Browse code

further fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@111693 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 21/12/2015 10:29:13
Showing21 changed files

... ...
@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
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-Version: 1.3.1
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-Date: 2015-10-13
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+Version: 1.3.2
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+Date: 2015-12-21
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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: This package provides a unified R/Bioconductor interface to the
... ...
@@ -21,7 +21,7 @@ Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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         S4Vectors, tools
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 Suggests: Biobase, knitr
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 LinkingTo: Rcpp
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-SystemRequirements:
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+SystemRequirements: GNU make
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 VignetteBuilder: knitr
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 LazyLoad: yes
27 27
 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
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 biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,
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         Sequencing
33 33
 NeedsCompilation: yes
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-Packaged: 2015-10-07 16:20:45 UTC; bodenhof
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@@ -8,13 +8,15 @@ citEntry(entry="Article",
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                              as.person("Christoph Horejs-Kainrath"),
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                              as.person("Sepp Hochreiter")),
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          journal="Bioinformatics",
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-         note="(accepted)",
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+         volume="31",
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+         number="24",
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+         pages="3997--3999",
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          year="2015",
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          doi="10.1093/bioinformatics/btv494",
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          textVersion =
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              paste("U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015)",
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                    "msa: an R package for multiple sequence alignment.",
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-                   "Bioinformatics (accepted).",
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+                   "Bioinformatics 31(24):3997-9999.",
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                    "DOI: 10.1093/bioinformatics/btv176.")
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 )
20 22
 
... ...
@@ -1,8 +1,16 @@
1 1
 Change history of package msa:
2 2
 ==============================
3 3
 
4
-Version 1.2.0:
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-- new branch for Bioconductor 3.2 release
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+Version 1.3.2:
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+- further fixes in Makefiles and Makevars files to account for changes
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+  in build system
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+- update of citation information
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+
9
+Version 1.3.1:
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+- fixes in Makefiles and Makevars files to account for changes in build system
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+
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+Version 1.3.0:
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+- new branch for Bioconductor 3.3 devel
6 14
 
7 15
 Version 1.1.3: 
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 - bug fix related to custom substitution matrices in the MUSCLE interface
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@@ -42,7 +42,7 @@ The following slots are defined for \code{MsaMetaData} objects:
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   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
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   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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 }
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 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},
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@@ -114,7 +114,7 @@
114 114
   
115 115
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
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   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
119 119
 }
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 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},
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@@ -30,7 +30,7 @@
30 30
   
31 31
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
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   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
35 35
 
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   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)
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@@ -134,7 +134,7 @@
134 134
   
135 135
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
136 136
   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
139 139
  
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   \url{http://www.clustal.org/download/clustalw_help.txt}
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@@ -82,7 +82,7 @@
82 82
   
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   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
84 84
   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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   \url{http://www.clustal.org/omega/README}
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@@ -84,7 +84,7 @@
84 84
    
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   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
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   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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   \url{http://www.clustal.org/download/clustalw_help.txt}
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@@ -91,7 +91,7 @@
91 91
   
92 92
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
93 93
   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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   \url{http://www.drive5.com/muscle/muscle.html}
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@@ -192,7 +192,7 @@
192 192
   
193 193
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
194 194
   (2015). msa: an R package for multiple sequence alignment. 
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-  \emph{Bioinformatics} (accepted). DOI:
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+  \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
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   \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
197 197
 
198 198
   \url{https://www.ctan.org/pkg/texshade}
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@@ -1,5 +1,5 @@
1 1
 ## Variant 1: deactivate OpenMP on Mac Platforms
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-CONFIGURE_FLAGS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
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+CONFIGURE_FLAGS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`
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 ## Variant 2: deactivate OpenMP generally
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 #CONFIGURE_FLAGS=--without-openmp 
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 ## Variant 3: let the configure script determine whether OpenMP is available
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@@ -44,9 +44,9 @@ all: clustalomega
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 clustalomega:
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 	./configure $(CONFIGURE_FLAGS); \
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 	export PKG_LIBS="$(PKG_LIBS) $(SHLIB_OPENMP_CFLAGS)"; \
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
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-	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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+	export PKG_CFLAGS="$(PKG_CFLAGS) $(SHLIB_OPENMP_CFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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 	cd src; \
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-	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
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+	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libClustalOmega.so $(CPPNames) && \
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 	ar rcs libClustalOmega.a $(OBJNames) && \
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 	cp libClustalOmega.a ../../
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@@ -38,8 +38,8 @@ clustalomega:
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 	cp windows/src/config.h src/; \
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 	cp windows/src/clustal-omega-config.h src/; \
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 	export PKG_LIBS="$(PKG_LIBS) -L"../../gc-7.2" -lgccpp72 -lgc72"; \
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \
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-	export PKG_CFLAGS="$(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()"`"; \
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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+	export PKG_CFLAGS="$(PKG_CFLAGS) -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -lgccpp -lgc"; \
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 	cd src; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o ClustalOmega.dll $(CPPNames) && \
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 	$(AR) rcs libClustalOmega.a $(OBJNames) && \
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@@ -7,7 +7,7 @@ all: clustalw
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 clustalw:
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 	./configure; \
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 	cd src; \
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-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`"; \
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-	"${R_HOME}/bin${R_ARCH_BIN}/R" CMD SHLIB -o libClustalW.so $(CPPNames) && \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \
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+	${R_HOME}/bin/R CMD SHLIB -o libClustalW.so $(CPPNames) && \
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 	ar rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.a ../../
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@@ -11,7 +11,7 @@ clustalw:
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 	cp windows/src/clustalw_version.h src/; \
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 	cp windows/src/config.h src/; \
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 	cd src; \
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-	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS) `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \
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+	export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. $(PKG_CXXFLAGS)"; \
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 	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o ClustalW.dll $(CPPNames) &&\
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 	$(AR) rcs libClustalW.a $(OBJNames) && \
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 	cp libClustalW.a ../../
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@@ -1,5 +1,5 @@
1
-PKG_LIBS=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "if (Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a  -Wl,--no-whole-archive')"`
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-PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e "Rcpp:::CxxFlags()"`
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+PKG_LIBS=`${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')"`
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+PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"
3 3
 
