[med-svn] [r-bioc-preprocesscore] 02/05: New upstream version 1.40.0
Andreas Tille
tille at debian.org
Wed Nov 8 10:11:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-preprocesscore.
commit cd49ba79651088451776861011da902f88a33d62
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 8 11:08:43 2017 +0100
New upstream version 1.40.0
---
DESCRIPTION | 10 +-
cleanup | 5 +
configure | 241 ++++++++++++++++++++++++++------------------
configure.in | 42 ++++----
src/Makevars | 3 -
src/rlm_anova.c | 4 +-
src/weightedkerneldensity.c | 6 +-
7 files changed, 180 insertions(+), 131 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index f5ece0c..d213ce3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
Package: preprocessCore
-Version: 1.38.1
+Version: 1.40.0
Title: A collection of pre-processing functions
-Author: Benjamin Milo Bolstad <bmb at bmbolstad.com>
-Maintainer: Benjamin Milo Bolstad <bmb at bmbolstad.com>
+Author: Ben Bolstad <bmb at bmbolstad.com>
+Maintainer: Ben Bolstad <bmb at bmbolstad.com>
Imports: stats
-Description: A library of core preprocessing routines
+Description: A library of core preprocessing routines.
License: LGPL (>= 2)
URL: https://github.com/bmbolstad/preprocessCore
Collate: normalize.quantiles.R quantile_extensions.R
@@ -13,4 +13,4 @@ Collate: normalize.quantiles.R quantile_extensions.R
LazyLoad: yes
biocViews: Infrastructure
NeedsCompilation: yes
-Packaged: 2017-05-05 22:14:47 UTC; biocbuild
+Packaged: 2017-10-30 22:37:04 UTC; biocbuild
diff --git a/cleanup b/cleanup
new file mode 100755
index 0000000..00b9411
--- /dev/null
+++ b/cleanup
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+rm -f config.status config.log
+rm -f src/Makevars
+rm -f src/*.o
diff --git a/configure b/configure
index 91a5c62..5577926 100755
--- a/configure
+++ b/configure
@@ -1,11 +1,9 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68.
+# Generated by GNU Autoconf 2.69.
#
#
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
-# Foundation, Inc.
+# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
#
#
# This configure script is free software; the Free Software Foundation
@@ -134,6 +132,31 @@ export LANGUAGE
# CDPATH.
(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+# Use a proper internal environment variable to ensure we don't fall
+ # into an infinite loop, continuously re-executing ourselves.
+ if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
+ _as_can_reexec=no; export _as_can_reexec;
+ # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+as_fn_exit 255
+ fi
+ # We don't want this to propagate to other subprocesses.
+ { _as_can_reexec=; unset _as_can_reexec;}
if test "x$CONFIG_SHELL" = x; then
as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
emulate sh
@@ -167,7 +190,8 @@ if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
else
exitcode=1; echo positional parameters were not saved.
fi
-test x\$exitcode = x0 || exit 1"
+test x\$exitcode = x0 || exit 1
+test -x / || exit 1"
as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
@@ -212,21 +236,25 @@ IFS=$as_save_IFS
if test "x$CONFIG_SHELL" != x; then :
- # We cannot yet assume a decent shell, so we have to provide a
- # neutralization value for shells without unset; and this also
- # works around shells that cannot unset nonexistent variables.
- # Preserve -v and -x to the replacement shell.
- BASH_ENV=/dev/null
- ENV=/dev/null
- (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
- export CONFIG_SHELL
- case $- in # ((((
- *v*x* | *x*v* ) as_opts=-vx ;;
- *v* ) as_opts=-v ;;
- *x* ) as_opts=-x ;;
- * ) as_opts= ;;
- esac
- exec "$CONFIG_SHELL" $as_opts "$as_myself" ${1+"$@"}
+ export CONFIG_SHELL
+ # We cannot yet assume a decent shell, so we have to provide a
+# neutralization value for shells without unset; and this also
+# works around shells that cannot unset nonexistent variables.
+# Preserve -v and -x to the replacement shell.
+BASH_ENV=/dev/null
+ENV=/dev/null
+(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+case $- in # ((((
+ *v*x* | *x*v* ) as_opts=-vx ;;
+ *v* ) as_opts=-v ;;
+ *x* ) as_opts=-x ;;
+ * ) as_opts= ;;
+esac
+exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
+# Admittedly, this is quite paranoid, since all the known shells bail
+# out after a failed `exec'.
