Browse code

various fixes; version number bumped to 1.27.1

UBodenhofer authored on 17/02/2022 12:58:20
Showing17 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: 1.27.0
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-Date: 2021-10-20
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+Version: 1.27.1
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+Date: 2022-02-17
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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
... ...
@@ -16,10 +16,10 @@ Description: The 'msa' package provides a unified R/Bioconductor interface to
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 URL: http://www.bioinf.jku.at/software/msa/
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 License: GPL (>= 2)
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 Copyright: See file inst/COPYRIGHT
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-Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0)
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+Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0)
20 20
 Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
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         S4Vectors, tools
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-Suggests: Biobase, knitr, seqinr, ape, phangorn
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+Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn
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 LinkingTo: Rcpp
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 SystemRequirements: GNU make
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 VignetteBuilder: knitr
... ...
@@ -33,9 +33,10 @@ msaConvert <- function(x, type=c("seqinr::alignment",
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             stop("conversion to 'ape::AAbin' only supported for ",
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                  "amino acid sequences")
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-        out <- .Call("SplitCharVector2Matrix", xn, "X")
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-        rownames(out) <- names(xn)
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-        class(out) <- "AAbin"
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+        if (requireNamespace("ape", quietly=TRUE))
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+            out <- ape::as.AAbin(x)
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+        else
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+            stop("conversion to 'AAbin' requires package 'ape'")
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     }
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     else if (type == "ape::DNAbin")
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     {
... ...
@@ -43,9 +44,10 @@ msaConvert <- function(x, type=c("seqinr::alignment",
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             stop("conversion to 'ape::DNAbin' only supported for ",
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                  "DNA sequences")
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-        out <- .Call("SplitCharVector2Matrix", tolower(xn), "n")
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-        rownames(out) <- names(xn)
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-        class(out) <- "DNAbin"
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+        if (requireNamespace("ape", quietly=TRUE))
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+            out <- ape::as.DNAbin(x)
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+        else
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+            stop("conversion to 'DNAbin' requires package 'ape'")
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     }
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     else if (type == "phangorn::phyDat")
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     {
... ...
@@ -1,6 +1,19 @@
1 1
 Change history of package msa:
2 2
 ==============================
3 3
 
4
+Version 1.27.1:
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+- workaround for problems running texi2dvi() on R 4.2.0; those occurred 
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+  during package checks when running some examples and the vignette code
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+- updated URLs and DOIs (now requires R version >= 3.3.0)
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+- fixed msaConvert() function to now work well with newer versions of the
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+  'ape' package (now requires at least version 5.2)
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+
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+Version 1.27.0:
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+- new branch for Bioconductor 3.15 devel
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+
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+Version 1.26.0:
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+- release as part of Bioconductor 3.14
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+
4 17
 Version 1.25.3:
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 - further changes to get rid of compiler warnings
6 19
 
... ...
@@ -43,7 +43,7 @@ The following slots are defined for \code{MsaMetaData} objects:
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   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
44 44
   (2015). msa: an R package for multiple sequence alignment. 
45 45
   \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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+  \doi{10.1093/bioinformatics/btv494}.
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 }
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 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},
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   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},
... ...
@@ -118,7 +118,7 @@
118 118
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
119 119
   (2015). msa: an R package for multiple sequence alignment. 
120 120
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
121
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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+  \doi{10.1093/bioinformatics/btv494}.
122 122
 }
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 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},
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   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},
... ...
@@ -31,36 +31,36 @@
31 31
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
32 32
   (2015). msa: an R package for multiple sequence alignment. 
33 33
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
34
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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+  \doi{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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   CLUSTAL W: improving the sensitivity of progressive multiple sequence
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   alignment through sequence weighting, position-specific gap penalties
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   and weight matrix choice.
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   \emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:
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-  \href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.
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+  \doi{10.1093/nar/22.22.4673}.
42 42
 
43 43
   Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W.,
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   Lopez, R., McWilliam, H., Remmert, M., Soeding, J., Thompson, J. D.,
45 45
   and Higgins, D. G. (2011) Fast, scalable generation of high-quality
46 46
   protein multiple sequence alignments using Clustal Omega.
47 47
   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:
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-  \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.
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+  \doi{10.1038/msb.2011.75}.
49 49
 
