[med-svn] [probabel] 01/03: Imported Upstream version 0.4.5
Andreas Tille
tille at debian.org
Fri Jul 10 05:01:25 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository probabel.
commit a17cb632fb26f02f95d8de5caad3020bec302d48
Author: Andreas Tille <tille at debian.org>
Date: Fri Jul 10 06:47:04 2015 +0200
Imported Upstream version 0.4.5
---
Makefile.in | 11 +-
aclocal.m4 | 153 +++++++++---
checks/Makefile.am | 18 +-
checks/Makefile.in | 28 ++-
checks/R-tests/Makefile.am | 15 +-
checks/R-tests/Makefile.in | 17 +-
checks/R-tests/run_model_coxph.R | 65 +++--
checks/R-tests/run_models_in_R_pacox.R | 85 ++++++-
checks/inputfiles/coxph_data_nocovar.txt | 201 +++++++++++++++
checks/test_cox_nocovar.sh | 82 +++++++
configure | 269 ++++++++++----------
configure.ac | 12 +-
doc/ChangeLog | 31 +++
doc/Makefile.in | 18 +-
doc/ProbABEL_manual.tex | 58 +++--
doc/pacoxph.1 | 5 +-
doc/palinear.1 | 2 +-
doc/palogist.1 | 4 +-
doc/probabel.1 | 2 +-
doc/probabel.pl.1 | 2 +-
examples/Makefile.in | 2 +-
src/Makefile.am | 24 +-
src/Makefile.in | 405 +++++++++++++++----------------
src/command_line_settings.cpp | 2 +-
src/config.h.in | 3 -
src/coxph_data.cpp | 100 ++++++--
src/fvlib/CastUtils.h | 3 +
src/main.cpp | 2 +-
src/phedata.cpp | 9 +-
29 files changed, 1100 insertions(+), 528 deletions(-)
diff --git a/Makefile.in b/Makefile.in
index 6a577d3..8b3f5f3 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -511,10 +511,16 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
+ @echo WARNING: "Support for shar distribution archives is" \
+ "deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
+ @echo WARNING: "Support for distribution archives compressed with" \
+ "legacy program 'compress' is deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
$(am__post_remove_distdir)
@@ -556,9 +562,10 @@ distcheck: dist
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
&& $(am__cd) $(distdir)/_build \
- && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ && ../configure \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
+ --srcdir=.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
diff --git a/aclocal.m4 b/aclocal.m4
index 913076e..6f74638 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,4 +1,4 @@
-# generated automatically by aclocal 1.13.3 -*- Autoconf -*-
+# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.13'
+[am__api_version='1.14'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.13.3], [],
+m4_if([$1], [1.14.1], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.13.3])dnl
+[AM_AUTOMAKE_VERSION([1.14.1])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
@@ -418,6 +418,12 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
+m4_define([AC_PROG_CC],
+m4_defn([AC_PROG_CC])
+[_AM_PROG_CC_C_O
+])
+
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
@@ -526,6 +532,48 @@ dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
AC_CONFIG_COMMANDS_PRE(dnl
[m4_provide_if([_AM_COMPILER_EXEEXT],
[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
+
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
+ fi
+fi
])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
@@ -534,7 +582,6 @@ dnl mangled by Autoconf and run in a shell conditional statement.
m4_define([_AC_COMPILER_EXEEXT],
m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
-
# When config.status generates a header, we must update the stamp-h file.
# This file resides in the same directory as the config header
# that is generated. The stamp files are numbered to have different names.
@@ -682,38 +729,6 @@ AC_MSG_RESULT([$_am_result])
rm -f confinc confmf
])
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
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-AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-AC_REQUIRE_AUX_FILE([compile])dnl
-# FIXME: we rely on the cache variable name because
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-set dummy $CC
-am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
-eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
-if test "$am_t" != yes; then
- # Losing compiler, so override with the script.
- # FIXME: It is wrong to rewrite CC.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__CC in this case,
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-dnl Make sure AC_PROG_CC is never called again, or it will override our
-dnl setting of CC.