4 4
 .PHONY: all mylibs
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@@ -1,7 +1,7 @@
1 1
 .PHONY: all ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a
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3 3
 PKG_LIBS=-Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive
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-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()"`
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+PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src"
5 5
 
6 6
 all: $(SHLIB)
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 $(SHLIB): ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a
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@@ -5,7 +5,7 @@ OBJNames = aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o al
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 all: muscle
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7 7
 muscle:
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-	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I"../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"
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-	"${R_HOME}/bin/R" CMD SHLIB -o libMuscle.so $(CPPNames)
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) -I../gc-7.2/include"
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+	${R_HOME}/bin${R_ARCH_BIN}/R CMD SHLIB -o libMuscle.so $(CPPNames)
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 	ar rcs libMuscle.a $(OBJNames)
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 	cp libMuscle.a ../
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@@ -6,7 +6,7 @@ all: muscle
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7 7
 muscle:
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 	export PKG_LIBS="$(PKG_LIBS) -L"../gc-7.2/" -lgc72 -lgccpp72"
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-	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${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::CxxFlags()"`"
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-	"${R_HOME}/bin${R_ARCH_BIN}/R.exe" CMD SHLIB -o Muscle.dll $(CPPNames)
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+	export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(PKG_CXXFLAGS) -I../gc-7.2/include/"
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+	${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD SHLIB -o Muscle.dll $(CPPNames)
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 	$(AR) rcs libMuscle.a $(OBJNames)
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 	cp libMuscle.a ../
... ...
@@ -9,8 +9,8 @@ all: gc72
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 gc72:
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 	export PKG_LIBS="$(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$(PRIVATE_INCLUDE_DIR) `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \
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-	export PKG_CXXFLAGS="$(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$(PRIVATE_INCLUDE_DIR) `${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "Rcpp:::CxxFlags()"`"; \
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+	export PKG_CFLAGS="$(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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 	${R_HOME}/bin${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); \
... ...
@@ -699,8 +699,9 @@ We envision the following changes/extensions in future versions of the package:
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 If you use this package for research that is published later, you are kindly
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 asked to cite it as follows:
701 701
 \begin{quotation}
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-\noindent E.~Bonatesta, C.~Horejs-Kainrath, and U.~Bodenhofer, (2015).
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-msa: An R Package for Multiple Sequence Alignment.
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+\noindent U.~Bodenhofer, E.~Bonatesta, C.~Horej\v{s}-Kainrath, and S.~Hochreiter (2015).
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+msa: an R package for multiple sequence alignment. {\em Bioinformatics} {\bf 31}(24):3997--3999.
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+DOI: \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{bioinformatics/btv494}.
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 \end{quotation}
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 To obtain a Bib\TeX\ entries of the reference, enter the
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 following into your R session:
... ...
@@ -715,8 +716,15 @@ bibliography below).
715 716
 \section{Change Log}
716 717
 
717 718
 \begin{description}
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-\item[Version 1.2.0:] \mbox{ }  \begin{itemize}
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-    \item new branch for Bioconductor 3.2 release
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+\item[Version 1.3.2:] \mbox{ }  \begin{itemize}
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+   \item further fixes in Makefiles and Makevars files to account for changes in build system
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+   \item update of citation information
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+  \end{itemize}
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+\item[Version 1.3.1:] \mbox{ }  \begin{itemize}
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+   \item fixes in Makefiles and Makevars files to account for changes in build system
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+  \end{itemize}
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+\item[Version 1.3.0:] \mbox{ }  \begin{itemize}
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+    \item new branch for Bioconductor 3.3 devel
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   \end{itemize}
721 729
 \item[Version 1.1.3:] \mbox{ }  \begin{itemize}
722 730
     \item bug fix related to custom substitution matrices