+$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
+exit 255
fi
if test x$as_have_required = xno; then :
@@ -328,6 +356,14 @@ $as_echo X"$as_dir" |
} # as_fn_mkdir_p
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+ test -f "$1" && test -x "$1"
+} # as_fn_executable_p
# as_fn_append VAR VALUE
# ----------------------
# Append the text in VALUE to the end of the definition contained in VAR. Take
@@ -449,6 +485,10 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits
chmod +x "$as_me.lineno" ||
{ $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
+ # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
+ # already done that, so ensure we don't try to do so again and fall
+ # in an infinite loop. This has already happened in practice.
+ _as_can_reexec=no; export _as_can_reexec
# Don't try to exec as it changes $[0], causing all sort of problems
# (the dirname of $[0] is not the place where we might find the
# original and so on. Autoconf is especially sensitive to this).
@@ -483,16 +523,16 @@ if (echo >conf$$.file) 2>/dev/null; then
# ... but there are two gotchas:
# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -p'.
+ # In both cases, we have to default to `cp -pR'.
ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
elif ln conf$$.file conf$$ 2>/dev/null; then
as_ln_s=ln
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
@@ -504,28 +544,8 @@ else
as_mkdir_p=false
fi
-if test -x / >/dev/null 2>&1; then
- as_test_x='test -x'
-else
- if ls -dL / >/dev/null 2>&1; then
- as_ls_L_option=L
- else
- as_ls_L_option=
- fi
- as_test_x='
- eval sh -c '\''
- if test -d "$1"; then
- test -d "$1/.";
- else
- case $1 in #(
- -*)set "./$1";;
- esac;
- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
- ???[sx]*):;;*)false;;esac;fi
- '\'' sh
- '
-fi
-as_executable_p=$as_test_x
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -652,6 +672,7 @@ SHELL'
ac_subst_files=''
ac_user_opts='
enable_option_checking
+enable_threading
'
ac_precious_vars='build_alias
host_alias
@@ -1117,8 +1138,6 @@ target=$target_alias
if test "x$host_alias" != x; then
if test "x$build_alias" = x; then
cross_compiling=maybe
- $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
- If a cross compiler is detected then cross compile mode will be used" >&2
elif test "x$build_alias" != "x$host_alias"; then
cross_compiling=yes
fi
@@ -1267,6 +1286,12 @@ if test -n "$ac_init_help"; then
cat <<\_ACEOF
+Optional Features:
+ --disable-option-checking ignore unrecognized --enable/--with options
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --disable-threading Disable threading
+
Some influential environment variables:
CC C compiler command
CFLAGS C compiler flags
@@ -1344,9 +1369,9 @@ test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
configure
-generated by GNU Autoconf 2.68
+generated by GNU Autoconf 2.69
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.
_ACEOF
@@ -1459,7 +1484,7 @@ $as_echo "$ac_try_echo"; } >&5
test ! -s conftest.err
} && test -s conftest$ac_exeext && {
test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
+ test -x conftest$ac_exeext
}; then :
ac_retval=0
else
@@ -1642,7 +1667,7 @@ This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by $as_me, which was
-generated by GNU Autoconf 2.68. Invocation command line was
+generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2022,7 +2047,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_CC="${ac_tool_prefix}gcc"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -2062,7 +2087,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_ac_ct_CC="gcc"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -2115,7 +2140,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_CC="${ac_tool_prefix}cc"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -2156,7 +2181,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
ac_prog_rejected=yes
continue
@@ -2214,7 +2239,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -2258,7 +2283,7 @@ do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
ac_cv_prog_ac_ct_CC="$ac_prog"
$as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
@@ -2704,8 +2729,7 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <stdarg.h>
#include <stdio.h>
-#include <sys/types.h>
-#include <sys/stat.h>
+struct stat;
/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
struct buf { int x; };
FILE * (*rcsopen) (struct buf *, struct stat *, int);
@@ -2929,6 +2953,12 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
@@ -3010,7 +3040,7 @@ do
for ac_prog in grep ggrep; do
for ac_exec_ext in '' $ac_executable_extensions; do
ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
- { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+ as_fn_executable_p "$ac_path_GREP" || continue