-m4_define([AC_PROG_CC],
- [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
-])
-
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
# Copyright (C) 1997-2013 Free Software Foundation, Inc.
@@ -784,6 +799,70 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
+# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+#
+# This file 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.
+
+# _AM_PROG_CC_C_O
+# ---------------
+# Like AC_PROG_CC_C_O, but changed for automake. We rewrite AC_PROG_CC
+# to automatically call this.
+AC_DEFUN([_AM_PROG_CC_C_O],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+AC_LANG_PUSH([C])dnl
+AC_CACHE_CHECK(
+ [whether $CC understands -c and -o together],
+ [am_cv_prog_cc_c_o],
+ [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i])
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+AC_LANG_POP([C])])
+
+# For backward compatibility.
+AC_DEFUN_ONCE([AM_PROG_CC_C_O], [AC_REQUIRE([AC_PROG_CC])])
+
+# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+#
+# This file 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.
+
+# AM_RUN_LOG(COMMAND)
+# -------------------
+# Run COMMAND, save the exit status in ac_status, and log it.
+# (This has been adapted from Autoconf's _AC_RUN_LOG macro.)
+AC_DEFUN([AM_RUN_LOG],
+[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
+ ($1) >&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ (exit $ac_status); }])
+
# Check to make sure that the build environment is sane. -*- Autoconf -*-
# Copyright (C) 1996-2013 Free Software Foundation, Inc.
diff --git a/checks/Makefile.am b/checks/Makefile.am
index b14a61e..2bc16fd 100644
--- a/checks/Makefile.am
+++ b/checks/Makefile.am
@@ -17,6 +17,7 @@ input_files_dir = inputfiles
phenofiles = $(input_files_dir)/height.txt \
$(input_files_dir)/logist_data.txt \
$(input_files_dir)/coxph_data.txt \
+ $(input_files_dir)/coxph_data_nocovar.txt \
$(input_files_dir)/mmscore_pheno.PHE
genofiles = $(input_files_dir)/test.mldose \
@@ -49,7 +50,7 @@ if BUILD_palogist
check_SCRIPTS += test_bt.sh
endif
if BUILD_pacoxph
-check_SCRIPTS += test_cox.sh
+check_SCRIPTS += test_cox.sh test_cox_nocovar.sh
endif
AM_TESTS_ENVIRONMENT= \
@@ -125,6 +126,18 @@ coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
coxph_prob_recess.out.txt coxph_prob_add.out.txt \
coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
+cleanfiles_cox_nocovar = coxph_dose_nocovar_add.out.txt \
+coxph_dose_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_over_domin.out.txt \
+coxph_prob_nocovar_fv_domin.out.txt \
+coxph_prob_nocovar_over_domin.out.txt \
+coxph_prob_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_recess.out.txt \
+coxph_prob_nocovar_domin.out.txt \
+coxph_prob_nocovar_recess.out.txt \
+coxph_prob_nocovar_add.out.txt \
+coxph_prob_nocovar_2df.out.txt \
+coxph_prob_nocovar_fv_2df.out.txt
dose_files = chr1.chunk1.dose chr1.chunk2.dose chr2.chunk1.dose \
chr2.chunk2.dose chr1.dose chr2.dose
@@ -147,4 +160,5 @@ cleanfiles_probabel_check = height.PHE $(dose_files) $(prob_files) \
cleanfiles_dose_check = test.mldose
CLEANFILES = $(cleanfiles_probabel_check) $(cleanfiles_dose_check) \
- $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) $(cleanfiles_cox)
+ $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) $(cleanfiles_cox) \
+ $(cleanfiles_cox_nocovar)
