Merge pull request #369 from thibautjombart/release/2.1.11

Prepare for CRAN release

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.1.10
-Date: 2023-01-25 22:44:37 UTC
-SHA: 67d986732c578ff8f65884b4ca622c39f36da995
+Version: 2.1.11
+Date: 2025-02-06 21:23:37 UTC
+SHA: 43a3b10c137ff05d1282f44eeab5d25418a7f841

ChangeLog

@@ -4,6 +4,16 @@ BUG FIX
 
 - genlight objects subset without any arguments to loci no longer gain an
   extra byte. (reported: @maxecoulter, #363)
+- internal C functions `bytesToInt()` and `bytesToDouble()` have a new
+  condition to prevent overflows (thanks for the suggested fix by Ivan Krylov)
+
+MISC
+
+- `spca_randtest()` has been updated with a new p argument to include a
+  Bonferroni correction (fixed in #368, but initially implemented by @valemon
+  in #247)
+- `find.clust()` data frame method now sets `scale = FALSE` to align with the
+  other methods. (reported: @cassondranewman, #362; fixed: @tiagomaie, #366)
 
 			CHANGES IN ADEGENET VERSION 2.1.10
 

DESCRIPTION

@@ -70,6 +70,9 @@ Authors@R:
               comment = c(ORCID = "0000-0003-3823-0373")),
        person(given = "Max",
               family = "Coulter",
+              role = "ctb"),
+       person(given = "Ivan",
+              family = "Krylov",
               role = "ctb")
        )
 Description: Toolset for the exploration of genetic and genomic

NAMESPACE

@@ -47,8 +47,6 @@ S3method(gengraph,genpop)
 S3method(gengraph,matrix)
 S3method(get.likelihood,seqTrack)
 S3method(graphMutations,DNAbin)
-S3method(is,genind)
-S3method(is,genpop)
 S3method(labels,haploGen)
 S3method(loadingplot,default)
 S3method(loadingplot,glPca)
@@ -70,7 +68,6 @@ S3method(print,haploGen)
 S3method(print,monmonier)
 S3method(print,spca)
 S3method(rbind,genlight)
-S3method(sample,haploGen)
 S3method(scatter,dapc)
 S3method(scatter,glPca)
 S3method(screeplot,spca)
@@ -128,6 +125,8 @@ export(genind2genpop)
 export(genpop)
 export(hier)
 export(hybridize)
+export(is.genind)
+export(is.genpop)
 export(loadingplot)
 export(makefreq)
 export(minorAllele)
@@ -142,6 +141,7 @@ export(read.genetix)
 export(read.snp)
 export(read.structure)
 export(repool)
+export(sample.haploGen)
 export(scaleGen)
 export(seqTrack)
 export(setPop)

R/basicMethods.R

@@ -543,14 +543,12 @@ print.genpopSummary <- function(x, ...){
 ###############
 # Methods "is"
 ###############
-#' @method is genind
 #' @export
 is.genind <- function(x){
   res <- ( is(x, "genind") & validObject(x))
   return(res)
 }
 
-#' @method is genpop
 #' @export
 is.genpop <- function(x){
   res <- ( is(x, "genpop") & validObject(x))

R/haploGen.R

@@ -526,7 +526,6 @@ plotHaploGen <- function(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", a
 ###################
 ## sample.haploGen
 ###################
-#' @method sample haploGen
 #' @export
 sample.haploGen <- function(x, n){
 ##sample.haploGen <- function(x, n, rDate=.rTimeSeq, arg.rDate=NULL){

R/import.R

@@ -62,7 +62,7 @@
 #'   for your samples. This is especially useful if you have a hierarchical or
 #'   factorial sampling design.
 #' @param hierarchy a hierarchical formula that explicitely defines hierarchical
-#'   levels in your strata. see \code{\link{hierarchy}} for details.
+#'   levels in your strata. 
 #' @param check.ploidy a boolean indicating if the ploidy should be checked (TRUE,
 #' default) or not (FALSE). Not checking the ploidy makes the import much faster,
 #' but might result in bugs/problems if the input file is misread or the ploidy is

