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minor fixes (see inst/NEWS); version number bumped to 1.5.4

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@119484 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 20/07/2016 13:18:53
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: 1.5.3
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-Date: 2016-06-23
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+Version: 1.5.4
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+Date: 2016-07-20
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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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@@ -292,10 +292,10 @@ msaClustalW <- function(inputSeqs,
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     # tree #
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     ########
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     ##calculate NJ tree
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-    params[["tree"]] <- checkLogicalParams("tree", params, FALSE)
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+    ## params[["tree"]] <- checkLogicalParams("tree", params, FALSE)
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     ##delete param in copy
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-    paramsCopy[["tree"]] <- NULL
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+    ## paramsCopy[["tree"]] <- NULL
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     #######
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     # pim #
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@@ -53,7 +53,7 @@ msaConvert <- function(x, type=c("seqinr::alignment",
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                  "DNA sequences")
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         if (requireNamespace("phangorn", quietly=TRUE))
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-            out <- as.phyDat(x)
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+            out <- phangorn::as.phyDat(x)
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         else
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             stop("conversion to 'phyDat' requires package 'phangorn'")
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     }
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@@ -1,6 +1,12 @@
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 Change history of package msa:
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 ==============================
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+Version 1.5.4:
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+- bug fix in msaClustalW(): unsupported parameter 'tree' deactivated
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+- fixes in ClustalOmega source code to ensure GCC6 compatibility
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+- fix in msaConvert() function to improve safety of call to suggested
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+  package 'phangorn'
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+
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 Version 1.5.3:
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 - additional conversions implemented for msaConvert() function
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 - corresponding changes in documentation
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@@ -44,7 +44,7 @@ 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) $(SHLIB_OPENMP_CXXFLAGS) -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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+	export PKG_CXXFLAGS="$(PKG_CXXFLAGS) $(SHLIB_OPENMP_CXXFLAGS) -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
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 	export PKG_CFLAGS="$(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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@@ -36,7 +36,8 @@
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 #include <string.h>     // strcmp, strstr
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 #include <stdio.h>    // printf
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 #include <stdlib.h>   // exit
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-#include <math.h>     // sqrt, pow
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+//#include <math.h>     // sqrt, pow
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+#include <cmath>     // sqrt, pow
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 #include <limits.h>   // INT_MIN
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 #include <float.h>    // FLT_MIN
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 #include <time.h>     // clock
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@@ -834,6 +834,12 @@ bibliography below).
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 \section{Change Log}
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 \begin{description}
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+\item[Version 1.5.4:] \mbox{ }  \begin{itemize}
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+   \item bug fix in \verb+msaClustalW()+: unsupported parameter `\verb+tree+' deactivated
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+   \item fixes in ClustalOmega source code to ensure GCC 6 compatibility
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+   \item fix in \verb+msaConvert()+ function to improve safety of call to suggested
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+  package \verb+phangorn+
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+  \end{itemize}
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 \item[Version 1.5.3:] \mbox{ }  \begin{itemize}
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    \item additional conversions implemented for \verb+msaConvert()+ function
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    \item corresponding changes in documentation