diff --git a/checks/Makefile.in b/checks/Makefile.in
index 452d1dd..9a03869 100644
--- a/checks/Makefile.in
+++ b/checks/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -79,7 +79,7 @@ POST_UNINSTALL = :
@BUILD_palinear_TRUE@ check_dose_input.sh test_qt.sh \
@BUILD_palinear_TRUE@ test_mms.sh
@BUILD_palogist_TRUE at am__append_2 = test_bt.sh
- at BUILD_pacoxph_TRUE@am__append_3 = test_cox.sh
+ at BUILD_pacoxph_TRUE@am__append_3 = test_cox.sh test_cox_nocovar.sh
subdir = checks
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/test-driver
@@ -427,6 +427,7 @@ input_files_dir = inputfiles
phenofiles = $(input_files_dir)/height.txt \
$(input_files_dir)/logist_data.txt \
$(input_files_dir)/coxph_data.txt \
+ $(input_files_dir)/coxph_data_nocovar.txt \
$(input_files_dir)/mmscore_pheno.PHE
genofiles = $(input_files_dir)/test.mldose \
@@ -519,6 +520,19 @@ coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
coxph_prob_recess.out.txt coxph_prob_add.out.txt \
coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
+cleanfiles_cox_nocovar = coxph_dose_nocovar_add.out.txt \
+coxph_dose_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_over_domin.out.txt \
+coxph_prob_nocovar_fv_domin.out.txt \
+coxph_prob_nocovar_over_domin.out.txt \
+coxph_prob_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_recess.out.txt \
+coxph_prob_nocovar_domin.out.txt \
+coxph_prob_nocovar_recess.out.txt \
+coxph_prob_nocovar_add.out.txt \
+coxph_prob_nocovar_2df.out.txt \
+coxph_prob_nocovar_fv_2df.out.txt
+
dose_files = chr1.chunk1.dose chr1.chunk2.dose chr2.chunk1.dose \
chr2.chunk2.dose chr1.dose chr2.dose
@@ -537,7 +551,8 @@ cleanfiles_probabel_check = height.PHE $(dose_files) $(prob_files) \
cleanfiles_dose_check = test.mldose
CLEANFILES = $(cleanfiles_probabel_check) $(cleanfiles_dose_check) \
- $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) $(cleanfiles_cox)
+ $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) $(cleanfiles_cox) \
+ $(cleanfiles_cox_nocovar)
all: all-am
@@ -763,6 +778,13 @@ test_cox.sh.log: test_cox.sh
--log-file $$b.log --trs-file $$b.trs \
$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
"$$tst" $(AM_TESTS_FD_REDIRECT)
+test_cox_nocovar.sh.log: test_cox_nocovar.sh
+ @p='test_cox_nocovar.sh'; \
+ b='test_cox_nocovar.sh'; \
+ $(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+ --log-file $$b.log --trs-file $$b.trs \
+ $(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+ "$$tst" $(AM_TESTS_FD_REDIRECT)
.test.log:
@p='$<'; \
$(am__set_b); \
diff --git a/checks/R-tests/Makefile.am b/checks/R-tests/Makefile.am
index a88ce6c..de8b661 100644
--- a/checks/R-tests/Makefile.am
+++ b/checks/R-tests/Makefile.am
@@ -104,5 +104,18 @@ coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
coxph_prob_recess.out.txt coxph_prob_add.out.txt \
coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
+cleanfiles_cox_nocovar = coxph_dose_nocovar_add.out.txt \
+coxph_dose_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_over_domin.out.txt \
+coxph_prob_nocovar_fv_domin.out.txt \
+coxph_prob_nocovar_over_domin.out.txt \
+coxph_prob_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_recess.out.txt \
+coxph_prob_nocovar_domin.out.txt \
+coxph_prob_nocovar_recess.out.txt \
+coxph_prob_nocovar_add.out.txt \
+coxph_prob_nocovar_2df.out.txt \
+coxph_prob_nocovar_fv_2df.out.txt
+
