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Various fixes related to Windows build; version number bumped to 1.17.1

UBodenhofer authored on 12/09/2019 07:42:34
Showing7 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: 1.17.0
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-Date: 2018-04-27
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+Version: 1.17.1
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+Date: 2019-09-12
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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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@@ -215,7 +215,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
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         jobname <- substr(file, 1, nchar(file) - 4)
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-        if (length(grep("[^\\w-/\\\\:.]", jobname, perl=TRUE)) > 0)
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+        if (length(grep("[^\\w\\-/\\\\:.]", jobname, perl=TRUE)) > 0)
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         {
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             warning("Cannot use file name '", file,
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                     "' because it contains invalid characters => \n",
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@@ -88,5 +88,8 @@ rm -rf src/ClustalOmega/src/argtable2/*.la
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 rm -rf src/ClustalOmega/src/argtable2/*.o
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 rm -rf src/ClustalOmega/src/argtable2/*.lo
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 rm -rf src/ClustalOmega/src/argtable2/Makefile
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+rm -rf src/ClustalOmega/src/exceptions4c/*.la
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+rm -rf src/ClustalOmega/src/exceptions4c/*.o
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+rm -rf src/ClustalOmega/src/exceptions4c/*.lo
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 rm -rf src/ClustalOmega/src/*.dll
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 rm -rf src/ClustalOmega/src/*.a
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@@ -1,6 +1,30 @@
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 Change history of package msa:
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 ==============================
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+Version 1.18.0:
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+- release as part of Bioconductor 3.10
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+
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+Version 1.7.1:
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+- fixed regular expression to comply with PCRE2
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+- fixed Windows makefile for gc lib
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+- fixed Windows cleanup script
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+- fixed src/Makevars.win
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+
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+Version 1.17.0:
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+- new branch for Bioconductor 3.10 devel
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+
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+Version 1.16.0:
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+- release as part of Bioconductor 3.9
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+
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+Version 1.15.0:
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+- new branch for Bioconductor 3.9 devel
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+
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+Version 1.14.0:
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+- release as part of Bioconductor 3.8
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+
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+Version 1.13.0:
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+- new branch for Bioconductor 3.8 devel
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+
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 Version 1.12.0:
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 - release as part of Bioconductor 3.7
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@@ -12,7 +12,7 @@ clean:
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 	cd src
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 ./libGC.a:
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-	make --file=msaMakefile.win --directory=gc-7.2
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+	make --file=msaMakefile.win --directory=gc-7.2 AR="$(AR)"
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 	@echo "----------------------------------------"
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 	@echo "------------------ GC  -----------------"
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 	@echo "----------------------------------------"
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@@ -20,7 +20,7 @@ clean:
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 	@echo "----------------------------------------"
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 ./libMuscle.a:
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-	make --file=msaMakefile.win --directory=Muscle
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+	make --file=msaMakefile.win --directory=Muscle AR="$(AR)"
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 	@echo "----------------------------------------"
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 	@echo "---------------- MUSCLE ----------------"
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 	@echo "----------------------------------------"
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@@ -28,7 +28,7 @@ clean:
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 	@echo "----------------------------------------"
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 ./libClustalW.a:
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-	make --file=msaMakefile.win --directory=ClustalW
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+	make --file=msaMakefile.win --directory=ClustalW AR="$(AR)"
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 	@echo "----------------------------------------"
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 	@echo "--------------- ClustalW ---------------"
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 	@echo "----------------------------------------"
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@@ -36,7 +36,7 @@ clean:
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 	@echo "----------------------------------------"
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 ./libClustalOmega.a:
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-	make --file=msaMakefile.win --directory=ClustalOmega
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+	make --file=msaMakefile.win --directory=ClustalOmega AR="$(AR)"
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 	@echo "----------------------------------------"
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 	@echo "------------- ClustalOmega -------------"
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 	@echo "----------------------------------------"
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@@ -13,6 +13,6 @@ gc72:
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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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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o gc72.dll *.c; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o gccpp72.dll -L. -lgc72 *.cpp; \
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-	ar rcs libGC.a $(OBJNamesGC); \
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-	ar rcs libGCcpp.a $(OBJNamesGCCPP); \
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+	$(AR) rcs libGC.a $(OBJNamesGC); \
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+	$(AR) rcs libGCcpp.a $(OBJNamesGCCPP); \
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 	cp libGC*.a ../
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@@ -890,6 +890,18 @@ bibliography below).
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 \section{Change Log}
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 \begin{description}
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+\item[Version 1.18.0:] release as part of Bioconductor 3.10
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+\item[Version 1.17.1:] \mbox{ }  \begin{itemize}
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+   \item fixed regular expression to comply with PCRE2
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+   \item fixed Windows makefile for gc lib
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+   \item fixed Windows cleanup script
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+   \item fixed\verb+ src/Makevars.win+
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+  \end{itemize}
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+\item[Version 1.17.0:] new branch for Bioconductor 3.10 devel
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+\item[Version 1.16.0:] release as part of Bioconductor 3.9
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+\item[Version 1.15.0:] new branch for Bioconductor 3.9 devel
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+\item[Version 1.14.0:] release as part of Bioconductor 3.8
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+\item[Version 1.13.0:] new branch for Bioconductor 3.8 devel
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 \item[Version 1.12.0:] release as part of Bioconductor 3.7
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 \item[Version 1.11.2:] \mbox{ }  \begin{itemize}
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    \item minor fix in ClustalW