50 50
   Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high 
51 51
   accuracy and high throughput.
52 52
   \emph{Nucleic Acids Res.} \bold{32}(5):1792-1797. DOI:
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-  \href{http://dx.doi.org/10.1093/nar/gkh340}{10.1093/nar/gkh340}.
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+  \doi{10.1093/nar/gkh340}.
54 54
 
55 55
   Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method 
56 56
   with reduced time and space complexity.
57 57
   \emph{BMC Bioinformatics} \bold{5}:113. DOI:
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-  \href{http://dx.doi.org/10.1186/1471-2105-5-113}{10.1186/1471-2105-5-113}.
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+  \doi{10.1186/1471-2105-5-113}.
59 59
 
60 60
   Beitz, E. (2000) TeXshade: shading and labeling of multiple
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   sequence alignments using LaTeX2e
62 62
   \emph{Bioinformatics} \bold{16}(2):135-139. DOI:
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-  \href{http://dx.doi.org/10.1093/bioinformatics/16.2.135}{10.1093/bioinformatics/16.2.135}.
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+  \doi{10.1093/bioinformatics/16.2.135}.
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 }  
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 \seealso{\code{\link{msa}},  \code{\link{msaClustalW}},
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   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},
... ...
@@ -135,7 +135,7 @@
135 135
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
136 136
   (2015). msa: an R package for multiple sequence alignment. 
137 137
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
138
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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+  \doi{10.1093/bioinformatics/btv494}.
139 139
  
140 140
   \url{http://www.clustal.org/download/clustalw_help.txt}
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... ...
@@ -148,24 +148,24 @@
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   alignment through sequence weighting, position-specific gap penalties
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   and weight matrix choice.
150 150
   \emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:
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-  \href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.
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+  \doi{10.1093/nar/22.22.4673}.
152 152
 
153 153
   Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W.,
154 154
   Lopez, R., McWilliam, H., Remmert, M., Soeding, J., Thompson, J. D.,
155 155
   and Higgins, D. G. (2011) Fast, scalable generation of high-quality
156 156
   protein multiple sequence alignments using Clustal Omega.
157 157
   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:
158
-  \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.
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+  \doi{10.1038/msb.2011.75}.
159 159
 
160 160
   Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high 
161 161
   accuracy and high throughput.
162 162
   \emph{Nucleic Acids Res.} \bold{32}(5):1792-1797. DOI:
163
-  \href{http://dx.doi.org/10.1093/nar/gkh340}{10.1093/nar/gkh340}.
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+  \doi{10.1093/nar/gkh340}.
164 164
 
165 165
   Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method 
166 166
   with reduced time and space complexity.
167 167
   \emph{BMC Bioinformatics} \bold{5}:113. DOI:
168
-  \href{http://dx.doi.org/10.1186/1471-2105-5-113}{10.1186/1471-2105-5-113}.
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+  \doi{10.1186/1471-2105-5-113}.
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 }  
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 \seealso{\code{\link{msaClustalW}},
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   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},
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@@ -65,7 +65,7 @@
65 65
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
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   (2015). msa: an R package for multiple sequence alignment. 
67 67
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
68
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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+  \doi{10.1093/bioinformatics/btv494}.
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 }
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 \seealso{\code{\link{msaPrettyPrint}},
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   \code{\linkS4class{MsaAAMultipleAlignment}},
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@@ -83,7 +83,7 @@
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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. 
85 85
   \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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+  \doi{10.1093/bioinformatics/btv494}.
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88 88
   \url{http://www.clustal.org/omega/README}
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@@ -92,7 +92,7 @@
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   and Higgins, D. G. (2011) Fast, scalable generation of high-quality
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   protein multiple sequence alignments using Clustal Omega.
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   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:
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-  \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.
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+  \doi{10.1038/msb.2011.75}.
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 }
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 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
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   \code{\linkS4class{MsaDNAMultipleAlignment}},
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@@ -87,7 +87,7 @@
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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. 
89 89
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
90
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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+  \doi{10.1093/bioinformatics/btv494}.
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   \url{http://www.clustal.org/download/clustalw_help.txt}
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... ...
@@ -96,7 +96,7 @@
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   alignment through sequence weighting, position-specific gap penalties
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   and weight matrix choice.
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   \emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:
99
-  \href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.
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+  \doi{10.1093/nar/22.22.4673}.
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 }
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 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
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   \code{\linkS4class{MsaDNAMultipleAlignment}},
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@@ -85,7 +85,7 @@
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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} \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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+  \doi{10.1093/bioinformatics/btv494}.
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 }
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 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
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   \code{\linkS4class{MsaDNAMultipleAlignment}},
... ...
@@ -90,7 +90,7 @@
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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} \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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+  \doi{10.1093/bioinformatics/btv494}.
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 }
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 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
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   \code{\linkS4class{MsaDNAMultipleAlignment}},
... ...
@@ -67,7 +67,7 @@
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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} \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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+  \doi{10.1093/bioinformatics/btv494}.
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 }
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 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
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   \code{\linkS4class{MsaDNAMultipleAlignment}},
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@@ -92,19 +92,19 @@
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   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
93 93
   (2015). msa: an R package for multiple sequence alignment. 
94 94
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
95
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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+  \doi{10.1093/bioinformatics/btv494}.
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   \url{http://www.drive5.com/muscle/muscle.html}
98 98
   