CLEANFILES = $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) \
- $(cleanfiles_cox)
+ $(cleanfiles_cox) $(cleanfiles_cox_nocovar)
diff --git a/checks/R-tests/Makefile.in b/checks/R-tests/Makefile.in
index df0a3ec..882ca29 100644
--- a/checks/R-tests/Makefile.in
+++ b/checks/R-tests/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -492,8 +492,21 @@ coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
coxph_prob_recess.out.txt coxph_prob_add.out.txt \
coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
+cleanfiles_cox_nocovar = coxph_dose_nocovar_add.out.txt \
+coxph_dose_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_over_domin.out.txt \
+coxph_prob_nocovar_fv_domin.out.txt \
+coxph_prob_nocovar_over_domin.out.txt \
+coxph_prob_nocovar_fv_add.out.txt \
+coxph_prob_nocovar_fv_recess.out.txt \
+coxph_prob_nocovar_domin.out.txt \
+coxph_prob_nocovar_recess.out.txt \
+coxph_prob_nocovar_add.out.txt \
+coxph_prob_nocovar_2df.out.txt \
+coxph_prob_nocovar_fv_2df.out.txt
+
CLEANFILES = $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) \
- $(cleanfiles_cox)
+ $(cleanfiles_cox) $(cleanfiles_cox_nocovar)
all: all-am
diff --git a/checks/R-tests/run_model_coxph.R b/checks/R-tests/run_model_coxph.R
index 1454953..7f0c2a9 100644
--- a/checks/R-tests/run_model_coxph.R
+++ b/checks/R-tests/run_model_coxph.R
@@ -15,8 +15,8 @@
##' output can be compared to the ProbABEL output.
##' @author L.C. Larsen
run.model <- function(model0.txt, model.txt,
- snpcomponent1, snpcomponent2="1") {
-
+ snpcomponent1, snpcomponent2="1",
+ verbose=FALSE) {
if (snpcomponent2 != "1") {
## SNP component 2 is not constant: assume we run the 2df
## model.
@@ -28,15 +28,31 @@ run.model <- function(model0.txt, model.txt,
resultR <- data.frame()
for (i in 3:dim(dose)[2]) {
+ if (verbose) print(paste("------- new iteration: i =", i))
indexHom <- 3 + ( i - 3 ) * 2
indexHet <- indexHom + 1
snp1 <- eval(parse(text=snpcomponent1))
snp2 <- eval(parse(text=snpcomponent2))
snp <- snp1 + snp2
+ mu <- rep(1., length(snp)) # Add a constant mean
noNA <- which( !is.na(snp) )
model.0 <- eval(parse(text=model0.txt))
+ ## Check the imputation R^2, if below threshold ProbABEL will
+ ## set the coefficients to NaN and skip the rest of this
+ ## iteration of the for loop.
+ rsq <- Rsq[i-2]
+ if (rsq < rsq.thresh ) {
+ if (twoDF) {
+ row <- c(rsq, NaN, NaN, NaN, NaN, NaN)
+ } else {
+ row <- c(rsq, NaN, NaN, NaN)
+ }
+ resultR <- rbind(resultR, row)
+ next
+ }
+
## Evaluate the model. The whole tryCatch is needed to catch
## problems with non-converging regression.
model = tryCatch({
@@ -49,11 +65,25 @@ run.model <- function(model0.txt, model.txt,
eval(parse(text=model.txt)),
war)
)
- })
+ },
+ error = function(err) {
+ return(list(
+ "Can't calculate model; some error occurred",
+ err)
+ )
+ })
- if ( grepl("infinite", model[[2]]$message) |
- grepl("singular", model[[2]]$message) ) {
- ## The model did not converge, fill the coefficients with
+ if (verbose) print(model)
+
+ if ( grepl("Inf", model[[2]]$message) |
+ grepl("infinite", model[[2]]$message) |
+ grepl("iterations", model[[2]]$message) |
+ ( grepl("singular", model[[2]]$message) &
+ (regexpr("variable 1$", model[[2]]$message)[[1]] != 33)
+ )
+ ) {
+ ## The model did not converge or some other
+ ## errors/warnings occurred, fill the coefficients with
## NaNs
if (twoDF) {
smA1A2 <- c(NaN, NaN)
