Merge branch 'ubsan-fix'

This merge marks the upload of version 1.1.1 into CRAN. Unfortunately, a valgrind and Address sanitizer issue has been found.
grunwaldlab · Jul 27, 2014 · 9a11cb9 · 9a11cb9
1 parent 0fce5f3
commit 9a11cb9
Show file tree

Hide file tree

Showing 18 changed files with 273 additions and 317 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: poppr
 Type: Package
 Title: an R package for genetic analysis of populations with mixed
     reproduction
-Version: 1.1.0
-Date: 2014-07-23
+Version: 1.1.1
+Date: 2014-07-26
 Author: Zhian N. Kamvar <[email protected]>, Javier F. Tabima
     <[email protected]>, Niklaus J. Grunwald
     <[email protected]>

diff --git a/NEWS b/NEWS
@@ -1,3 +1,10 @@
+poppr 1.1.1
+===========
+BUG FIX
+* Fixed bug where the loss and add options for Bruvo's distance were switched. 
+* Fixed illegal memory access error by UBSAN. Made memory management of internal C functions more sane. (Addresses issue #2).
+* Fixed directional quotes and em-dashes produced by Mavericks (Addresses issue #3).
+
 poppr 1.1.0
 ===========
 NEW FEATURES

diff --git a/R/amova.r b/R/amova.r
@@ -172,7 +172,7 @@
 #' @references Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of
 #' molecular variance inferred from metric distances among DNA haplotypes:
 #' application to human mitochondrial DNA restriction data. \emph{Genetics},
-#' \strong{131}, 479–491.
+#' \strong{131}, 479-491.
 #' 
 #' @seealso \code{\link[ade4]{amova}} \code{\link{clonecorrect}}
 #'   \code{\link{diss.dist}} \code{\link{missingno}}

diff --git a/R/distances.r b/R/distances.r
@@ -155,49 +155,49 @@ diss.dist <- function(x, percent=FALSE, mat=FALSE){
 #' @keywords nei rogers rodgers reynolds coancestry edwards angular provesti
 #' @references
 #' Nei, M. (1972) Genetic distances between populations. American Naturalist,
-#' 106, 283–292. 
+#' 106, 283-292. 
 #' 
 #' Nei M. (1978) Estimation of average heterozygosity and genetic
-#' distance from a small number of individuals. Genetics, 23, 341–369. 
+#' distance from a small number of individuals. Genetics, 23, 341-369. 
 #' 
 #' Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall,
 #' London.
 #' 
 #' Edwards, A.W.F. (1971) Distance between populations on the basis of gene
-#' frequencies. Biometrics, 27, 873–881. 
+#' frequencies. Biometrics, 27, 873-881. 
 #' 
 #' Cavalli-Sforza L.L. and Edwards A.W.F.
 #' (1967) Phylogenetic analysis: models and estimation procedures. Evolution,
-#' 32, 550–570. 
+#' 32, 550-570. 
 #' 
 #' Hartl, D.L. and Clark, A.G. (1989) Principles of population
 #' genetics. Sinauer Associates, Sunderland, Massachussetts (p. 303).
 #' 
 #' Reynolds, J. B., B. S. Weir, and C. C. Cockerham. (1983) Estimation of the
 #' coancestry coefficient: basis for a short-term genetic distance. Genetics,
-#' 105, 767–779.
+#' 105, 767-779.
 #' 
 #' Rogers, J.S. (1972) Measures of genetic similarity and genetic distances.
-#' Studies in Genetics, Univ. Texas Publ., 7213, 145–153. 
+#' Studies in Genetics, Univ. Texas Publ., 7213, 145-153. 
 #' 
 #' Avise, J. C. (1994)
 #' Molecular markers, natural history and evolution. Chapman & Hall, London.
 #' 
 #' Prevosti A. (1974) La distancia genetica entre poblaciones. Miscellanea
-#' Alcobe, 68, 109–118. 
+#' Alcobe, 68, 109-118. 
 #' 
 #' Prevosti A., Oca\~na J. and Alonso G. (1975) Distances
 #' between populations of Drosophila subobscura, based on chromosome
-#' arrangements frequencies. Theoretical and Applied Genetics, 45, 231–241. 
+#' arrangements frequencies. Theoretical and Applied Genetics, 45, 231-241. 
 #' 
 #' For more information on dissimilarity indexes: 
 #' 
 #' Gower J. and Legendre P. (1986)
 #' Metric and Euclidean properties of dissimilarity coefficients. Journal of
-#' Classification, 3, 5–48 
+#' Classification, 3, 5-48 
 #' 
 #' Legendre P. and Legendre L. (1998) Numerical Ecology,
-#' Elsevier Science B.V. 20, pp274–288.
+#' Elsevier Science B.V. 20, pp274-288.
 #' @export
 #' @examples
 #' 

