[Genabel-commits] r758 - in pkg/ProbABEL: . doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 12 00:41:45 CEST 2011
Author: lckarssen
Date: 2011-08-12 00:41:45 +0200 (Fri, 12 Aug 2011)
New Revision: 758
Added:
pkg/ProbABEL/doc/Makefile.am
pkg/ProbABEL/doc/Makefile.in
Removed:
pkg/ProbABEL/doc/Makefile
Modified:
pkg/ProbABEL/Makefile.am
pkg/ProbABEL/Makefile.in
pkg/ProbABEL/configure
pkg/ProbABEL/configure.ac
pkg/ProbABEL/src/Makefile.am
pkg/ProbABEL/src/Makefile.in
pkg/ProbABEL/src/probabel.pl
Log:
- in probabel.pl the location for the probabel config file is now set
to /etc/, the default location it will end up. Before it still
pointed to the location the probabel.pl file was in. However, a
better fix would be to somehow put in the actual value of the
--sysconfdir option to ./configure.
- The PDF of the LaTeX documentation is now only generated if the
pdflatex binary can be found. So now we also build the documentation
using autotools.
Modified: pkg/ProbABEL/Makefile.am
===================================================================
--- pkg/ProbABEL/Makefile.am 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/Makefile.am 2011-08-11 22:41:45 UTC (rev 758)
@@ -1,10 +1,8 @@
+## Process this file with automake to produce Makefile.in
+
AUTOMAKE_OPTIONS = foreign
-SUBDIRS = src
+SUBDIRS = src doc
-docfiles = doc/ProbABEL_manual.pdf doc/ProbABEL_manual.tex \
- doc/QuickStart.txt doc/short_coxph_data.txt doc/short_height.out.csv \
- doc/short_height.txt doc/short_logist_data.txt doc/test_regression.R \
- doc/COPYING doc/LICENSE doc/INSTALL doc/CHANGES.LOG doc/TODO
examplefiles = \
examples/height_ngp2_robust_int1_over_domin.out.txt.save \
examples/test.prob.fvi examples/mmscore_gen.prob.fvd \
@@ -60,7 +58,5 @@
examples/impute_with_missing_add.out.txt.save \
examples/height_ngp2_robust_domin.out.txt.save examples/height.txt
-dist_doc_DATA = $(docfiles)
-
exampledir = $(pkgdatadir)/examples
dist_example_DATA = $(examplefiles)
Modified: pkg/ProbABEL/Makefile.in
===================================================================
--- pkg/ProbABEL/Makefile.in 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/Makefile.in 2011-08-11 22:41:45 UTC (rev 758)
@@ -33,10 +33,9 @@
PRE_UNINSTALL = :
POST_UNINSTALL = :
subdir = .
-DIST_COMMON = $(am__configure_deps) $(dist_doc_DATA) \
- $(dist_example_DATA) $(srcdir)/Makefile.am \
- $(srcdir)/Makefile.in $(top_srcdir)/configure compile depcomp \
- install-sh missing
+DIST_COMMON = $(am__configure_deps) $(dist_example_DATA) \
+ $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+ $(top_srcdir)/configure compile depcomp install-sh missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -77,8 +76,8 @@
am__base_list = \
sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-am__installdirs = "$(DESTDIR)$(docdir)" "$(DESTDIR)$(exampledir)"
-DATA = $(dist_doc_DATA) $(dist_example_DATA)
+am__installdirs = "$(DESTDIR)$(exampledir)"
+DATA = $(dist_example_DATA)
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
@@ -168,6 +167,7 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
+PDFLATEX = @PDFLATEX@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
@@ -216,12 +216,7 @@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
AUTOMAKE_OPTIONS = foreign
-SUBDIRS = src
-docfiles = doc/ProbABEL_manual.pdf doc/ProbABEL_manual.tex \