@@ -66,30 +96,21 @@ run.model <- function(model0.txt, model.txt,
## No convergence problems, we can trust the
## coefficients.
coeff <- summary(model[[1]])$coefficients
+ # The SNP coefficient(s) is/are in the last row(s) of coeff
+ nr <- nrow(coeff)
if (twoDF) {
- smA1A2 <- coeff[4, c("coef", "se(coef)")]
- smA1A1 <- coeff[5, c("coef", "se(coef)")]
+ smA1A2 <- coeff[nr - 1, c("coef", "se(coef)")]
+ smA1A1 <- coeff[nr, c("coef", "se(coef)")]
} else {
- sm <- coeff[4, c("coef", "se(coef)")]
+ sm <- coeff[nr, c("coef", "se(coef)")]
}
lrt <- 2 * ( model[[1]]$loglik[2] - model.0$loglik[2] )
}
- ## Check the imputation R^2, if below threshold ProbABEL will
- ## set the coefficients to NaN.
- rsq <- Rsq[i-2]
if (twoDF) {
- if( rsq < rsq.thresh ) {
- row <- c(rsq, NaN, NaN, NaN, NaN, NaN)
- } else {
- row <- c(rsq, smA1A2[1], smA1A2[2], smA1A1[1], smA1A1[2], lrt)
- }
+ row <- c(rsq, smA1A2[1], smA1A2[2], smA1A1[1], smA1A1[2], lrt)
} else {
- if( rsq < rsq.thresh ) {
- row <- c(rsq, NaN, NaN, NaN)
- } else {
- row <- c(rsq, sm[1], sm[2], lrt)
- }
+ row <- c(rsq, sm[1], sm[2], lrt)
}
resultR <- rbind(resultR, row)
diff --git a/checks/R-tests/run_models_in_R_pacox.R b/checks/R-tests/run_models_in_R_pacox.R
index 992f6c5..4ac670a 100644
--- a/checks/R-tests/run_models_in_R_pacox.R
+++ b/checks/R-tests/run_models_in_R_pacox.R
@@ -53,8 +53,8 @@ cat("Comparing R output with ProbABEL output\t\t")
source(paste0(srcdir, "run_model_coxph.R"))
model.fn.0 <-
- "coxph( Surv(fupt_chd, chd)[noNA] ~ sex[noNA] + age[noNA] + othercov[noNA] )"
-model.fn <- "coxph( Surv(fupt_chd, chd) ~ sex + age + othercov + snp1 )"
+ "coxph( Surv(fupt_chd, chd)[noNA] ~ mu[noNA] + sex[noNA] + age[noNA] + othercov[noNA] )"
+model.fn <- "coxph( Surv(fupt_chd, chd) ~ mu + sex + age + othercov + snp1 )"
## Additive model, dosages
snpdose <- "dose[, i]"
@@ -109,4 +109,85 @@ rownames(prob.2df.R) <- NULL
stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
cat("2df\n")
+
+
+cat("\nRun the same checks, but without any covariates (see bug #1266)\n")
+cat("Running ProbABEL...\t\t\t\t")
+tmp <- system(paste0("bash ", tests.path, "test_cox_nocovar.sh 2> /dev/null"),
+ intern=TRUE)
+cat("OK\n")
+
+dose.add.PA <- read.table("coxph_dose_nocovar_add.out.txt",
+ head=TRUE)[, colsAddDose]
+prob.add.PA <- read.table("coxph_prob_nocovar_add.out.txt",
+ head=TRUE)[, colsAddProb]
+prob.dom.PA <- read.table("coxph_prob_nocovar_domin.out.txt",
+ head=TRUE)[, colsDom]
+prob.rec.PA <- read.table("coxph_prob_nocovar_recess.out.txt",
+ head=TRUE)[, colsRec]
+prob.odom.PA <- read.table("coxph_prob_nocovar_over_domin.out.txt",
+ head=TRUE)[, colsOdom]
+prob.2df.PA <- read.table("coxph_prob_nocovar_2df.out.txt",
+ head=TRUE)[, cols2df]
+
+model.fn.0 <-
+ "coxph( Surv(fupt_chd, chd)[noNA] ~ mu[noNA] )"
