[IMP] Users can overwrite the package compiler

frahik · Oct 17, 2019 · 7a75ff9 · 7a75ff9
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BMTME
 Title: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis
-Version: 1.0.11
+Version: 1.0.12
 Date: 2019-9-30
 Language: en-US
 Authors@R: c(person("Francisco Javier", "Luna-Vazquez", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5370-7152")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+BMTME v1.0.12
+==============
+
+Changes:
+
+ * [FIX] Users can overwrite the package compiler.
+
 BMTME v1.0.11
 ==============
 

diff --git a/README.Rmd b/README.Rmd
@@ -10,22 +10,36 @@ output: github_document
   </h4>
 
   <p align="center">
-  <a href="https://www.tidyverse.org/lifecycle/#maturing">
-    <img src="https://img.shields.io/badge/lifecycle-maturing-blue.svg" alt="Maturing"> </a>
-  <a href="https://travis-ci.org/frahik/BMTME">
-    <img src="https://travis-ci.org/frahik/BMTME.svg?branch=master" alt="Travis build status"> </a> 
-  <a href='https://coveralls.io/github/frahik/BMTME'>
+    <a href="https://www.tidyverse.org/lifecycle/#maturing">
+      <img src="https://img.shields.io/badge/lifecycle-maturing-blue.svg" alt="Maturing">
+    </a>
+    <a href="https://www.gnu.org/licenses/lgpl-3.0">
+      <img src="https://img.shields.io/badge/License-LGPL%20v3-blue.svg" alt="LGPL, Version 3.0">
+    </a>
+    <a href="http://www.repostatus.org/#active">
+      <img src="https://www.repostatus.org/badges/latest/active.svg" alt="The project has reached a stable, usable state and is being actively developed.">
+    </a> 
+    <a href="https://cran.r-project.org/package=BMTME">
+      <img src="http://cranlogs.r-pkg.org/badges/BMTME" alt="Dowloads from the CRAN">
+    </a> 
+  </p>
+
+  <p align="center">
+    <a href="https://travis-ci.org/frahik/BMTME">
+      <img src="https://travis-ci.org/frahik/BMTME.svg?branch=master" alt="Travis build status">
+    </a>
     <a href="https://ci.appveyor.com/project/frahik/bmtme">
-    <img src="https://ci.appveyor.com/api/projects/status/r2vog9sa30yutl5n?svg=true" alt="Appveyor build status"> </a>
-    <img src='https://coveralls.io/repos/github/frahik/BMTME/badge.svg?branch=master' alt='Coverage Status'/> </a>
-  <a href="https://www.gnu.org/licenses/lgpl-3.0">
-    <img src="https://img.shields.io/badge/License-LGPL%20v3-blue.svg" alt="LGPL, Version 3.0"> </a>
-  <a href="http://www.repostatus.org/#active">
-    <img src="https://www.repostatus.org/badges/latest/active.svg" alt="The project has reached a stable, usable state and is being actively developed."> </a>
-  <a href="">
-    <img src="http://cranlogs.r-pkg.org/badges/BMTME" alt="Dowloads from the CRAN"> </a>
-  <a href="https://cran.r-project.org/package=BMTME">
-    <img src="http://www.r-pkg.org/badges/version-ago/BMTME" alt="CRAN"> </a>
+      <img src="https://ci.appveyor.com/api/projects/status/r2vog9sa30yutl5n?svg=true" alt="Appveyor build status">
+    </a>
+    <a href='https://coveralls.io/github/frahik/BMTME'>
+      <img src='https://coveralls.io/repos/github/frahik/BMTME/badge.svg?branch=master' alt='Coverage Status'/>
+    </a> 
+    <a href="https://cran.r-project.org/package=BMTME">
+      <img src="http://www.r-pkg.org/badges/version-ago/BMTME" alt="CRAN">
+    </a>
+    <a href="https://cran.r-project.org/package=BMTME">
+      <img src="https://cranchecks.info/badges/summary/BMTME" alt="CRAN">
+    </a>
   </p>
 
   <h4 align="center">

diff --git a/README.md b/README.md
@@ -6,36 +6,42 @@
 
 <h3 align="center">
 
-Bayesian Multi-Trait Multi-Environment | Development version 1.0.10
+Bayesian Multi-Trait Multi-Environment | Development version 1.0.12
 