diff --git a/R/internal.r b/R/internal.r
@@ -93,7 +93,7 @@ NULL
 #'   Restrepo, William E. Fry, Gregory A. Forbes, Valerie J. Fieland, Martha
 #'   Cardenas, and Niklaus J. Grünwald. "The Irish potato famine pathogen
 #'   \emph{Phytophthora infestans} originated in central Mexico rather than the Andes."
-#'   Proceedings of the National Academy of Sciences 111:8791–8796.
+#'   Proceedings of the National Academy of Sciences 111:8791-8796.
 #==============================================================================#
 NULL
 #==============================================================================#
@@ -108,8 +108,8 @@ NULL
 #'   were sampled across 3 years (2009, 2010, and 2011) in a total of four
 #'   trees, where one tree was sampled in all three years, for a total of 6
 #'   within-tree populations. Within each year, samples in the spring were taken
-#'   from affected blossoms (termed “BB” for blossom blight) and in late summer
-#'   from affected fruits (termed “FR” for fruit rot). There are a total of 694 
+#'   from affected blossoms (termed "BB" for blossom blight) and in late summer
+#'   from affected fruits (termed "FR" for fruit rot). There are a total of 694 
 #'   isolates with 65 to 173 isolates within each canopy population that were 
 #'   characterized using a set of 13 microsatellite markers.
 #' @format a \code{\linkS4class{genclone}} object with 3 hierarchical levels 

diff --git a/R/poppr.R b/R/poppr.R
@@ -62,18 +62,18 @@
 #' }
 #' @section Genetic distances:
 #' \itemize{
-#' \item \code{\link{bruvo.dist}} - Bruvo’s distance
+#' \item \code{\link{bruvo.dist}} - Bruvo's distance
 #' \item \code{\link{diss.dist}} - Absolute genetic distance (see provesti.dist)
-#' \item \code{\link{nei.dist}} - Nei’s 1978 genetic distance
-#' \item \code{\link{rogers.dist}} - Rogers’ euclidean distance
-#' \item \code{\link{reynolds.dist}} - Reynolds’ coancestry distance
-#' \item \code{\link{edwards.dist}} - Edwards’ angular distance
-#' \item \code{\link{provesti.dist}} - Provesti’s absolute genetic distance
+#' \item \code{\link{nei.dist}} - Nei's 1978 genetic distance
+#' \item \code{\link{rogers.dist}} - Rogers' euclidean distance
+#' \item \code{\link{reynolds.dist}} - Reynolds' coancestry distance
+#' \item \code{\link{edwards.dist}} - Edwards' angular distance
+#' \item \code{\link{provesti.dist}} - Provesti's absolute genetic distance
 #' }
 #' @section Bootstrapping:
 #' \itemize{
 #' \item \code{\link{aboot}} - Creates a bootstrapped dendrogram for any distance measure
-#' \item \code{\link{bruvo.boot}} - Produces dendrograms with bootstrap support based on Bruvo’s distance
+#' \item \code{\link{bruvo.boot}} - Produces dendrograms with bootstrap support based on Bruvo's distance
 #' }
 #' @section Analysis:
 #' \itemize{
@@ -93,7 +93,7 @@
 #' \itemize{
 #' \item \code{\link{plot_poppr_msn}} - Plots minimum spanning networks produced in poppr with scale bar and legend
 #' \item \code{\link{greycurve}} - Helper to determine the appropriate parameters for adjusting the grey level for msn functions
-#' \item \code{\link{bruvo.msn}} - Produces minimum spanning networks based off Bruvo’s distance colored by population
+#' \item \code{\link{bruvo.msn}} - Produces minimum spanning networks based off Bruvo's distance colored by population
 #' \item \code{\link{poppr.msn}} - Produces a minimum spanning network for any pairwise distance matrix related to the data
 #' \item \code{\link{info_table}} - Creates a heatmap representing missing data or observed ploidy
 #' \item \code{\link{genotype_curve}} - Creates a series of boxplots to demonstrate how many markers are needed to represent the diversity of your data. 