- doc/QuickStart.txt doc/short_coxph_data.txt doc/short_height.out.csv \
- doc/short_height.txt doc/short_logist_data.txt doc/test_regression.R \
- doc/COPYING doc/LICENSE doc/INSTALL doc/CHANGES.LOG doc/TODO
-
+SUBDIRS = src doc
examplefiles = \
examples/height_ngp2_robust_int1_over_domin.out.txt.save \
examples/test.prob.fvi examples/mmscore_gen.prob.fvd \
@@ -277,7 +272,6 @@
examples/impute_with_missing_add.out.txt.save \
examples/height_ngp2_robust_domin.out.txt.save examples/height.txt
-dist_doc_DATA = $(docfiles)
exampledir = $(pkgdatadir)/examples
dist_example_DATA = $(examplefiles)
all: all-recursive
@@ -317,26 +311,6 @@
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
$(am__aclocal_m4_deps):
-install-dist_docDATA: $(dist_doc_DATA)
- @$(NORMAL_INSTALL)
- test -z "$(docdir)" || $(MKDIR_P) "$(DESTDIR)$(docdir)"
- @list='$(dist_doc_DATA)'; test -n "$(docdir)" || list=; \
- for p in $$list; do \
- if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- echo "$$d$$p"; \
- done | $(am__base_list) | \
- while read files; do \
- echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(docdir)'"; \
- $(INSTALL_DATA) $$files "$(DESTDIR)$(docdir)" || exit $$?; \
- done
-
-uninstall-dist_docDATA:
- @$(NORMAL_UNINSTALL)
- @list='$(dist_doc_DATA)'; test -n "$(docdir)" || list=; \
- files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
- test -n "$$files" || exit 0; \
- echo " ( cd '$(DESTDIR)$(docdir)' && rm -f" $$files ")"; \
- cd "$(DESTDIR)$(docdir)" && rm -f $$files
install-dist_exampleDATA: $(dist_example_DATA)
@$(NORMAL_INSTALL)
test -z "$(exampledir)" || $(MKDIR_P) "$(DESTDIR)$(exampledir)"
@@ -673,7 +647,7 @@
all-am: Makefile $(DATA)
installdirs: installdirs-recursive
installdirs-am:
- for dir in "$(DESTDIR)$(docdir)" "$(DESTDIR)$(exampledir)"; do \
+ for dir in "$(DESTDIR)$(exampledir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: install-recursive
@@ -722,7 +696,7 @@
info-am:
-install-data-am: install-dist_docDATA install-dist_exampleDATA
+install-data-am: install-dist_exampleDATA
install-dvi: install-dvi-recursive
@@ -768,7 +742,7 @@
ps-am:
-uninstall-am: uninstall-dist_docDATA uninstall-dist_exampleDATA
+uninstall-am: uninstall-dist_exampleDATA
.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
install-am install-strip tags-recursive
@@ -780,15 +754,14 @@
distclean distclean-generic distclean-tags distcleancheck \
distdir distuninstallcheck dvi dvi-am html html-am info \
info-am install install-am install-data install-data-am \
- install-dist_docDATA install-dist_exampleDATA install-dvi \
- install-dvi-am install-exec install-exec-am install-html \
- install-html-am install-info install-info-am install-man \
- install-pdf install-pdf-am install-ps install-ps-am \
- install-strip installcheck installcheck-am installdirs \
- installdirs-am maintainer-clean maintainer-clean-generic \
- mostlyclean mostlyclean-generic pdf pdf-am ps ps-am tags \
- tags-recursive uninstall uninstall-am uninstall-dist_docDATA \
- uninstall-dist_exampleDATA
+ install-dist_exampleDATA install-dvi install-dvi-am \
+ install-exec install-exec-am install-html install-html-am \
+ install-info install-info-am install-man install-pdf \
+ install-pdf-am install-ps install-ps-am install-strip \
+ installcheck installcheck-am installdirs installdirs-am \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am uninstall-dist_exampleDATA