+model.fn <- "coxph( Surv(fupt_chd, chd) ~ mu + snp1 )"
+
+
+cat("Comparing R output with ProbABEL output\t\t")
+
+## Additive model, dosages
+snpdose <- "dose[, i]"
+dose.add.R <- run.model(model.fn.0, model.fn, snpdose)
+colnames(dose.add.R) <- colsAddDose
+rownames(dose.add.R) <- NULL
+stopifnot( all.equal(dose.add.PA, dose.add.R, tol=tol) )
+cat("additive ")
+
+
+## Additive model, probabilities
+snpprob <- "doseFromProb[, i]"
+prob.add.R <- run.model(model.fn.0, model.fn, snpprob)
+colnames(prob.add.R) <- colsAddProb
+rownames(prob.add.R) <- NULL
+stopifnot( all.equal(prob.add.PA, prob.add.R, tol=tol) )
+cat("additive ")
+
+## dominant model
+snpprob <- "prob[, indexHom] + prob[, indexHet]"
+prob.dom.R <- run.model(model.fn.0, model.fn, snpprob)
+colnames(prob.dom.R) <- colsDom
+rownames(prob.dom.R) <- NULL
+stopifnot( all.equal(prob.dom.PA, prob.dom.R, tol=tol) )
+cat("dominant ")
+
+## recessive model
+snpprob <- "prob[, indexHom]"
+prob.rec.R <- run.model(model.fn.0, model.fn, snpprob)
+colnames(prob.rec.R) <- colsRec
+rownames(prob.rec.R) <- NULL
+stopifnot( all.equal(prob.rec.PA, prob.rec.R, tol=tol) )
+cat("recessive ")
+
+## over-dominant model
+snpprob <- "prob[, indexHet]"
+prob.odom.R <- run.model(model.fn.0, model.fn, snpprob)
+colnames(prob.odom.R) <- colsOdom
+rownames(prob.odom.R) <- NULL
+stopifnot( all.equal(prob.odom.PA, prob.odom.R, tol=tol) )
+cat("overdominant ")
+
+
+## 2df model
+model.fn <-
+ "coxph( Surv(fupt_chd, chd) ~ mu+ snp1 + snp2 )"
+snpd1 <- "prob[, indexHet]"
+snpd2 <- "prob[, indexHom]"
+prob.2df.R <- run.model(model.fn.0, model.fn, snpd1, snpd2)
+colnames(prob.2df.R) <- cols2df
+rownames(prob.2df.R) <- NULL
+stopifnot( all.equal(prob.2df.PA, prob.2df.R, tol=tol) )
+cat("2df\n")
+
cat("\t\t\t\t\t\tOK\n")
diff --git a/checks/inputfiles/coxph_data_nocovar.txt b/checks/inputfiles/coxph_data_nocovar.txt
new file mode 100644
index 0000000..c6ca38b
--- /dev/null
+++ b/checks/inputfiles/coxph_data_nocovar.txt
@@ -0,0 +1,201 @@
+id fupt_chd chd
+id636728 3.187930645 0
+id890314 2.099691952 0
+id102874 9.133488079 1
+id200949 7.525406804 0
+id336491 6.798229522 0
+id988766 6.149545358 0
+id21999 1.013546103 1
+id433893 1.282853098 0
+id688932 8.340206657 0
+id394203 3.392345681 1
+id995678 9.587748608 0
+id694339 1.25827049 0
+id256455 5.414840139 0
+id14836 6.177914833 1
+id817128 2.940033056 1
+id803325 9.619267566 0
+id521287 0.320487323 1
+id701472 7.101945547 0
+id850010 6.780876558 1
+id268483 7.903947419 0
+id738781 1.086018804 0
+id28411 1.254350142 1
+id541635 9.057035035 1
+id751101 1.303018406 0
+id826300 6.735484141 1
+id884387 9.097303962 0
+id492414 4.756845946 0
+id268871 4.018189958 0
+id627354 8.874035732 0
+id503932 0.091310535 0
+id163442 3.240808272 0
+id317797 9.050109718 0
+id687857 7.992764162 0
+id871570 2.353719529 0