diff --git a/man/Pinf.Rd b/man/Pinf.Rd
@@ -19,6 +19,6 @@ Goss, Erica M., Javier F. Tabima, David EL Cooke, Silvia
   Restrepo, William E. Fry, Gregory A. Forbes, Valerie J. Fieland, Martha
   Cardenas, and Niklaus J. Grünwald. "The Irish potato famine pathogen
   \emph{Phytophthora infestans} originated in central Mexico rather than the Andes."
-  Proceedings of the National Academy of Sciences 111:8791–8796.
+  Proceedings of the National Academy of Sciences 111:8791-8796.
 }
 
diff --git a/man/genetic_distance.Rd b/man/genetic_distance.Rd
@@ -64,49 +64,49 @@ Daniel Chessel (ade4)
 }
 \references{
 Nei, M. (1972) Genetic distances between populations. American Naturalist,
-106, 283–292.
+106, 283-292.
 
 Nei M. (1978) Estimation of average heterozygosity and genetic
-distance from a small number of individuals. Genetics, 23, 341–369.
+distance from a small number of individuals. Genetics, 23, 341-369.
 
 Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall,
 London.
 
 Edwards, A.W.F. (1971) Distance between populations on the basis of gene
-frequencies. Biometrics, 27, 873–881.
+frequencies. Biometrics, 27, 873-881.
 
 Cavalli-Sforza L.L. and Edwards A.W.F.
 (1967) Phylogenetic analysis: models and estimation procedures. Evolution,
-32, 550–570.
+32, 550-570.
 
 Hartl, D.L. and Clark, A.G. (1989) Principles of population
 genetics. Sinauer Associates, Sunderland, Massachussetts (p. 303).
 
 Reynolds, J. B., B. S. Weir, and C. C. Cockerham. (1983) Estimation of the
 coancestry coefficient: basis for a short-term genetic distance. Genetics,
-105, 767–779.
+105, 767-779.
 
 Rogers, J.S. (1972) Measures of genetic similarity and genetic distances.
-Studies in Genetics, Univ. Texas Publ., 7213, 145–153.
+Studies in Genetics, Univ. Texas Publ., 7213, 145-153.
 
 Avise, J. C. (1994)
 Molecular markers, natural history and evolution. Chapman & Hall, London.
 
 Prevosti A. (1974) La distancia genetica entre poblaciones. Miscellanea
-Alcobe, 68, 109–118.
+Alcobe, 68, 109-118.
 
 Prevosti A., Oca\~na J. and Alonso G. (1975) Distances
 between populations of Drosophila subobscura, based on chromosome
-arrangements frequencies. Theoretical and Applied Genetics, 45, 231–241.
+arrangements frequencies. Theoretical and Applied Genetics, 45, 231-241.
 
