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

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.27.0

-Date: 2021-10-20

+Version: 1.27.1

+Date: 2022-02-17

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

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

 Description: The 'msa' package provides a unified R/Bioconductor interface to

@@ -16,10 +16,10 @@ Description: The 'msa' package provides a unified R/Bioconductor interface to

 URL: http://www.bioinf.jku.at/software/msa/

 License: GPL (>= 2)

 Copyright: See file inst/COPYRIGHT

-Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)

+Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0)

 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),

         S4Vectors, tools

-Suggests: Biobase, knitr, seqinr, ape, phangorn

+Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn

 LinkingTo: Rcpp

 SystemRequirements: GNU make

 VignetteBuilder: knitr

@@ -33,9 +33,10 @@ msaConvert <- function(x, type=c("seqinr::alignment",

             stop("conversion to 'ape::AAbin' only supported for ",

                  "amino acid sequences")

-        out <- .Call("SplitCharVector2Matrix", xn, "X")

-        rownames(out) <- names(xn)

-        class(out) <- "AAbin"

+        if (requireNamespace("ape", quietly=TRUE))

+            out <- ape::as.AAbin(x)

+        else

+            stop("conversion to 'AAbin' requires package 'ape'")

     }

     else if (type == "ape::DNAbin")

     {

@@ -43,9 +44,10 @@ msaConvert <- function(x, type=c("seqinr::alignment",

             stop("conversion to 'ape::DNAbin' only supported for ",

                  "DNA sequences")

-        out <- .Call("SplitCharVector2Matrix", tolower(xn), "n")

-        rownames(out) <- names(xn)

-        class(out) <- "DNAbin"

+        if (requireNamespace("ape", quietly=TRUE))

+            out <- ape::as.DNAbin(x)

+        else

+            stop("conversion to 'DNAbin' requires package 'ape'")

     }

     else if (type == "phangorn::phyDat")

     {

@@ -1,6 +1,19 @@

 Change history of package msa:

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

+Version 1.27.1:

+- workaround for problems running texi2dvi() on R 4.2.0; those occurred 

+  during package checks when running some examples and the vignette code

+- updated URLs and DOIs (now requires R version >= 3.3.0)

+- fixed msaConvert() function to now work well with newer versions of the

+  'ape' package (now requires at least version 5.2)

+

+Version 1.27.0:

+- new branch for Bioconductor 3.15 devel

+

+Version 1.26.0:

+- release as part of Bioconductor 3.14

+

 Version 1.25.3:

 - further changes to get rid of compiler warnings

@@ -43,7 +43,7 @@ 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} \bold{31}(24):3997-3999. DOI:

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

+  \doi{10.1093/bioinformatics/btv494}.

 }

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

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

@@ -118,7 +118,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

 }

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

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

@@ -31,36 +31,36 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

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

   CLUSTAL W: improving the sensitivity of progressive multiple sequence

   alignment through sequence weighting, position-specific gap penalties

   and weight matrix choice.

   \emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:

-  \href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.

+  \doi{10.1093/nar/22.22.4673}.

   Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W.,

   Lopez, R., McWilliam, H., Remmert, M., Soeding, J., Thompson, J. D.,

   and Higgins, D. G. (2011) Fast, scalable generation of high-quality

   protein multiple sequence alignments using Clustal Omega.

   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:

-  \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.

+  \doi{10.1038/msb.2011.75}.

   Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high 

   accuracy and high throughput.

   \emph{Nucleic Acids Res.} \bold{32}(5):1792-1797. DOI:

-  \href{http://dx.doi.org/10.1093/nar/gkh340}{10.1093/nar/gkh340}.

+  \doi{10.1093/nar/gkh340}.

   Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method 

   with reduced time and space complexity.

   \emph{BMC Bioinformatics} \bold{5}:113. DOI:

-  \href{http://dx.doi.org/10.1186/1471-2105-5-113}{10.1186/1471-2105-5-113}.

+  \doi{10.1186/1471-2105-5-113}.

   Beitz, E. (2000) TeXshade: shading and labeling of multiple

   sequence alignments using LaTeX2e

   \emph{Bioinformatics} \bold{16}(2):135-139. DOI:

-  \href{http://dx.doi.org/10.1093/bioinformatics/16.2.135}{10.1093/bioinformatics/16.2.135}.

+  \doi{10.1093/bioinformatics/16.2.135}.

 }  

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

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

@@ -135,7 +135,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

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

@@ -148,24 +148,24 @@

   alignment through sequence weighting, position-specific gap penalties

   and weight matrix choice.

   \emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:

-  \href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.