# Tell versions [3.59,3.63) of GNU make to not export all variables.
Modified: pkg/ProbABEL/configure
===================================================================
--- pkg/ProbABEL/configure 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/configure 2011-08-11 22:41:45 UTC (rev 758)
@@ -597,6 +597,9 @@
ac_subst_vars='am__EXEEXT_FALSE
am__EXEEXT_TRUE
LTLIBOBJS
+HAVE_PDFLATEX_FALSE
+HAVE_PDFLATEX_TRUE
+PDFLATEX
LIBOBJS
EGREP
GREP
@@ -5119,8 +5122,64 @@
done
-ac_config_files="$ac_config_files Makefile src/Makefile"
+# Check for presence of pdfLaTeX
+# Extract the first word of "pdflatex", so it can be a program name with args.
+set dummy pdflatex; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_PDFLATEX+set}" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$PDFLATEX"; then
+ ac_cv_prog_PDFLATEX="$PDFLATEX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+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
+ ac_cv_prog_PDFLATEX="pdflatex"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+fi
+fi
+PDFLATEX=$ac_cv_prog_PDFLATEX
+if test -n "$PDFLATEX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PDFLATEX" >&5
+$as_echo "$PDFLATEX" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+if test -z "$PDFLATEX"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: Unable to create PDF version of the user manual." >&5
+$as_echo "$as_me: WARNING: Unable to create PDF version of the user manual." >&2;}
+fi
+
+ if test -n "$PDFLATEX"; then
+ HAVE_PDFLATEX_TRUE=
+ HAVE_PDFLATEX_FALSE='#'
+else
+ HAVE_PDFLATEX_TRUE='#'
+ HAVE_PDFLATEX_FALSE=
+fi
+
+
+
+# Files to be generated by autotools
+ac_config_files="$ac_config_files Makefile src/Makefile doc/Makefile"
+
+# Create output files
cat >confcache <<\_ACEOF
# This file is a shell script that caches the results of configure
# tests run on this system so they can be shared between configure
@@ -5239,6 +5298,10 @@
as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
+if test -z "${HAVE_PDFLATEX_TRUE}" && test -z "${HAVE_PDFLATEX_FALSE}"; then
+ as_fn_error $? "conditional \"HAVE_PDFLATEX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
+fi
: ${CONFIG_STATUS=./config.status}
ac_write_fail=0
@@ -5846,6 +5909,7 @@
"depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
"Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
"src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+ "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
*) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;;
esac
Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/configure.ac 2011-08-11 22:41:45 UTC (rev 758)
@@ -31,4 +31,21 @@
AC_FUNC_MALLOC
AC_CHECK_FUNCS([pow putenv sqrt strdup strncasecmp])
-AC_OUTPUT(Makefile src/Makefile)
+
+# Check for presence of pdfLaTeX
+AC_CHECK_PROG(PDFLATEX, pdflatex, pdflatex)
+if test -z "$PDFLATEX"; then
+ AC_MSG_WARN([Unable to create PDF version of the user manual.])
+fi
+
+AM_CONDITIONAL([HAVE_PDFLATEX], test -n "$PDFLATEX")
+
+
+# Files to be generated by autotools
+AC_CONFIG_FILES([
+ Makefile
+ src/Makefile
+ doc/Makefile
+])
+# Create output files
+AC_OUTPUT
Deleted: pkg/ProbABEL/doc/Makefile
===================================================================
--- pkg/ProbABEL/doc/Makefile 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/doc/Makefile 2011-08-11 22:41:45 UTC (rev 758)
@@ -1,45 +0,0 @@
-MANNAME = ProbABEL_manual
-MANTEXSRC = $(MANNAME).tex
-MANAUX = $(patsubst %.tex, %.aux, $(MANTEXSRC))
-MANPDF = $(patsubst %.tex, %.pdf, $(MANTEXSRC))
-
-.PHONY: clean clean_doc
-
-$(MANPDF): $(MANTEXSRC) $(MANAUX)
- @echo === Making final PDF ===
- pdflatex $(MANTEXSRC)
- @while ( grep "Rerun to " \
- $(MANNAME).log > /dev/null ); do \
- echo '** Re-running LaTeX **'; \
- pdflatex $(MANTEXSRC); \
- done
- pdflatex $(MANTEXSRC)
-
-
-# A target needed to keep track of the nr. of LaTeX runs
-.btmp:
-
-
-clean_doc:
- rm -f *~ *.log *.idx *.out *.toc *.aux
- rm -rf auto
-
-clean: clean_doc
- rm -f $(MANPDF)
- rm -f .btmp
-
-%.aux: %.tex $(MANSRC)
- @echo === Making $< file ===
- pdflatex $(MANTEXSRC)
-# Look for citations. Make sure grep never returns an error code.