 For more information on dissimilarity indexes:
 
 Gower J. and Legendre P. (1986)
 Metric and Euclidean properties of dissimilarity coefficients. Journal of
-Classification, 3, 5–48
+Classification, 3, 5-48
 
 Legendre P. and Legendre L. (1998) Numerical Ecology,
-Elsevier Science B.V. 20, pp274–288.
+Elsevier Science B.V. 20, pp274-288.
 }
 \seealso{
 \code{\link{aboot}} \code{\link{diss.dist}} \code{\link{poppr.amova}}

diff --git a/man/monpop.Rd b/man/monpop.Rd
@@ -16,8 +16,8 @@ This is microsatellite data for a population of the haploid
   were sampled across 3 years (2009, 2010, and 2011) in a total of four
   trees, where one tree was sampled in all three years, for a total of 6
   within-tree populations. Within each year, samples in the spring were taken
-  from affected blossoms (termed “BB” for blossom blight) and in late summer
-  from affected fruits (termed “FR” for fruit rot). There are a total of 694
+  from affected blossoms (termed "BB" for blossom blight) and in late summer
+  from affected fruits (termed "FR" for fruit rot). There are a total of 694
   isolates with 65 to 173 isolates within each canopy population that were
   characterized using a set of 13 microsatellite markers.
 }

diff --git a/man/poppr-package.Rd b/man/poppr-package.Rd
@@ -73,21 +73,21 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package.
 \section{Genetic distances}{
 
 \itemize{
-\item \code{\link{bruvo.dist}} - Bruvo’s distance
+\item \code{\link{bruvo.dist}} - Bruvo's distance
 \item \code{\link{diss.dist}} - Absolute genetic distance (see provesti.dist)
-\item \code{\link{nei.dist}} - Nei’s 1978 genetic distance
-\item \code{\link{rogers.dist}} - Rogers’ euclidean distance
-\item \code{\link{reynolds.dist}} - Reynolds’ coancestry distance
-\item \code{\link{edwards.dist}} - Edwards’ angular distance
-\item \code{\link{provesti.dist}} - Provesti’s absolute genetic distance
+\item \code{\link{nei.dist}} - Nei's 1978 genetic distance
+\item \code{\link{rogers.dist}} - Rogers' euclidean distance
+\item \code{\link{reynolds.dist}} - Reynolds' coancestry distance
+\item \code{\link{edwards.dist}} - Edwards' angular distance
+\item \code{\link{provesti.dist}} - Provesti's absolute genetic distance
 }
 }
 
 \section{Bootstrapping}{
 
 \itemize{
 \item \code{\link{aboot}} - Creates a bootstrapped dendrogram for any distance measure
-\item \code{\link{bruvo.boot}} - Produces dendrograms with bootstrap support based on Bruvo’s distance
+\item \code{\link{bruvo.boot}} - Produces dendrograms with bootstrap support based on Bruvo's distance
 }
 }
 
@@ -113,7 +113,7 @@ This package relies on the \pkg{\link[adegenet]{adegenet}} package.
 \itemize{
 \item \code{\link{plot_poppr_msn}} - Plots minimum spanning networks produced in poppr with scale bar and legend
 \item \code{\link{greycurve}} - Helper to determine the appropriate parameters for adjusting the grey level for msn functions
-\item \code{\link{bruvo.msn}} - Produces minimum spanning networks based off Bruvo’s distance colored by population
+\item \code{\link{bruvo.msn}} - Produces minimum spanning networks based off Bruvo's distance colored by population
 \item \code{\link{poppr.msn}} - Produces a minimum spanning network for any pairwise distance matrix related to the data
 \item \code{\link{info_table}} - Creates a heatmap representing missing data or observed ploidy
 \item \code{\link{genotype_curve}} - Creates a series of boxplots to demonstrate how many markers are needed to represent the diversity of your data.

diff --git a/man/poppr.amova.Rd b/man/poppr.amova.Rd
@@ -124,7 +124,7 @@ amova.cc.test
 Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of
 molecular variance inferred from metric distances among DNA haplotypes:
 application to human mitochondrial DNA restriction data. \emph{Genetics},
-\strong{131}, 479–491.
+\strong{131}, 479-491.
 }
 \seealso{
 \code{\link[ade4]{amova}} \code{\link{clonecorrect}}