -lgc72 *.cpp; \
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 	$(AR) rcs libGC.a $(OBJNamesGC); \