# Check for GNU ac_path_GREP and select it if it is found.
# Check for GNU $ac_path_GREP
case `"$ac_path_GREP" --version 2>&1` in
@@ -3076,7 +3106,7 @@ do
for ac_prog in egrep; do
for ac_exec_ext in '' $ac_executable_extensions; do
ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
- { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+ as_fn_executable_p "$ac_path_EGREP" || continue
# Check for GNU ac_path_EGREP and select it if it is found.
# Check for GNU $ac_path_EGREP
case `"$ac_path_EGREP" --version 2>&1` in
@@ -3310,22 +3340,45 @@ if test "x$use_pthread_stack_min" = xno; then
fi
-
-if test "x${use_pthreads}" = "xno"; then
- echo "------------------------------------------"
- echo " Unable to find pthreads on this system. "
- echo " Building a single-threaded version. "
- echo "------------------------------------------"
+# Check whether --enable-threading was given.
+if test "${enable_threading+set}" = set; then :
+ enableval=$enable_threading;
fi
-if test "x${use_pthreads}" = "xyes"; then
- $as_echo "#define USE_PTHREADS 1" >>confdefs.h
+
+
+if test "x$enable_threading" != "xno" ; then :
+
+ if test "x${use_pthreads}" = "xno"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: ------------------------------------------" >&5
+$as_echo "$as_me: ------------------------------------------" >&6;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Unable to find pthreads on this system. " >&5
+$as_echo "$as_me: Unable to find pthreads on this system. " >&6;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Building a single-threaded version. " >&5
+$as_echo "$as_me: Building a single-threaded version. " >&6;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: ------------------------------------------" >&5
+$as_echo "$as_me: ------------------------------------------" >&6;}
+ fi
+
+
+ if test "x${use_pthreads}" = "xyes"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Enabling threading for preprocessCore" >&5
+$as_echo "$as_me: Enabling threading for preprocessCore" >&6;}
+ $as_echo "#define USE_PTHREADS 1" >>confdefs.h
+
+ fi
+
+else
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Disabling threading for\ preprocessCore" >&5
+$as_echo "$as_me: Disabling threading for\ preprocessCore" >&6;}
fi
+
ac_config_files="$ac_config_files src/Makevars"
cat >confcache <<\_ACEOF
@@ -3771,16 +3824,16 @@ if (echo >conf$$.file) 2>/dev/null; then
# ... but there are two gotchas:
# 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
# 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -p'.
+ # In both cases, we have to default to `cp -pR'.
ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
elif ln conf$$.file conf$$ 2>/dev/null; then
as_ln_s=ln
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
else
- as_ln_s='cp -p'
+ as_ln_s='cp -pR'
fi
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
@@ -3840,28 +3893,16 @@ else
as_mkdir_p=false
fi
-if test -x / >/dev/null 2>&1; then
- as_test_x='test -x'
-else
- if ls -dL / >/dev/null 2>&1; then
- as_ls_L_option=L
- else
- as_ls_L_option=
- fi
- as_test_x='
- eval sh -c '\''
- if test -d "$1"; then
- test -d "$1/.";
- else
- case $1 in #(
- -*)set "./$1";;
- esac;
- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
- ???[sx]*):;;*)false;;esac;fi
- '\'' sh
- '
-fi
-as_executable_p=$as_test_x
+
+# as_fn_executable_p FILE
+# -----------------------
+# Test if FILE is an executable regular file.
+as_fn_executable_p ()
+{
+ test -f "$1" && test -x "$1"
+} # as_fn_executable_p
+as_test_x='test -x'
+as_executable_p=as_fn_executable_p
# Sed expression to map a string onto a valid CPP name.
as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
@@ -3883,7 +3924,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# values after options handling.
ac_log="
This file was extended by $as_me, which was
-generated by GNU Autoconf 2.68. Invocation command line was
+generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
@@ -3936,10 +3977,10 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
config.status
-configured by $0, generated by GNU Autoconf 2.68,
+configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2012 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
@@ -4016,7 +4057,7 @@ fi
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
if \$ac_cs_recheck; then
- set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ set X $SHELL '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
shift
\$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
CONFIG_SHELL='$SHELL'
diff --git a/configure.in b/configure.in
index d0bba06..6ac257a 100644
--- a/configure.in
+++ b/configure.in
@@ -1,12 +1,6 @@
dnl
-dnl Configuration things for affyR.
-dnl (http://www.cbs.dtu.dk/laurent/download/affyR/
-dnl What is below (and in the other configuration fiels
-dnl was taken from different configuration scripts for R version 1.3.0.