- @grep "^\\\\citation" $(MANAUX) > .btmp.new || true
-# If the citations are not changed, don't do anything. Otherwise replace
-# the .btmp file to make sure Bibtex will be run.
- @if ( diff .btmp.new .btmp > /dev/null ); then \
- rm .btmp.new; \
- else \
- mv .btmp.new .btmp; \
- fi
-
-# $(DOCS): $()
-# cd $(DOCDIR); pdflatex $(DOCSRC)
Added: pkg/ProbABEL/doc/Makefile.am
===================================================================
--- pkg/ProbABEL/doc/Makefile.am (rev 0)
+++ pkg/ProbABEL/doc/Makefile.am 2011-08-11 22:41:45 UTC (rev 758)
@@ -0,0 +1,47 @@
+## Process this file with automake to produce Makefile.in
+
+dist_doc_DATA = ProbABEL_manual.tex QuickStart.txt \
+ short_coxph_data.txt short_height.out.csv \
+ short_height.txt short_logist_data.txt test_regression.R \
+ COPYING LICENSE INSTALL CHANGES.LOG TODO
+
+
+if HAVE_PDFLATEX
+MANNAME = ProbABEL_manual
+MANPDF = $(MANNAME).pdf
+MANTEXSRC = $(MANNAME).tex
+MANAUX = $(MANNAME).aux
+doc_DATA = $(MANPDF)
+
+CLEANFILES = $(MANPDF) $(MANNAME).log $(MANNAME).idx $(MANNAME).out \
+ $(MANNAME).toc $(MANAUX) .btmp
+
+endif
+
+
+# Several make rules to generate the PDF from the LaTeX source
+.aux.pdf:
+ @echo === Making final PDF ===
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC)
+ @while ( grep "Rerun to " \
+ $(srcdir)/$(MANNAME).log ); do \
+ echo '** Re-running LaTeX **'; \
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC); \
+ done
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC)
+
+.tex.aux:
+ @echo === Making $@ file ===
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC)
+## Look for citations. Make sure grep never returns an error code.
+ @grep "^\\\\citation" $(MANAUX) > .btmp.new || true
+## If the citations are not changed, don't do anything. Otherwise replace
+## the .btmp file to make sure BibTeX will be run.
