Merge pull request #73 from mmollina/testless

Testless
mmollina · Mar 6, 2024 · 7bcae98 · 7bcae98
2 parents f7e8d07 + 6c1d431
commit 7bcae98
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: mappoly
 Type: Package
 Title: Genetic Linkage Maps in Autopolyploids
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: c(person(given = "Marcelo",
                     family = "Mollinari",
                     role = c("aut", "cre"),

diff --git a/MAPpoly.Rproj b/MAPpoly.Rproj
@@ -14,7 +14,7 @@ LaTeX: pdfLaTeX
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source --resave-data
+PackageInstallArgs: --no-multiarch --with-keep.source --resave-data --use-LTO
 PackageBuildArgs: --resave-data
 PackageCheckArgs: --no-vignettes --as-cran --install-args=--build
 PackageRoxygenize: rd,collate,namespace,vignette
diff --git a/NAMESPACE b/NAMESPACE
@@ -113,7 +113,6 @@ export(split_and_rephase)
 export(summary_maps)
 export(update_framework_map)
 export(update_map)
-export(update_missing)
 import(RCurl)
 import(Rcpp)
 import(fields)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# MAPpoly version 0.4.1
+ - Addressed the `--use-LTO` installation failure issue
+
 # MAPpoly version 0.4.0
  - Functions to build maps in individual parents
  - Functions to merge individual maps

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,6 +1,22 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+calc_genoprob_cpp <- function(m, geno, ph1, ph2, rf, probs, verbose) {
+    .Call('_mappoly_calc_genoprob_cpp', PACKAGE = 'mappoly', m, geno, ph1, ph2, rf, probs, verbose)
+}
+
+calc_genprob_haplo_cpp <- function(m, n_mrk, n_ind, haplo, emit, rf, probs, verbose) {
+    .Call('_mappoly_calc_genprob_haplo_cpp', PACKAGE = 'mappoly', m, n_mrk, n_ind, haplo, emit, rf, probs, verbose)
+}
+
+calc_genprob_haplo_highprec_cpp <- function(m, n_mrk, n_ind, haplo, emit, rf, probs, verbose) {
+    .Call('_mappoly_calc_genprob_haplo_highprec_cpp', PACKAGE = 'mappoly', m, n_mrk, n_ind, haplo, emit, rf, probs, verbose)
+}
+
+loglike_hmm_cpp <- function(m, geno, ph1, ph2, rf, verbose) {
+    .Call('_mappoly_loglike_hmm_cpp', PACKAGE = 'mappoly', m, geno, ph1, ph2, rf, verbose)
+}
+
 .vcf_get_probabilities <- function(mat, pl_pos) {
     .Call('_mappoly_vcf_get_probabilities', PACKAGE = 'mappoly', mat, pl_pos)
 }

diff --git a/R/calc_genoprob.R b/R/calc_genoprob.R
@@ -96,17 +96,17 @@ calc_genoprob <- function(input.map, step = 0,  phase.config = "best", verbose =
     phQ[rownames(Dtemp)] <- phQtemp
     seq.rf.pseudo <- mf_h(diff(map.pseudo))
   }
-  for (j in 1:nrow(D))
-    D[j, D[j, ]  ==  input.map$info$ploidy + 1] <- dp[j] + dq[j] + 1 + as.numeric(dp[j] == 0 || dq[j] == 0)
-  res.temp <- .Call("calc_genoprob",
-                  ploidy,
-                  t(D),
-                  phP,
-                  phQ,
-                  seq.rf.pseudo,
-                  as.numeric(rep(0, choose(ploidy, ploidy/2)^2 * n.mrk * n.ind)),
-                  verbose = verbose,
-                  PACKAGE = "mappoly")
+  for (j in 1:nrow(D)){
+    D[j, D[j, ]  ==  input.map$info$ploidy + 1] <- dp[j] + dq[j] + 1 + 
+      as.numeric(dp[j] == 0 || dq[j] == 0)    
+  }
+  res.temp <- calc_genoprob_cpp(ploidy,
+                                t(D),
+                                phP,
+                                phQ,
+                                seq.rf.pseudo,
+                                as.numeric(rep(0, choose(ploidy, ploidy/2)^2 * n.mrk * n.ind)),
+                                verbose = verbose)
   if(verbose) cat("\n")
   dim(res.temp[[1]]) <- c(choose(ploidy,ploidy/2)^2,n.mrk,n.ind)
   dimnames(res.temp[[1]]) <- list(kronecker(apply(combn(letters[1:ploidy],ploidy/2),2, paste, collapse = ""),