+dnl Configuration things for preprocessCore
dnl
-dnl Acknowledgments: The author(s) of the R configure scripts, Kurt Hornik for the tip with autoconf.
-dnl
-dnl Laurent 2001
AC_INIT("DESCRIPTION")
@@ -29,6 +23,7 @@ AC_PROG_CC
AC_PROG_CPP
+AC_LANG(C)
@@ -48,13 +43,13 @@ fi
AC_MSG_CHECKING([if PTHREAD_STACK_MIN is defined])
-AC_COMPILE_IFELSE([
+AC_COMPILE_IFELSE([AC_LANG_SOURCE([
#include <pthread.h>
#include <limits.h>
int main () {size_t stacksize = PTHREAD_STACK_MIN + 0x4000;
}
- ],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])
+ ])],[use_pthread_stack_min=yes], [use_pthread_stack_min=no])
AC_MSG_RESULT($use_pthread_stack_min)
if test "x$use_pthread_stack_min" = xno; then
@@ -62,17 +57,28 @@ if test "x$use_pthread_stack_min" = xno; then
fi
+AC_ARG_ENABLE([threading],
+ AS_HELP_STRING([--disable-threading],[Disable threading]))
-if test "x${use_pthreads}" = "xno"; then
- echo "------------------------------------------"
- echo " Unable to find pthreads on this system. "
- echo " Building a single-threaded version. "
- echo "------------------------------------------"
-fi
-if test "x${use_pthreads}" = "xyes"; then
- AC_DEFINE(USE_PTHREADS, 1)
-fi
+AS_IF([test "x$enable_threading" != "xno" ],[
+ if test "x${use_pthreads}" = "xno"; then
+ AC_MSG_NOTICE(------------------------------------------)
+ AC_MSG_NOTICE( Unable to find pthreads on this system. )
+ AC_MSG_NOTICE( Building a single-threaded version. )
+ AC_MSG_NOTICE(------------------------------------------)
+ fi
+
+
+ if test "x${use_pthreads}" = "xyes"; then
+ AC_MSG_NOTICE(Enabling threading for preprocessCore)
+ AC_DEFINE(USE_PTHREADS, 1)
+ fi
+ ],
+ [
+ AC_MSG_NOTICE(Disabling threading for preprocessCore)
+ ])
+
diff --git a/src/Makevars b/src/Makevars
deleted file mode 100644
index efaa3e7..0000000
--- a/src/Makevars
+++ /dev/null
@@ -1,3 +0,0 @@
-PKG_CFLAGS = -g -O2 -Wall -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1
-PKG_LIBS = -lpthread $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
-PKG_CPPFLAGS = -I/usr/local/include
diff --git a/src/rlm_anova.c b/src/rlm_anova.c
index b32c8a3..48a6f0f 100644
--- a/src/rlm_anova.c
+++ b/src/rlm_anova.c
@@ -1155,9 +1155,9 @@ void rlm_compute_se_anova(double *Y, int y_rows,int y_cols, double *beta, double
i = RLM_SE_Method_3_anova(Kappa, XTX, W, y_rows,y_cols, se_estimates,varcov);
if (i){
for (i=0; i <n; i++){
- printf("%2.1f ", PsiFn(resids[i]/scale,k1,1));
+ // printf("%2.1f ", PsiFn(resids[i]/scale,k1,1));
}
- printf("\n");
+ //printf("\n");
}
}
}
diff --git a/src/weightedkerneldensity.c b/src/weightedkerneldensity.c
index 9e93f51..19ca4dd 100644
--- a/src/weightedkerneldensity.c
+++ b/src/weightedkerneldensity.c
@@ -747,7 +747,7 @@ static double IQR(double *x, int length){
double lowindex, highindex;
double lowfloor, highfloor;
double lowceil, highceil;
- int low_i, high_i;
+ /* int low_i, high_i; */
double low_h, high_h;
@@ -762,8 +762,8 @@ static double IQR(double *x, int length){
lowceil = ceil(lowindex);
highceil = ceil(highindex);
- low_i = lowindex > lowfloor;
- high_i = highindex > highfloor;
+ /*low_i = lowindex > lowfloor;
+ high_i = highindex > highfloor; */
qslow = x[(int)lowfloor];
qshigh = x[(int)highfloor];
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-preprocesscore.git
More information about the debian-med-commit
mailing list