R/strataMethods.R

@@ -216,7 +216,7 @@
 #'   levels of the strata. An example of a hierarchical formula would
 #'   be:\tabular{r}{ \code{~Country/City/Neighborhood}} This convention was
 #'   chosen as it becomes easier to type and makes intuitive sense when defining
-#'   a \code{\link{hierarchy}}. Note: it is important to use hiearchical
+#'   a hierarchy. Note: it is important to use hiearchical
 #'   formulas when specifying hierarchies as other types of formulas (eg. 
 #'   \code{~Country*City*Neighborhood}) will give incorrect results.}
 #'   

cran-comments.md

@@ -1 +1 @@
-This update fixes an error thrown by LLVM in C23 mode by removing the `typedef short bool` definition in `snpbin.h`
+This fixes a buffer overflow that was negatively affecting dartR.base

docker/testing/Dockerfile

@@ -1,9 +1,9 @@
-FROM rocker/drd
+FROM rocker/r-devel-san
 
 MAINTAINER Thibaut Jombart <[email protected]>
 
 RUN apt-get update && apt-get upgrade -y
-RUN apt-get install libssl-dev libxml2-dev pandoc pandoc-citeproc libblas-dev liblapack-dev git qpdf -y
+RUN apt-get install -y libcurl4-openssl-dev libssl-dev libfontconfig1-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev gdal-bin proj-bin libgdal-dev libproj-dev libgmp3-dev jags libfftw3-dev
 
 ## add guest user
 
@@ -15,35 +15,24 @@ RUN chmod a+rw /usr/local/lib/R/site-library -R
 
 ## install CRAN packages
 
-RUN echo 'options(download.file.method = "libcurl", repos = c(CRAN = "https://cran.ma.imperial.ac.uk"))' > ~/.Rprofile
+# RUN echo 'options(download.file.method = "libcurl", repos = c(CRAN = "https://cran.ma.imperial.ac.uk"))' > ~/.Rprofile
 
 RUN r -e "install.packages('devtools')" \
- && r -e "install.packages('roxygen2')" \
- && r -e "install.packages('testthat')" \
- && r -e "install.packages('rmarkdown')" \
- && r -e "install.packages('adegenet', dependencies = c('Depends', 'Imports'))" \
- && r -e "install.packages('pegas')" \
- && r -e "install.packages('hierfstat')" \
- && r -e "install.packages('poppr')" \
- && r -e "install.packages('akima')" \
- && r -e "install.packages('maps')" \
- && r -e "install.packages('splancs')" \
- && r -e "install.packages('tripack')"
+ && r -e "install.packages('adegenet', dependencies = TRUE)"
 
-
-
-## install devel packages (github)
-
-RUN r -e "devtools::install_github('thibautjombart/adegenet')"
+RUN r -e 'install.packages("BiocManager")' \
+ && r -e 'BiocManager::install("SNPRelate")' \
+ && r -e 'install.packages("dartR.base")'
 
 
 ## clone repos to get sources
+RUN apt-get install -y git
 
 RUN su guest
 RUN mkdir ~/dev
 WORKDIR /home/guest/dev
 
-RUN git clone https://github.com/thibautjombart/adegenet
+COPY . .
 
 WORKDIR /home/guest/
-RUN ls='ls --color=auto'
+CMD Rscript -e 'library(dartR.base); gl.pcoa(testset.gl)'

inst/CITATION

@@ -1,7 +1,7 @@
 citHeader("To cite the adegenet package:")
 
-citEntry(
-entry="Article",
+bibentry(
+bibtype="Article",
 title = "adegenet: a R package for the multivariate analysis of genetic markers",
 journal= "Bioinformatics",
 year = "2008",
@@ -13,8 +13,8 @@ textVersion = "Jombart, T. (2008) adegenet: a R package for the multivariate ana
 )
 