+  \doi{10.1093/nar/22.22.4673}.

   Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W.,

   Lopez, R., McWilliam, H., Remmert, M., Soeding, J., Thompson, J. D.,

   and Higgins, D. G. (2011) Fast, scalable generation of high-quality

   protein multiple sequence alignments using Clustal Omega.

   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:

-  \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.

+  \doi{10.1038/msb.2011.75}.

   Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high 

   accuracy and high throughput.

   \emph{Nucleic Acids Res.} \bold{32}(5):1792-1797. DOI:

-  \href{http://dx.doi.org/10.1093/nar/gkh340}{10.1093/nar/gkh340}.

+  \doi{10.1093/nar/gkh340}.

   Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method 

   with reduced time and space complexity.

   \emph{BMC Bioinformatics} \bold{5}:113. DOI:

-  \href{http://dx.doi.org/10.1186/1471-2105-5-113}{10.1186/1471-2105-5-113}.

+  \doi{10.1186/1471-2105-5-113}.

 }  

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

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

@@ -65,7 +65,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msaPrettyPrint}},

   \code{\linkS4class{MsaAAMultipleAlignment}},

@@ -83,7 +83,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

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

@@ -92,7 +92,7 @@

   and Higgins, D. G. (2011) Fast, scalable generation of high-quality

   protein multiple sequence alignments using Clustal Omega.

   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:

-  \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.

+  \doi{10.1038/msb.2011.75}.

 }

 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}},

@@ -87,7 +87,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

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

@@ -96,7 +96,7 @@

   alignment through sequence weighting, position-specific gap penalties

   and weight matrix choice.

   \emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:

-  \href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.

+  \doi{10.1093/nar/22.22.4673}.

 }

 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}},

@@ -85,7 +85,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}},

@@ -90,7 +90,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}},

@@ -67,7 +67,7 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

 }

 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}},

@@ -92,19 +92,19 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

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

   Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high 

   accuracy and high throughput.

   \emph{Nucleic Acids Res.} \bold{32}(5):1792-1797. DOI:

-  \href{http://dx.doi.org/10.1093/nar/gkh340}{10.1093/nar/gkh340}.

+  \doi{10.1093/nar/gkh340}.

   Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method 

   with reduced time and space complexity.

   \emph{BMC Bioinformatics} \bold{5}:113. DOI:

-  \href{http://dx.doi.org/10.1186/1471-2105-5-113}{10.1186/1471-2105-5-113}.

+  \doi{10.1186/1471-2105-5-113}.

 }

 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},

   \code{\linkS4class{MsaDNAMultipleAlignment}},

@@ -199,14 +199,14 @@

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

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

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

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

+  \doi{10.1093/bioinformatics/btv494}.

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

   Beitz, E. (2000) TeXshade: shading and labeling of multiple

   sequence alignments using LaTeX2e

   \emph{Bioinformatics} \bold{16}(2):135-139. DOI:

-  \href{http://dx.doi.org/10.1093/bioinformatics/16.2.135}{10.1093/bioinformatics/16.2.135}.

+  \doi{10.1093/bioinformatics/16.2.135}.

 }

 \seealso{\code{\link{msaCheckNames}}

 }

@@ -223,6 +223,7 @@ myAlignment <- msa(mySeqs)

 msaPrettyPrint(myAlignment, output="asis", askForOverwrite=FALSE)

 ## create PDF file according to some custom settings

+\dontrun{

 tmpFile <- tempfile(pattern="msa", tmpdir=".", fileext=".pdf")

 tmpFile

 msaPrettyPrint(myAlignment, file=tmpFile, output="pdf",

@@ -230,7 +231,6 @@ msaPrettyPrint(myAlignment, file=tmpFile, output="pdf",

                showConsensus="bottom", logoColors="rasmol",

                verbose=FALSE, askForOverwrite=FALSE)

-\dontrun{

 library(Biobase)

 openPDF(tmpFile)}

 }

@@ -171,7 +171,7 @@ which allows for pretty-printing multiple alignments using the \LaTeX\ package

 \shade. As an example, the following \R\ code creates a PDF file

 \verb+myfirstAlignment.pdf+ which is shown in

 Figure~\ref{fig:myFirstAlignment}:

-<<IntegratePDF2>>=

+<<IntegratePDF2,eval=FALSE>>=

 msaPrettyPrint(myFirstAlignment, output="pdf", showNames="none",

                showLogo="none", askForOverwrite=FALSE, verbose=FALSE)

 @

new file mode 100644

Binary files /dev/null and b/vignettes/myFirstAlignment.pdf differ