support installation without OpenMP

README.md

@@ -55,13 +55,18 @@ Analysis. arXiv:1710.11028 [stat].
 ### Installation
 
 You can install the `pCMF` R package with the following R command:
+```R
+devtools::install_git("https://gitlab.inria.fr/gdurif/pCMF", subdir="pkg", branch="prod")
+```
 
+If you don't have OpenMP installed on your machine (for instance on MacOS), you can run the following command:
 ```R
-devtools::install_git("https://gitlab.inria.fr/gdurif/pCMF", subdir="pkg")
+devtools::install_git("https://gitlab.inria.fr/gdurif/pCMF", subdir="pkg", branch="prod_no_omp")
 ```
+**Note:** We encourage you to install a compiler (e.g. gcc) that supports OpenMP in order 
+to benefit from multi-core computing and improve computation performance.
 
 To install the `devtools` package, you can run:
-
 ```R
 install.packages("devtools")
 ```
@@ -70,8 +75,19 @@ You can also use the git repository available at <https://gitlab.inria.fr/gdurif
 then build and install the package with Rstudio (the [project file](./pCMF.Rproj) 
 is set accordingly) or with the R command line tools.
 
-Once you cloned the git repository, you can also run:
+To clone the repository, you can do:
+```bash
+git clone https://gitlab.inria.fr/gdurif/pCMF.git
+```
+**Note:** if you don't have OpenMP on your system (c.f. previously), after cloning
+the repository, you should do:
+```bash
+cd pCMF
+git fetch origin prod_no_omp
+git checkout prod_no_omp
+```
 
+Once you cloned the git repository, you can run to install the `pCMF` package:
 ```R
 devtools::install("/path/to/pCMF/pkg") # you should edit the path
 ```

pkg/DESCRIPTION

@@ -2,7 +2,7 @@ Package: pCMF
 Type: Package
 Title: Probabilistic Factorization of Count Matrices
 Version: 1.0
-Date: 2018-07-04
+Date: 2018-10-25
 Author: Ghislain Durif
 Maintainer: Ghislain Durif <gd.dev@libertymail.net>
 Description: Routines for probabilistic count matrices factorization (pCMF). 

pkg/src/gap_factor_model.cpp

@@ -23,8 +23,11 @@
 * \date 07/02/2018
 */
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 

pkg/src/run_gap_factor.cpp

@@ -23,14 +23,11 @@
 * \date 03/04/2018
 */
 
-#include <omp.h>
-// [[Rcpp::plugins(openmp)]]
 #include <Rcpp.h>
 #include <RcppEigen.h>
 
 #include "algorithm_variational_EM.h"
 #include "gap_factor_model.h"
-#include "utils/random.h"
 #include "wrapper_gap_factor.h"
 
 // [[Rcpp::depends(RcppEigen)]]

pkg/src/run_poisson_nmf.cpp

@@ -23,15 +23,11 @@
 * \date 26/02/2018
 */
 
-#include <omp.h>
-// [[Rcpp::plugins(openmp)]]
 #include <Rcpp.h>
 #include <RcppEigen.h>
-#include <stdio.h>
 
 #include "algorithm_simple_factor.h"
 #include "poisson_nmf.h"
-#include "utils/random.h"
 #include "wrapper_matrix_factor.h"
 
 // [[Rcpp::depends(RcppEigen)]]

pkg/src/run_sparse_gap_factor.cpp

@@ -23,14 +23,11 @@
 * \date 10/04/2018
 */
 
-#include <omp.h>
-// [[Rcpp::plugins(openmp)]]
 #include <Rcpp.h>
 #include <RcppEigen.h>
 
 #include "algorithm_variational_EM.h"
 #include "sparse_gap_factor_model.h"
-#include "utils/random.h"
 #include "wrapper_sparse_gap_factor.h"
 
 // [[Rcpp::depends(RcppEigen)]]

pkg/src/run_zi_gap_factor.cpp

@@ -23,15 +23,11 @@
 * \date 10/04/2018
 */
 
-#include <omp.h>
-// [[Rcpp::plugins(openmp)]]
 #include <Rcpp.h>
 #include <RcppEigen.h>
-#include <stdio.h>
 
 #include "algorithm_variational_EM.h"
 #include "zi_gap_factor_model.h"
-#include "utils/random.h"
 #include "wrapper_gap_factor.h"
 
 // [[Rcpp::depends(RcppEigen)]]

pkg/src/run_zi_sparse_gap_factor.cpp

@@ -23,14 +23,11 @@
 * \date 10/04/2018
 */
 
-#include <omp.h>
-// [[Rcpp::plugins(openmp)]]
 #include <Rcpp.h>
 #include <RcppEigen.h>
 
 #include "algorithm_variational_EM.h"
 #include "zi_sparse_gap_factor_model.h"
-#include "utils/random.h"
 #include "wrapper_sparse_gap_factor.h"
 
 // [[Rcpp::depends(RcppEigen)]]

pkg/src/sparse_gap_factor_model.cpp

@@ -23,8 +23,11 @@
  * \date 10/04/2018
  */
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 

pkg/src/test_gap_factor_algo.cpp

@@ -18,8 +18,11 @@
 
 #ifdef _DEV
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 #include <stdio.h>

pkg/src/test_simple_algo.cpp

@@ -18,8 +18,11 @@
 
 #ifdef _DEV
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 #include <stdio.h>

pkg/src/wrapper_gap_factor.h

@@ -27,8 +27,11 @@
 #ifndef GAP_FACTOR_WRAPPER_H
 #define GAP_FACTOR_WRAPPER_H
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 #include <stdio.h>

pkg/src/wrapper_matrix_factor.h

@@ -27,8 +27,11 @@
 #ifndef MATRIX_FACTOR_WRAPPER_H
 #define MATRIX_FACTOR_WRAPPER_H
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 #include <stdio.h>

pkg/src/wrapper_sparse_gap_factor.h

@@ -27,8 +27,11 @@
 #ifndef SPARSE_GAP_FACTOR_WRAPPER_H
 #define SPARSE_GAP_FACTOR_WRAPPER_H
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 #include <stdio.h>

pkg/src/zi_gap_factor_model.cpp

@@ -23,8 +23,11 @@
 * \date 10/04/2018
 */
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>
 

pkg/src/zi_sparse_gap_factor_model.cpp

@@ -23,8 +23,11 @@
  * \date 10/04/2018
  */
 
+#if defined(_OPENMP)
 #include <omp.h>
 // [[Rcpp::plugins(openmp)]]
+#endif
+
 #include <Rcpp.h>
 #include <RcppEigen.h>