@@ -1,8 +1,8 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.3.1

-Date: 2015-10-13

+Version: 1.3.2

+Date: 2015-12-21

 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer

 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

 Description: This package provides a unified R/Bioconductor interface to the

@@ -21,7 +21,7 @@ Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),

         S4Vectors, tools

 Suggests: Biobase, knitr

 LinkingTo: Rcpp

-SystemRequirements:

+SystemRequirements: GNU make

 VignetteBuilder: knitr

 LazyLoad: yes

 Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R

@@ -31,4 +31,3 @@ Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R

 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,

         Sequencing

 NeedsCompilation: yes

-Packaged: 2015-10-07 16:20:45 UTC; bodenhof

@@ -8,13 +8,15 @@ citEntry(entry="Article",

                              as.person("Christoph Horejs-Kainrath"),

                              as.person("Sepp Hochreiter")),

          journal="Bioinformatics",

-         note="(accepted)",

+         volume="31",

+         number="24",

+         pages="3997--3999",

          year="2015",

          doi="10.1093/bioinformatics/btv494",

          textVersion =

              paste("U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015)",

                    "msa: an R package for multiple sequence alignment.",

-                   "Bioinformatics (accepted).",

+                   "Bioinformatics 31(24):3997-9999.",

                    "DOI: 10.1093/bioinformatics/btv176.")

 )

@@ -1,8 +1,16 @@

 Change history of package msa:

 ==============================

-Version 1.2.0:

-- new branch for Bioconductor 3.2 release

+Version 1.3.2:

+- further fixes in Makefiles and Makevars files to account for changes

+  in build system

+- update of citation information

+

+Version 1.3.1:

+- fixes in Makefiles and Makevars files to account for changes in build system

+

+Version 1.3.0:

+- new branch for Bioconductor 3.3 devel

 Version 1.1.3: 

 - bug fix related to custom substitution matrices in the MUSCLE interface

@@ -42,7 +42,7 @@ The following slots are defined for \code{MsaMetaData} objects:

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},

@@ -114,7 +114,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},

@@ -30,7 +30,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)

@@ -134,7 +134,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.clustal.org/download/clustalw_help.txt}

@@ -82,7 +82,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.clustal.org/omega/README}

@@ -84,7 +84,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.clustal.org/download/clustalw_help.txt}

@@ -91,7 +91,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.drive5.com/muscle/muscle.html}

@@ -192,7 +192,7 @@

   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

   (2015). msa: an R package for multiple sequence alignment. 

-  \emph{Bioinformatics} (accepted). DOI:

+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:

   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{https://www.ctan.org/pkg/texshade}

@@ -1,5 +1,5 @@

 ## Variant 1: deactivate OpenMP on Mac Platforms

-CONFIGURE_FLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`

+CONFIGURE_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`

 ## Variant 2: deactivate OpenMP generally

 #CONFIGURE_FLAGS=--without-openmp 

 ## Variant 3: let the configure script determine whether OpenMP is available

@@ -44,9 +44,9 @@ all: clustalomega

 clustalomega:

 	./configure $(CONFIGURE_FLAGS); \

 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \

-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \

-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \

+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \

+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \

 	cd src; \

-	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalOmega.so $(CPPNames) && \

+	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \

 	ar rcs libClustalOmega.a $(OBJNames) && \

 	cp libClustalOmega.a ../../

@@ -38,8 +38,8 @@ clustalomega:

 	cp windows/src/config.h src/; \

 	cp windows/src/clustal-omega-config.h src/; \

 	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.2" -lgccpp72 -lgc72"; \

-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \

-	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" -lgccpp -lgc `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \

+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \

+	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \

 	cd src; \

 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o ClustalOmega.dll $(CPPNames) && \

 	$(AR) rcs libClustalOmega.a $(OBJNames) && \

@@ -7,7 +7,7 @@ all: clustalw

 clustalw:

