From 09be724c07686930c4c3771ef2e5532fd4134a30 Mon Sep 17 00:00:00 2001
From: Benjamin Christoffersen <boennecd@gmail.com>
Date: Fri, 3 Jan 2020 10:10:16 +0100
Subject: [PATCH] fix lto issue prepare for submission

---
 NEWS.md               |  1 +
 TODO                  |  4 +---
 cran-comments.md      | 34 +++++++++++++---------------------
 src/Makevars          |  1 +
 src/R_BLAS_LAPACK.cpp | 22 +++++++++++++++++-----
 5 files changed, 33 insertions(+), 29 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index cbabb60..02b6dbb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
 # pargm 0.1.4
 * `stop`s when there are more variables than observations. Previously, this 
   caused a crash.
+* handle Fortran string length argument.
 
 # pargm 0.1.3
 * Fix bug found with Valgrind.
diff --git a/TODO b/TODO
index 510a712..598113e 100644
--- a/TODO
+++ b/TODO
@@ -1,7 +1,5 @@
 make a function which can take a function input which yields the input for
 each chunk to allow for larger data sets that do not fit in memory
-make a method like `speedglm` which computes the cross product of the weighted
-design matrix which is faster but less stable
-the Armadillo `rows` may be slow when the copy is made? 
+the Armadillo `rows` may be slow when the copy is made?
 there may be an overhead with the current abstract family class
 fix issue with order in `summary.glm`
diff --git a/cran-comments.md b/cran-comments.md
index 63f8a16..91adbe2 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,24 +1,16 @@
 ## Test environments
-* Ubuntu 18.04 LTS
-  R version 3.5.3
-* Ubuntu 14.04.5 LTS (on travis-ci with codename: trusty)
-  R version 3.5.2
-* win-builder (devel and release)
-* Local Ubuntu 18.04 with R 3.5.2 and with clang 6.0.0 with ASAN and 
+* Ubuntu 18.04 LTS with gcc 8.3.0
+  R version 3.6.1
+* Ubuntu 16.04 LTS (on travis-ci)
+  R version 3.6.1
+* Ubuntu 18.04 LTS with gcc 8.3.0 with --enable-lto
+  R devel (2019-11-06 r77376)
+* Ubuntu 18.04 LTS with clang 6.0.0 with ASAN and 
   UBSAN checks
-* The following rhub platforms:
-  fedora-clang-devel
-  fedora-gcc-devel
-  debian-gcc-patched
-  debian-gcc-devel
-  debian-gcc-release
-  linux-x86_64-rocker-gcc-san
-  solaris-x86-patched
-
+  R devel (2019-11-06 r77376)
+* win-builder (devel and release)
+* `rhub::check_on_solaris()`
+  
 ## R CMD check results
-There were no ERRORs, or WARNINGs. There is a NOTE on `fedora-gcc-devel`
-on rhub, my local machine, and `debian-gcc-release` on rhub about the size 
-of the package.
-
-## Resubmission
-`R CMD check --use-valgrind --as-cran` passes without any errors.
+The LTO issue have been solved. There is a note about the size of the 
+package on some platforms.
diff --git a/src/Makevars b/src/Makevars
index 22ebc63..dd9d6cc 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1 +1,2 @@
+PKG_CPPFLAGS = -DUSE_FC_LEN_T
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/R_BLAS_LAPACK.cpp b/src/R_BLAS_LAPACK.cpp
index 57a9280..a0d4aef 100644
--- a/src/R_BLAS_LAPACK.cpp
+++ b/src/R_BLAS_LAPACK.cpp
@@ -1,6 +1,15 @@
-#include <Rcpp.h>
+#include <Rconfig.h>
 #include <R_ext/BLAS.h>
+#ifndef FCLEN
+#define FCLEN
+#endif
+#ifndef FCONE
+#define FCONE
+#endif
 #include <R_ext/Lapack.h>
+
+#include <Rcpp.h>
+
 #include <R_ext/Applic.h>
 #include "R_BLAS_LAPACK.h"
 
@@ -27,7 +36,7 @@ namespace R_BLAS_LAPACK {
         &n, &nrhs,
         A, &n,
         B, &n,
-        &info);
+        &info FCONE FCONE FCONE);
 
     if(info != 0){
       std::stringstream str;
@@ -42,7 +51,8 @@ namespace R_BLAS_LAPACK {
               const double* tau, double* c, const int* ldc,
               double* work, const int* lwork, int* info){
     F77_CALL(dormqr)(
-        side, trans, m, n, k, a, lda, tau, c, ldc, work, lwork, info);
+        side, trans, m, n, k, a, lda, tau, c, ldc, work, lwork, info
+        FCONE FCONE);
   }
 
   void dgeqp3(const int* m, const int* n, double* a, const int* lda,
@@ -65,13 +75,15 @@ namespace R_BLAS_LAPACK {
              const double *alpha, const double *a, const int *lda,
              const double *x, const int *incx, const double *beta,
              double *y, const int *incy){
-    F77_CALL(dgemv)(trans, m, n, alpha, a, lda, x, incx, beta, y, incy);
+    F77_CALL(dgemv)(trans, m, n, alpha, a, lda, x, incx, beta, y, incy
+                    FCONE);
   }
 
   void dsyrk(const char *uplo, const char *trans,
              const int *n, const int *k,
              const double *alpha, const double *a, const int *lda,
              const double *beta, double *c, const int *ldc){
-    F77_CALL(dsyrk)(uplo, trans, n, k, alpha, a, lda, beta, c, ldc);
+    F77_CALL(dsyrk)(uplo, trans, n, k, alpha, a, lda, beta, c, ldc
+                    FCONE FCONE);
   }
 }