Browse code

Disable threading when flexiblas is found

Ben Bolstad authored on 25/02/2021 00:52:20
Showing1 changed files
... ...
@@ -55,7 +55,14 @@ if test "x$use_pthread_stack_min" = xno; then
55 55
 fi
56 56
 
57 57
 
58
-
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+AC_MSG_CHECKING([if R is using flexiblas])
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+BLAS_LIBS=`"${R_HOME}/bin/R" CMD config BLAS_LIBS`
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+if echo "${BLAS_LIBS}" | grep flexiblas > /dev/null; then
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+    AC_MSG_RESULT([flexiblas found. preprocessCore specific threading will be disabled])
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+    use_pthreads=no
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+else
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+    AC_MSG_RESULT([flexiblas not found. preprocessCore threading will not be disabled])
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+fi
59 66
 
60 67
 AC_ARG_ENABLE([threading],
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 	AS_HELP_STRING([--disable-threading],[Disable threading]))
Browse code

Reverting openblas usage check

Francisco D. MorĂ³n-Duran authored on 29/07/2019 13:58:02
Showing1 changed files
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@@ -55,14 +55,6 @@ if test "x$use_pthread_stack_min" = xno; then
55 55
 fi
56 56
 
57 57
 
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-AC_MSG_CHECKING([if R is using openblas])
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-BLAS_LIBS=`"${R_HOME}/bin/R" CMD config BLAS_LIBS`
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-if echo "${BLAS_LIBS}" | grep openblas > /dev/null; then
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-    AC_MSG_RESULT([openblas found. preprocessCore threading will be disabled])
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-    use_pthreads=no
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-else
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-    AC_MSG_RESULT([openblas not found. preprocessCore threading will not be disabled])
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-fi
66 58
 
67 59
 
68 60
 AC_ARG_ENABLE([threading],
Browse code

Update configure.in for checking if R uses openblas

Ben Bolstad authored on 12/05/2019 15:31:51
Showing1 changed files
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@@ -25,8 +25,6 @@ AC_PROG_CPP
25 25
 
26 26
 AC_LANG(C)
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-
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-
30 28
 # Checks for libraries.
31 29
 use_pthreads=no
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 AC_SEARCH_LIBS([pthread_create], [pthread],
... ...
@@ -57,10 +55,21 @@ if test "x$use_pthread_stack_min" = xno; then
57 55
 fi
58 56
 
59 57
 
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+AC_MSG_CHECKING([if R is using openblas])
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+BLAS_LIBS=`"${R_HOME}/bin/R" CMD config BLAS_LIBS`
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+if echo "${BLAS_LIBS}" | grep openblas > /dev/null; then
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+    AC_MSG_RESULT([openblas found. preprocessCore threading will be disabled])
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+    use_pthreads=no
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+else
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+    AC_MSG_RESULT([openblas not found. preprocessCore threading will not be disabled])
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+fi
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+
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+
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 AC_ARG_ENABLE([threading],
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 	AS_HELP_STRING([--disable-threading],[Disable threading]))
62 70
 
63 71
 
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+
64 73
 AS_IF([test "x$enable_threading" != "xno" ],[
65 74
 	    if test "x${use_pthreads}" = "xno"; then
66 75
 	       AC_MSG_NOTICE(------------------------------------------)
Browse code

fix typo

Ben Bolstad authored on 04/09/2017 16:36:43
Showing1 changed files
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@@ -76,7 +76,7 @@ AS_IF([test "x$enable_threading" != "xno" ],[
76 76
 	    fi
77 77
 	    ],
78 78
 	    [
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-	    AC_MSG_NOTICE(Disabling threading for\ preprocessCore)
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+	    AC_MSG_NOTICE(Disabling threading for preprocessCore)
80 80
 	    ])
81 81
 
82 82
 
Browse code

small configure script message cleanup

Ben Bolstad authored on 02/09/2017 16:48:33
Showing1 changed files
... ...
@@ -76,7 +76,7 @@ AS_IF([test "x$enable_threading" != "xno" ],[
76 76
 	    fi
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 	    ],
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 	    [
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-	    AC_MSG_NOTICE("Disabling threading for\n preprocessCore")
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+	    AC_MSG_NOTICE(Disabling threading for\ preprocessCore)
80 80
 	    ])
81 81
 
82 82
 
Browse code

Update configure.in to provide "--disable-threading"

Ben Bolstad authored on 02/09/2017 03:40:30
Showing1 changed files
... ...
@@ -1,12 +1,6 @@
1 1
 dnl
2
-dnl Configuration things for affyR.
3
-dnl (http://www.cbs.dtu.dk/laurent/download/affyR/
4
-dnl What is below (and in the other configuration fiels 
5
-dnl was taken from different configuration scripts for R version 1.3.0.
2
+dnl Configuration things for preprocessCore
6 3
 dnl
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-dnl Acknowledgments: The author(s) of the R configure scripts, Kurt Hornik for the tip with autoconf.
8
-dnl
9
-dnl Laurent 2001
10 4
 
