Moved mixsqp from Suggests to Imports.

DESCRIPTION

@@ -2,7 +2,7 @@ Package: mashr
 Type: Package
 Encoding: UTF-8
 Title: Multivariate Adaptive Shrinkage 
-Version: 0.2.20.0583
+Version: 0.2.20.0584
 Date: 2019-02-11
 Authors@R: c(person("Matthew","Stephens",role=c("aut","cre"),
                     email="[email protected]"),
@@ -27,15 +27,15 @@ Imports:
     rmeta,
     Rcpp (>= 0.12.11),
     mvtnorm,
-    abind
+    abind,
+    mixsqp
 LinkingTo:
     Rcpp, 
     RcppArmadillo,
     RcppGSL
 Suggests:
     MASS,
     REBayes,
-    mixsqp,
     flashr,
     corrplot,
     testthat,

R/opt.R

@@ -16,17 +16,10 @@ optimize_pi = function(matrix_lik, pi_init = NULL,
   if (optmethod == "mixIP")
    if (!requireNamespace("REBayes",quietly = TRUE)) {
      warning(paste("optmethod = \"mixIP\" requires REBayes package;",
-                   "switching to optmethod = \"mixEM\""))
-     optmethod <- "mixEM"
+                   "switching to optmethod = \"mixSQP\""))
+     optmethod <- "mixSQP"
    }
 
-  if (optmethod == "mixSQP")
-    if (!requireNamespace("mixsqp",quietly = TRUE)) {
-      warning(paste("optmethod = \"mixSQP\" requires mixsqp package;",
-                    "switching to optmethod = \"mixEM\""))
-      optmethod <- "mixEM"
-    }
-
   if(optmethod == "mixIP"){control = ashr:::set_control_mixIP(control)
   }else if(optmethod == 'mixEM' || optmethod == 'cxxMixSquarem'){
     control = ashr:::set_control_squarem(control, nrow(matrix_lik))

README.md

@@ -42,13 +42,14 @@ repository useful for your work, please cite:
 
 Please follow these steps to install mashr.
 
-1. Unlike most packages available on CRAN, mashr is not precompiled;
-   therefore, you will need to make sure that your R installation is
-   properly set up to compile packages with C++ source; in particular,
-   the C++ compiler programs supported by your version of R should be
-   installed on your computer, and R should be correctly configured to
-   call these compilers. See the [CRAN documentation][cran-docs]
-   for more information.
+1. Unlike most packages available on CRAN, mashr is not precompiled,
+   and therefore to install mashr you will need to make sure that your
+   R installation is properly set up to compile packages with C++
+   source; in particular, the C++ compiler programs supported by your
+   version of R should be installed on your computer, and R should be
+   correctly configured to call these compilers when installing
+   packages from source. For more information, see the
+   [CRAN documentation][cran-docs].
 
 2. Install the [latest release][mashr-release-latest] of the mashr
    package using [devtools][devtools]:
@@ -58,15 +59,20 @@ Please follow these steps to install mashr.
     devtools::install_github("stephenslab/mashr")
     ```
 
-   This command should have automatically retrieved and installed the
-   latest version of the ashr package from Github. If it did not, you
-   can install the ashr package separately using devtools:
+   This command should automatically install any missing dependencies
+   that are available from CRAN. This command should also
+   automatically retrieve and install the latest version of the ashr
+   package from Github. If it does not, you can install the ashr
+   package separately using devtools:
 
    ```R
    devtools::install_github("stephens999/ashr")
    ```
 
-3. Several additional packages are needed to build vignettes:
+3. By default, the `devtools::install_github` function does not build
+   the vignettes. If you would like to build the vignettes, you will
+   need to several additional packages, including [flashr][flashr],
+   that are used only in the vignettes:
 
    ```R
    install.packages(c("kableExtra","corrplot"))