 
-citEntry(
-entry="Article",
+bibentry(
+bibtype="Article",
 title = "adegenet 1.3-1: new tools for the analysis of genome-wide SNP data",
 journal= "Bioinformatics",
 year = "2011",

man/auxil.Rd

@@ -5,6 +5,7 @@
 \alias{.rmspaces}
 \alias{.genlab}
 \alias{.readExt}
+\alias{.render.server.info}
 \alias{corner}
 \alias{num2col}
 \alias{fac2col}
@@ -50,6 +51,7 @@
     \item \code{.rmspaces}: remove peripheric spaces in a character string. 
     \item \code{.genlab}: generate labels in a correct alphanumeric ordering. 
     \item \code{.readExt}: read the extension of a given file. 
+    \item \code{.render.server.info} used to display session information for the dapcServer
   }
 
   Color palettes include:

man/pairDist.Rd

@@ -45,7 +45,7 @@ pairDistPlot(x, \dots)
     object. For \code{\linkS4class{genind}} objects, pairwise squared
     Euclidean distances are computed from the allele data. For
     \code{DNAbin} objects, distances are computed uing
-    \code{\link{dist.dna}}, and '...' is used to pass arguments to the
+    \code{dist.dna}, and '...' is used to pass arguments to the
     function.  }
 
   \item{grp}{a factor defining a grouping of individuals.}

src/snpbin.c

@@ -146,11 +146,11 @@ void bytesToBinInt(unsigned char *vecbytes, int *vecsize, int *vecres){
     temp = (int *) calloc(8, sizeof(int));
 
     for(i=0;i<*vecsize;i++){
-	byteToBinInt(vecbytes[i], temp);
-	for(j=0;j<=7;j++){
-	    vecres[j+idres] = temp[j];
-	}
-	idres = idres + 8;
+        byteToBinInt(vecbytes[i], temp);
+        for(j=0;j<=7;j++){
+            vecres[j+idres] = temp[j];
+        }
+        idres = idres + 8;
     }
 
     free(temp);
@@ -186,19 +186,20 @@ void bytesToInt(unsigned char *vecbytes, int *veclength, int *nbvec, int *vecres
 
     /* initialize result vector to 0 */
     for(i=0; i < *reslength; i++){
-	vecres[i]=0;
+        vecres[i]=0;
     }
 
     /* build output */
     for(k=0;k<*nbvec;k++){ /* for all input vector */
-	idres = 0;
-	for(i=0;i<*veclength;i++){ /* for one input vector */
-	    byteToBinInt(vecbytes[i+ k* *veclength], temp); /* byte -> 8 int (0/1)*/
-	    for(j=0;j<=7;j++){ /* fill in the result*/
-		vecres[j+idres] += temp[j];
-	    }
-	    idres = idres + 8;
-	}
+        idres = 0;
+        for(i=0;i<*veclength;i++){ /* for one input vector */
+            byteToBinInt(vecbytes[i+ k* *veclength], temp); /* byte -> 8 int (0/1)*/
+            for(j=0;j<=7;j++){ /* fill in the result*/
+                if (j+idres >= *reslength) break; // do not decode padding bytes
+                vecres[j+idres] += temp[j];
+            }
+            idres = idres + 8;
+        }
     }
     free(temp);
 } /* end bytesToInt */
@@ -214,18 +215,19 @@ void bytesToDouble(unsigned char *vecbytes, int *veclength, int *nbvec, double *
 
     /* initialize result vector to 0 */
     for(i=0; i < *reslength; i++){
-	vecres[i]=0.0;
+      vecres[i]=0.0;
     }
 
     for(k=0;k<*nbvec;k++){ /* for all input vector */
-	idres = 0;
-	for(i=0;i<*veclength;i++){ /* for one input vector */
-	    byteToBinDouble(vecbytes[i+ k* *veclength], temp); /* byte -> 8 double (0/1)*/
-	    for(j=0;j<=7;j++){ /* fill in the result*/
-		vecres[j+idres] += temp[j];
-	    }
-	    idres = idres + 8;
-	}
+        idres = 0;
+        for(i=0;i<*veclength;i++){ /* for one input vector */
+            byteToBinDouble(vecbytes[i+ k* *veclength], temp); /* byte -> 8 double (0/1)*/
+            for(j=0;j<=7;j++){ /* fill in the result*/
+                if (j+idres >= *reslength) break; // do not decode padding bytes
+                vecres[j+idres] += temp[j];
+            }
+            idres = idres + 8;
+        }
     }
     free(temp);
 } /* end bytesToInt */