11 5
 
12 6
 AC_INIT("DESCRIPTION")
... ...
@@ -29,6 +23,7 @@ AC_PROG_CC
29 23
 AC_PROG_CPP
30 24
 
31 25
 
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+AC_LANG(C)
32 27
 
33 28
 
34 29
 
... ...
@@ -48,13 +43,13 @@ fi
48 43
 
49 44
 
50 45
 AC_MSG_CHECKING([if PTHREAD_STACK_MIN is defined])
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-AC_COMPILE_IFELSE([
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+AC_COMPILE_IFELSE([AC_LANG_SOURCE([
52 47
 	#include <pthread.h>
53 48
 	#include <limits.h>
54 49
 
55 50
       int main () {size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
56 51
 }     	  
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-    ],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])
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+    ])],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])
58 53
 AC_MSG_RESULT($use_pthread_stack_min)
59 54
 
60 55
 if test "x$use_pthread_stack_min" = xno; then
... ...
@@ -62,17 +57,28 @@ if test "x$use_pthread_stack_min" = xno; then
62 57
 fi
63 58
 
64 59
 
60
+AC_ARG_ENABLE([threading],
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+	AS_HELP_STRING([--disable-threading],[Disable threading]))
65 62
 
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-if test "x${use_pthreads}" = "xno"; then
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-  echo "------------------------------------------"
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-  echo " Unable to find pthreads on this system.  "
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-  echo " Building a single-threaded version.      "
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-  echo "------------------------------------------"
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-fi
72 63
 
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-if test "x${use_pthreads}" = "xyes"; then
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-  AC_DEFINE(USE_PTHREADS, 1)
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-fi
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+AS_IF([test "x$enable_threading" != "xno" ],[
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+	    if test "x${use_pthreads}" = "xno"; then
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+	       AC_MSG_NOTICE(------------------------------------------)
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+	       AC_MSG_NOTICE( Unable to find pthreads on this system.  )
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+	       AC_MSG_NOTICE( Building a single-threaded version.      )
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+	       AC_MSG_NOTICE(------------------------------------------)
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+	    fi
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+
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+
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+	    if test "x${use_pthreads}" = "xyes"; then
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+  	       AC_MSG_NOTICE(Enabling threading for preprocessCore)
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+  	       AC_DEFINE(USE_PTHREADS, 1)
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+	    fi
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+	    ],
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+	    [
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+	    AC_MSG_NOTICE("Disabling threading for\n preprocessCore")
80
+	    ])
81
+
76 82
 
77 83
 
78 84
 
Browse code

setting up git-svn bridge

Bioconductor Git-SVN Bridge authored on 31/08/2014 21:28:19
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,80 @@
1
+dnl
2
+dnl Configuration things for affyR.
3
+dnl (http://www.cbs.dtu.dk/laurent/download/affyR/
4
+dnl What is below (and in the other configuration fiels 
5
+dnl was taken from different configuration scripts for R version 1.3.0.
6
+dnl
7
+dnl Acknowledgments: The author(s) of the R configure scripts, Kurt Hornik for the tip with autoconf.
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+dnl
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+dnl Laurent 2001
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+
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+
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+AC_INIT("DESCRIPTION")
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+
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+dnl
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+dnl Are things (still) the same ?
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+dnl (taken from the 'writing R extensions manual')
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+
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+dnl Now find the compiler and compiler flags to use
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+: ${R_HOME=`R RHOME`}
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+if test -z "${R_HOME}"; then
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+       echo "could not determine R_HOME"
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+       exit 1
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+fi
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+CC=`"${R_HOME}/bin/R" CMD config CC`
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+CPP=`"${R_HOME}/bin/R" CMD config CPP`
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+CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
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+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
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+AC_PROG_CC
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+AC_PROG_CPP
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+
31
+
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+
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+
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+
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+# Checks for libraries.
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+use_pthreads=no
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+AC_SEARCH_LIBS([pthread_create], [pthread],
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+  [use_pthreads=yes])
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+
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+# Checks for header files.
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+AC_HEADER_STDC
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+AC_CHECK_HEADERS([stdlib.h])
43
+
44
+if test "x${have_pthreads}" = xyes; then
45
+  AC_CHECK_HEADERS([pthread.h], [],
46
+    [use_pthreads=no])
47
+fi
48
+
49
+
50
+AC_MSG_CHECKING([if PTHREAD_STACK_MIN is defined])
51
+AC_COMPILE_IFELSE([
52
+	#include <pthread.h>
53
+	#include <limits.h>
54
+
55
+      int main () {size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
56
+}     	  
57
+    ],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])
58
+AC_MSG_RESULT($use_pthread_stack_min)
59
+
60
+if test "x$use_pthread_stack_min" = xno; then
61
+	use_pthreads=no
62
+fi
63
+
64
+
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+
66
+if test "x${use_pthreads}" = "xno"; then
67
+  echo "------------------------------------------"
68
+  echo " Unable to find pthreads on this system.  "
69
+  echo " Building a single-threaded version.      "
70
+  echo "------------------------------------------"
71
+fi
72
+
73
+if test "x${use_pthreads}" = "xyes"; then
74
+  AC_DEFINE(USE_PTHREADS, 1)
75
+fi
76
+
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+
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+
79
+
80
+AC_OUTPUT(src/Makevars)