diff --git a/R/haplotype_map_utils.R b/R/haplotype_map_utils.R
@@ -258,27 +258,23 @@ calc_genoprob_haplo <- function(ploidy, n.mrk, n.ind, haplo, emit = NULL,
   }
   mrk.names <- names(haplo)
   if(highprec){
-    res.temp <- .Call("calc_genprob_haplo_highprec",
-                      ploidy,
-                      n.mrk,
-                      n.ind,
-                      haplo,
-                      emit,
-                      rf_vec,
-                      as.numeric(rep(0, choose(ploidy, ploidy/2)^2 * n.mrk * n.ind)),
-                      verbose,
-                      PACKAGE = "mappoly")
+    res.temp <- calc_genprob_haplo_highprec_cpp(ploidy,
+                                                n.mrk,
+                                                n.ind,
+                                                haplo,
+                                                emit,
+                                                rf_vec,
+                                                as.numeric(rep(0, choose(ploidy, ploidy/2)^2 * n.mrk * n.ind)),
+                                                verbose)
   } else{
-    res.temp <- .Call("calc_genprob_haplo",
-                      ploidy,
-                      n.mrk,
-                      n.ind,
-                      haplo,
-                      emit,
-                      rf_vec,
-                      as.numeric(rep(0, choose(ploidy, ploidy/2)^2 * n.mrk * n.ind)),
-                      verbose,
-                      PACKAGE = "mappoly")
+    res.temp <- calc_genprob_haplo_cpp(ploidy,
+                                       n.mrk,
+                                       n.ind,
+                                       haplo,
+                                       emit,
+                                       rf_vec,
+                                       as.numeric(rep(0, choose(ploidy, ploidy/2)^2 * n.mrk * n.ind)),
+                                       verbose)
   }
   if(verbose) cat("\n")
   dim(res.temp[[1]]) <- c(choose(ploidy,ploidy/2)^2,n.mrk,n.ind)

diff --git a/R/loglike_hmm.R b/R/loglike_hmm.R
@@ -43,14 +43,12 @@ loglike_hmm <- function(input.map, input.data = NULL, verbose = FALSE)
     D[j, D[j, ]  ==  input.map$info$ploidy + 1] <- dp[j] + dq[j] + 1 + as.numeric(dp[j] == 0 || dq[j] == 0)
   for(i in 1:length(input.map$maps)){
     rf.temp <- input.map$maps[[i]]$seq.rf
-    res.temp <- .Call("loglike_hmm",
-                    input.map$info$ploidy,
-                    t(D),
-                    lapply(input.map$maps[[i]]$seq.ph$P, function(x) x-1),
-                    lapply(input.map$maps[[i]]$seq.ph$Q, function(x) x-1),
-                    rf.temp,
-                    verbose,
-                    PACKAGE = "mappoly")
+    res.temp <- loglike_hmm_cpp(input.map$info$ploidy,
+                                t(D),
+                                lapply(input.map$maps[[i]]$seq.ph$P, function(x) x-1),
+                                lapply(input.map$maps[[i]]$seq.ph$Q, function(x) x-1),
+                                rf.temp,
+                                verbose)
     input.map$maps[[i]]$loglike <- res.temp[[1]]
   }
   return(input.map)

diff --git a/R/utils.R b/R/utils.R
@@ -478,21 +478,7 @@ mp_pallet2 <- colorRampPalette(c("#911eb4", "#000075","#4363d8","#42d4f4","#4699
 mp_pallet3 <- colorRampPalette(c("#ffe119", "#f58231","#e6194b","#808000","#9a6324", "#800000","#911eb4", "#000075","#4363d8","#42d4f4","#469990", "#3cb44b"))
 