99 99
   Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high 
100 100
   accuracy and high throughput.
101 101
   \emph{Nucleic Acids Res.} \bold{32}(5):1792-1797. DOI:
102
-  \href{http://dx.doi.org/10.1093/nar/gkh340}{10.1093/nar/gkh340}.
102
+  \doi{10.1093/nar/gkh340}.
103 103
 
104 104
   Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method 
105 105
   with reduced time and space complexity.
106 106
   \emph{BMC Bioinformatics} \bold{5}:113. DOI:
107
-  \href{http://dx.doi.org/10.1186/1471-2105-5-113}{10.1186/1471-2105-5-113}.
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+  \doi{10.1186/1471-2105-5-113}.
108 108
 }
109 109
 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
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   \code{\linkS4class{MsaDNAMultipleAlignment}},
... ...
@@ -199,14 +199,14 @@
199 199
   U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
200 200
   (2015). msa: an R package for multiple sequence alignment. 
201 201
   \emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
202
-  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
202
+  \doi{10.1093/bioinformatics/btv494}.
203 203
 
204 204
   \url{https://www.ctan.org/pkg/texshade}
205 205
 
206 206
   Beitz, E. (2000) TeXshade: shading and labeling of multiple
207 207
   sequence alignments using LaTeX2e
208 208
   \emph{Bioinformatics} \bold{16}(2):135-139. DOI:
209
-  \href{http://dx.doi.org/10.1093/bioinformatics/16.2.135}{10.1093/bioinformatics/16.2.135}.
209
+  \doi{10.1093/bioinformatics/16.2.135}.
210 210
 }
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 \seealso{\code{\link{msaCheckNames}}
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 }
... ...
@@ -223,6 +223,7 @@ myAlignment <- msa(mySeqs)
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 msaPrettyPrint(myAlignment, output="asis", askForOverwrite=FALSE)
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 ## create PDF file according to some custom settings
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+\dontrun{
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 tmpFile <- tempfile(pattern="msa", tmpdir=".", fileext=".pdf")
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 tmpFile
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 msaPrettyPrint(myAlignment, file=tmpFile, output="pdf",
... ...
@@ -230,7 +231,6 @@ msaPrettyPrint(myAlignment, file=tmpFile, output="pdf",
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                showConsensus="bottom", logoColors="rasmol",
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                verbose=FALSE, askForOverwrite=FALSE)
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-\dontrun{
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 library(Biobase)
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 openPDF(tmpFile)}
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 }
... ...
@@ -171,7 +171,7 @@ which allows for pretty-printing multiple alignments using the \LaTeX\ package
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 \shade. As an example, the following \R\ code creates a PDF file
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 \verb+myfirstAlignment.pdf+ which is shown in
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 Figure~\ref{fig:myFirstAlignment}:
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-<<IntegratePDF2>>=
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+<<IntegratePDF2,eval=FALSE>>=
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 msaPrettyPrint(myFirstAlignment, output="pdf", showNames="none",
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                showLogo="none", askForOverwrite=FALSE, verbose=FALSE)
177 177
 @
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new file mode 100644
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Binary files /dev/null and b/vignettes/myFirstAlignment.pdf differ