+ @if ( diff .btmp.new .btmp > /dev/null ); then \
+ rm .btmp.new; \
+ else \
+ mv .btmp.new .btmp; \
+ fi
+
+# A target needed to keep track of the nr. of LaTeX runs
+.btmp:
Added: pkg/ProbABEL/doc/Makefile.in
===================================================================
--- pkg/ProbABEL/doc/Makefile.in (rev 0)
+++ pkg/ProbABEL/doc/Makefile.in 2011-08-11 22:41:45 UTC (rev 758)
@@ -0,0 +1,429 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
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+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
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+INSTALL_HEADER = $(INSTALL_DATA)
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+NORMAL_INSTALL = :
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+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+subdir = doc
+DIST_COMMON = $(dist_doc_DATA) $(srcdir)/Makefile.am \
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+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
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+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
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+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+dist_doc_DATA = ProbABEL_manual.tex QuickStart.txt \
+ short_coxph_data.txt short_height.out.csv \
+ short_height.txt short_logist_data.txt test_regression.R \
+ COPYING LICENSE INSTALL CHANGES.LOG TODO
+
+ at HAVE_PDFLATEX_TRUE@MANNAME = ProbABEL_manual
+ at HAVE_PDFLATEX_TRUE@MANPDF = $(MANNAME).pdf
+ at HAVE_PDFLATEX_TRUE@MANTEXSRC = $(MANNAME).tex
+ at HAVE_PDFLATEX_TRUE@MANAUX = $(MANNAME).aux
+ at HAVE_PDFLATEX_TRUE@doc_DATA = $(MANPDF)
+ at HAVE_PDFLATEX_TRUE@CLEANFILES = $(MANPDF) $(MANNAME).log $(MANNAME).idx $(MANNAME).out \
+ at HAVE_PDFLATEX_TRUE@ $(MANNAME).toc $(MANAUX) .btmp
+
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .aux .pdf .tex
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
+ $(AUTOMAKE) --gnu doc/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-dist_docDATA: $(dist_doc_DATA)
+ @$(NORMAL_INSTALL)
+ test -z "$(docdir)" || $(MKDIR_P) "$(DESTDIR)$(docdir)"
+ @list='$(dist_doc_DATA)'; test -n "$(docdir)" || list=; \
+ for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(docdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(docdir)" || exit $$?; \
+ done
+
+uninstall-dist_docDATA:
+ @$(NORMAL_UNINSTALL)
+ @list='$(dist_doc_DATA)'; test -n "$(docdir)" || list=; \
+ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+ test -n "$$files" || exit 0; \
+ echo " ( cd '$(DESTDIR)$(docdir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(docdir)" && rm -f $$files
+install-docDATA: $(doc_DATA)
+ @$(NORMAL_INSTALL)
+ test -z "$(docdir)" || $(MKDIR_P) "$(DESTDIR)$(docdir)"
+ @list='$(doc_DATA)'; test -n "$(docdir)" || list=; \
+ for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ echo "$$d$$p"; \
+ done | $(am__base_list) | \
+ while read files; do \
+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(docdir)'"; \
+ $(INSTALL_DATA) $$files "$(DESTDIR)$(docdir)" || exit $$?; \
+ done
+
+uninstall-docDATA:
+ @$(NORMAL_UNINSTALL)
+ @list='$(doc_DATA)'; test -n "$(docdir)" || list=; \
+ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+ test -n "$$files" || exit 0; \
+ echo " ( cd '$(DESTDIR)$(docdir)' && rm -f" $$files ")"; \
+ cd "$(DESTDIR)$(docdir)" && rm -f $$files
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+ list='$(DISTFILES)'; \
+ dist_files=`for file in $$list; do echo $$file; done | \
+ sed -e "s|^$$srcdirstrip/||;t" \
+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+ case $$dist_files in \
+ */*) $(MKDIR_P) `echo "$$dist_files" | \
+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+ sort -u` ;; \
+ esac; \
+ for file in $$dist_files; do \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ if test -d $$d/$$file; then \
+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test -d "$(distdir)/$$file"; then \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+ fi; \
+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+ else \
+ test -f "$(distdir)/$$file" \
+ || cp -p $$d/$$file "$(distdir)/$$file" \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+ for dir in "$(DESTDIR)$(docdir)" "$(DESTDIR)$(docdir)"; do \
+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+ done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am: install-dist_docDATA install-docDATA
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-dist_docDATA uninstall-docDATA
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+ distclean-generic distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am \
+ install-dist_docDATA install-docDATA install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-ps install-ps-am \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic pdf pdf-am ps ps-am uninstall uninstall-am \
+ uninstall-dist_docDATA uninstall-docDATA
+
+
+# Several make rules to generate the PDF from the LaTeX source
+.aux.pdf:
+ @echo === Making final PDF ===
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC)
+ @while ( grep "Rerun to " \
+ $(srcdir)/$(MANNAME).log ); do \
+ echo '** Re-running LaTeX **'; \
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC); \
+ done
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC)
+
+.tex.aux:
+ @echo === Making $@ file ===
+ $(PDFLATEX) $(srcdir)/$(MANTEXSRC)
+ @grep "^\\\\citation" $(MANAUX) > .btmp.new || true
+ @if ( diff .btmp.new .btmp > /dev/null ); then \
+ rm .btmp.new; \
+ else \
+ mv .btmp.new .btmp; \
+ fi
+
+# A target needed to keep track of the nr. of LaTeX runs
+.btmp:
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/src/Makefile.am 2011-08-11 22:41:45 UTC (rev 758)