 #' Update missing information
-#'
-#' Updates the missing data in the dosage matrix of an object of class 
-#' \code{mappoly.data} given a new probability threshold
-#' @param input.data an object of class \code{mappoly.data}
-#' @param prob.thres probability threshold to associate a marker call to a 
-#'     dosage. Markers with maximum genotype probability smaller than 'prob.thres' 
-#'     are considered as missing data for the dosage calling purposes
-#' @examples
-#' \donttest{
-#' data.updated = update_missing(hexafake.geno.dist, prob.thres = 0.5)
-#' print(hexafake.geno.dist)
-#' print(data.updated)
-#' }
-#' @author Marcelo Mollinari, \email{[email protected]}
-#' @export
+#' @keywords internal
 update_missing <- function(input.data, prob.thres = 0.95){
   geno.dose <- dist_prob_to_class(geno = input.data$geno, prob.thres = prob.thres)
   if(geno.dose$flag)

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,32 +1,51 @@
 ## Re-submission of MAPpoly package
 
-This is a re-submission of MAPpoly package. This version (0.4.0), contains the following changes
+This is a re-submission of the MAPpoly package. This version includes changes to address the issues that led to its archival on CRAN, specifically the failure in installing the package using `--use-LTO`. We have made corrections to ensure compatibility and successful installation with `--use-LTO`.
 
-  - Update DESCRIPTION file
-  - Functions to build maps in individual parents
-  - Functions to merge individual maps
-  - Imputation functions based on map
-  - Functions to edit order interactively
-  - Fix minor bugs 
+Changes in this submission include:
+
+  - Addressed the `--use-LTO` installation failure issue
 
 Thank you for reviewing our re-submission!
 
 ## Test environments
-* local R installation (macOS Somona 14.3.1), R 4.3.2
-* local R installation (Ubuntu 22.04), R 4.3.2
+* local R installation (macOS Sonoma 14.3.1), R 4.3.3
+   - Apple clang version 14.0.0 (clang-1400.0.29.202)
+   - GNU Fortran (GCC) 12.2.0
+* local R installation (Ubuntu 22.04), R 4.3.3
+   - gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+   - GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+   - Compiled using the following configuration:
+
+      ./configure \
+       --prefix=/opt/R/${R_VERSION} \
+       --enable-R-shlib \
+       --enable-memory-profiling \
+       --with-blas \
+       --with-lapack\
+       --enable-lto=R
+
+    And installed using `R CMD INSTALL --use-LTO mappoly_0.4.1.tar.gz`
+* local R installation (Ubuntu 22.04), R devel
+   - Intel(R) oneAPI DPC++/C++ Compiler 2024.0.2 (2024.0.2.20231213)
+   - ifx (IFX) 2024.0.2 20231213
+
 * Win-builder (release and devel)
 
+
 ## R CMD check results 
 
 0 errors | 0 warnings | 2 notes
 
- - on local macOS: R 4.3.2
+ - on local macOS: R 4.3.3
    * installed size is 8.2Mb
      sub-directories of 1Mb or more:
        * R:      2.8Mb
        * data:   3.0Mb
-   * GNU make is a SystemRequirements.      
-
+   * GNU make is a SystemRequirements.
+
+ - Checked with `--use-LTO` flag: Installation successful without any errors or warnings.
+
 ## Downstream dependencies
 
 We checked 3 reverse dependencies (3 from CRAN + 0 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

diff --git a/man/update_missing.Rd b/man/update_missing.Rd