 </h4>
 
 <p align="center">
 
 <a href="https://www.tidyverse.org/lifecycle/#maturing">
 <img src="https://img.shields.io/badge/lifecycle-maturing-blue.svg" alt="Maturing">
-</a> <a href="https://travis-ci.org/frahik/BMTME">
-<img src="https://travis-ci.org/frahik/BMTME.svg?branch=master" alt="Travis build status">
-</a> <a href='https://coveralls.io/github/frahik/BMTME'>
-<a href="https://ci.appveyor.com/project/frahik/bmtme">
-<img src="https://ci.appveyor.com/api/projects/status/r2vog9sa30yutl5n?svg=true" alt="Appveyor build status">
-</a>
-<img src='https://coveralls.io/repos/github/frahik/BMTME/badge.svg?branch=master' alt='Coverage Status'/>
 </a> <a href="https://www.gnu.org/licenses/lgpl-3.0">
 <img src="https://img.shields.io/badge/License-LGPL%20v3-blue.svg" alt="LGPL, Version 3.0">
 </a> <a href="http://www.repostatus.org/#active">
 <img src="https://www.repostatus.org/badges/latest/active.svg" alt="The project has reached a stable, usable state and is being actively developed.">
-</a> <a href="">
+</a> <a href="https://cran.r-project.org/package=BMTME">
 <img src="http://cranlogs.r-pkg.org/badges/BMTME" alt="Dowloads from the CRAN">
+</a>
+
+</p>
+
+<p align="center">
+
+<a href="https://travis-ci.org/frahik/BMTME">
+<img src="https://travis-ci.org/frahik/BMTME.svg?branch=master" alt="Travis build status">
+</a> <a href="https://ci.appveyor.com/project/frahik/bmtme">
+<img src="https://ci.appveyor.com/api/projects/status/r2vog9sa30yutl5n?svg=true" alt="Appveyor build status">
+</a> <a href='https://coveralls.io/github/frahik/BMTME'>
+<img src='https://coveralls.io/repos/github/frahik/BMTME/badge.svg?branch=master' alt='Coverage Status'/>
 </a> <a href="https://cran.r-project.org/package=BMTME">
 <img src="http://www.r-pkg.org/badges/version-ago/BMTME" alt="CRAN">
-</a>
+</a> <a href="https://cran.r-project.org/package=BMTME">
+<img src="https://cranchecks.info/badges/summary/BMTME" alt="CRAN"> </a>
 
 </p>
 
 <h4 align="center">
 
-\[Last README update: 2019-09-30\]
+\[Last README update: 2019-10-17\]
 
 </h4>
 
@@ -55,7 +61,7 @@ Bayesian Multi-Trait Multi-Environment | Development version 1.0.10
 
 <h2 id="news">
 
-News of this version (1.0.10)
+News of this version (1.0.12)
 
 </h2>
 
@@ -139,7 +145,7 @@ citation('BMTME')
     ##   Francisco Javier Luna-Vazquez, Fernando H. Toledo, Osval Antonio
     ##   Montesinos-Lopez, Abelardo Montesinos-Lopez and Jose Crossa
     ##   (2019). BMTME: Bayesian Multi-Trait Multi-Environment for
-    ##   Genomic Selection Analysis. R package version 1.0.10.
+    ##   Genomic Selection Analysis. R package version 1.0.12.
     ##   https://github.com/frahik/BMTME
     ## 
     ## A BibTeX entry for LaTeX users is
@@ -148,7 +154,7 @@ citation('BMTME')
     ##     title = {BMTME: Bayesian Multi-Trait Multi-Environment for Genomic Selection Analysis},
     ##     author = {Francisco Javier Luna-Vazquez and Fernando H. Toledo and Osval Antonio Montesinos-Lopez and Abelardo Montesinos-Lopez and Jose Crossa},
     ##     year = {2019},
-    ##     note = {R package version 1.0.10},
+    ##     note = {R package version 1.0.12},
     ##     url = {https://github.com/frahik/BMTME},
     ##   }
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -20,21 +20,9 @@ This does
 
 clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64
 -o BMTME.so RcppExports.o Sample_IW.o -lstdc++
--L/data/gannet/ripley/R/R-clang/lib -lRlapack
--L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath
 
 The hard-coded inclusion of g++'s C++ library is wrong and harmful.
 
-I don't know what you think
-
-CC=ccache clang -Qunused-arguments
-CXX=ccache clang++ -Qunused-arguments
-
-does, but users cannot override these in src/Makevars so this should be
-cleaned up.
-
-Please correct ASAP and before Oct 12 to retain the package on CRAN.
-
 ## Special comments
 
 This version implements the corrections mentioned in the last round of comments

diff --git a/src/Makevars b/src/Makevars
@@ -1 +1 @@
-PKG_LIBS = -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/Makevars.win b/src/Makevars.win