 	./configure; \

 	cd src; \

-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \

-	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalW.so $(CPPNames) && \

+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \

+	${R_HOME}/bin/R CMD SHLIB -o libClustalW.so $(CPPNames) && \

 	ar rcs libClustalW.a $(OBJNames) && \

 	cp libClustalW.a ../../

@@ -11,7 +11,7 @@ clustalw:

 	cp windows/src/clustalw_version.h src/; \

 	cp windows/src/config.h src/; \

 	cd src; \

-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \

+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \

 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o ClustalW.dll $(CPPNames) &&\

 	$(AR) rcs libClustalW.a $(OBJNames) && \

 	cp libClustalW.a ../../

@@ -1,5 +1,5 @@

-PKG_LIBS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive')"`

-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`

+PKG_LIBS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive')"`

+PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"

 .PHONY: all mylibs

@@ -1,7 +1,7 @@

 .PHONY: all ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a

 PKG_LIBS=-Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive

-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`

+PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"

 all: $(SHLIB)

 $(SHLIB): ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a

@@ -5,7 +5,7 @@ OBJNames = aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o al

 all: muscle

 muscle:

-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I"../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"

-	"${R_HOME}/bin/R" CMD SHLIB -o libMuscle.so $(CPPNames)

+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I../gc-7.2/include"

+	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libMuscle.so $(CPPNames)

 	ar rcs libMuscle.a $(OBJNames)

 	cp libMuscle.a ../

@@ -6,7 +6,7 @@ all: muscle

 muscle:

 	export PKG_LIBS="$(PKG_LIBS) -L"../gc-7.2/" -lgc72 -lgccpp72"

-	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I"../gc-7.2/include/" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::CxxFlags()"`"

-	"${R_HOME}/bin${R_ARCH_BIN}/R.exe" CMD SHLIB -o Muscle.dll $(CPPNames)

+	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I../gc-7.2/include/"

+	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o Muscle.dll $(CPPNames)

 	$(AR) rcs libMuscle.a $(OBJNames)

 	cp libMuscle.a ../

@@ -9,8 +9,8 @@ all: gc72

 gc72:

 	export PKG_LIBS="$(PKG_LIBS) -I$(AO_INCLUDE_DIR) -I$(INCLUDE_DIR) -I$(PRIVATE_INCLUDE_DIR)"; \

-	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) `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \

-	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) `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \

+	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)"; \

+	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)"; \

 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o gc72.dll *.c; \

 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o gccpp72.dll -L. -lgc72 *.cpp; \

 	ar rcs libGC.a $(OBJNamesGC); \

@@ -699,8 +699,9 @@ We envision the following changes/extensions in future versions of the package:

 If you use this package for research that is published later, you are kindly

 asked to cite it as follows:

 \begin{quotation}

-\noindent E.~Bonatesta, C.~Horejs-Kainrath, and U.~Bodenhofer, (2015).

-msa: An R Package for Multiple Sequence Alignment.

+\noindent U.~Bodenhofer, E.~Bonatesta, C.~Horej\v{s}-Kainrath, and S.~Hochreiter (2015).

+msa: an R package for multiple sequence alignment. {\em Bioinformatics} {\bf 31}(24):3997--3999.

+DOI: \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{bioinformatics/btv494}.

 \end{quotation}

 To obtain a Bib\TeX\ entries of the reference, enter the

 following into your R session:

@@ -715,8 +716,15 @@ bibliography below).

 \section{Change Log}

 \begin{description}

-\item[Version 1.2.0:] \mbox{ }  \begin{itemize}

-    \item new branch for Bioconductor 3.2 release

+\item[Version 1.3.2:] \mbox{ }  \begin{itemize}

+   \item further fixes in Makefiles and Makevars files to account for changes in build system

+   \item update of citation information

+  \end{itemize}

+\item[Version 1.3.1:] \mbox{ }  \begin{itemize}

+   \item fixes in Makefiles and Makevars files to account for changes in build system

+  \end{itemize}

+\item[Version 1.3.0:] \mbox{ }  \begin{itemize}

+    \item new branch for Bioconductor 3.3 devel

   \end{itemize}

 \item[Version 1.1.3:] \mbox{ }  \begin{itemize}

     \item bug fix related to custom substitution matrices