@@ -1,7 +1,9 @@
+## Process this file with automake to produce Makefile.in
+
## Using wildcards in these lists doesn't work. Also GNU make's ($wildcard,) doesn't
## work. It gives warning message about portability, but in the end doesn't work,
## I tried :-).
-REGFILES = data.h mematrix.h reg1.h usage.h main.cpp version.h mematri1.h
+REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h version.h
## Filevector files:
FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
@@ -28,7 +30,6 @@
bin_PROGRAMS = palinear palogist pacoxph
-#bin_PROGRAMS = pacoxph
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palinear_CXXFLAGS = -DLINEAR
Modified: pkg/ProbABEL/src/Makefile.in
===================================================================
--- pkg/ProbABEL/src/Makefile.in 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/src/Makefile.in 2011-08-11 22:41:45 UTC (rev 758)
@@ -186,6 +186,7 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
+PDFLATEX = @PDFLATEX@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
STRIP = @STRIP@
@@ -233,7 +234,7 @@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-REGFILES = data.h mematrix.h reg1.h usage.h main.cpp version.h mematri1.h
+REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h version.h
FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp \
fvlib/frutil.cpp fvlib/Logger.cpp fvlib/RealHandlerWrapper.cpp \
@@ -254,7 +255,6 @@
COXBASE = coxfit2 chinv2 cholesky2 chsolve2 dmatrix
COXSRC = $(COXBASE:=.c)
-#bin_PROGRAMS = pacoxph
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palinear_CXXFLAGS = -DLINEAR
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
@@ -280,9 +280,9 @@
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --foreign src/Makefile
+ $(AUTOMAKE) --gnu src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
Modified: pkg/ProbABEL/src/probabel.pl
===================================================================
--- pkg/ProbABEL/src/probabel.pl 2011-07-28 10:29:42 UTC (rev 757)
+++ pkg/ProbABEL/src/probabel.pl 2011-08-11 22:41:45 UTC (rev 758)
@@ -6,16 +6,16 @@
#
# Description: Handy perl wrapper for ProbABEL functions
#
-# Version: 1.4
+# Version: 1.5
# Created: 28-Oct-2008
# Revision: none
-# last modification: 07-Jan-2011
+# last modification: 11-Aug-2011
#
# Author: Lennart C. Karssen,
# Maksim V. Struchalin,
# Yurii S. Aulchenko
# Company: Erasmus MC,
-# Epidemiology & Biostatistics Department,
+# Department of Epidemiology,
# The Netherlands.
# Email: l.karssen at erasmusmc.nl,
# m.struchalin at erasmusmc.nl,
@@ -26,8 +26,8 @@
-$version="1.4";
-$release_data="07-Jan-2011";
+$version="1.5";
+$release_data="11-Aug-2011";
$_2df_file_postfix = "_2df.out.txt";
$_add_file_postfix = "_add.out.txt";
@@ -42,7 +42,7 @@
$separator_filename = "_._chr_._";
$base_path = "./";
-$config = $base_path . "probabel_config.cfg";
+$config = "/etc/probabel_config.cfg";
@method = ("linear","logistic","coxph");
@anprog = ($base_path . "palinear", $base_path . "palogist", $base_path . "pacoxph");
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