+id724067 1.617985994 1
+id874076 3.099430273 0
+id927863 3.64738684 0
+id369805 0.973580503 0
+id668376 0.567035975 0
+id717362 6.77104712 1
+id665504 8.956792361 0
+id336637 7.196501733 0
+id60633 5.086557706 0
+id848600 8.270336349 1
+id169514 9.421256192 0
+id690732 9.952887485 0
+id684760 3.361963101 0
+id553502 5.557606017 1
+id214917 6.535326783 0
+id849169 7.903922417 1
+id941921 2.305853849 0
+id784646 3.120883065 1
+id520954 8.756848347 1
+id996355 7.326814334 0
+id96730 6.664821662 0
+id673442 3.081616083 0
+id68305 3.525197877 1
+id653025 7.231586593 0
+id208543 4.622250109 0
+id335725 5.924295793 1
+id980400 2.35961827 0
+id869939 0.736202662 0
+id297563 6.641749611 0
+id852663 5.124175591 0
+id162070 7.910906314 0
+id272875 9.825455416 1
+id163787 2.471002157 0
+id422204 2.915218179 0
+id120197 3.367355865 0
+id33660 4.407010904 1
+id803855 8.755961077 0
+id255048 7.749378138 0
+id690936 7.543593942 0
+id126807 0.251036587 0
+id99016 6.491002725 0
+id883847 1.088929613 0
+id354523 9.618060855 1
+id737255 4.133744506 1
+id990941 5.646270286 0
+id25464 8.272429793 0
+id918375 0.723567779 0
+id537828 4.0147246 0
+id682778 9.130628394 0
+id587547 7.44191196 0
+id670874 4.512303089 0
+id444459 8.723388559 0
+id777456 4.115325335 1
+id452384 2.067203142 0
+id826975 8.348432332 0
+id519567 6.785076383 0
+id84292 7.634117891 0
+id124432 5.099839207 1
+id800145 8.551368147 0
+id153857 3.556301609 0
+id587157 8.758929135 1
+id506262 6.238330685 1
+id634462 0.905623161 0
+id687592 0.290071515 0
+id955526 1.838730964 0
+id181850 0.144560173 1
+id159506 6.045008786 1
+id609051 6.873427527 1
+id963886 0.853758289 0
+id405792 3.909860553 1
+id494172 7.480072965 0
+id964637 3.816858446 0
+id799355 1.226117869 1
+id157111 4.166491482 1
+id114524 8.645968152 0
+id954931 0.158490245 0
+id827034 0.702377072 0
+id689645 2.0658374 0
+id281585 4.640052191 1
+id885624 3.615978697 0
+id577871 2.230068497 0
+id238796 5.161400753 0
+id481035 7.693009686 0
+id972713 6.34411768 1
+id905484 4.55801149 0
+id713511 6.721560405 1
+id512328 4.431789868 0
+id703534 8.974882244 1
+id409904 4.845419164 0
+id577169 1.384047668 0
+id813971 6.785385478 0
+id558483 0.27946972 0
+id892784 1.505769901 0
+id611178 3.97305697 1
+id192732 7.859877791 0
+id917280 1.39759155 0
+id435876 4.928142177 0
+id980722 0.72730016 1
+id308273 3.466919258 1
+id476685 8.925909139 0
+id315883 7.79623385 0
+id935945 3.491058239 1
+id991781 6.268341084 0
+id65199 2.65595714 0
+id226233 6.409789501 0
+id860183 7.567894972 0
+id295209 0.983143735 1
+id544964 1.927387219 0
+id648663 7.914653713 0
+id710165 9.981244413 0
+id392593 7.418579368 0
+id129945 9.344802496 0
+id382621 1.828452452 0
+id901440 9.496967232 0
+id39847 8.962161053 0
+id526460 1.855905599 0
+id477473 1.89081994 1
+id448194 4.814151059 0
+id904184 8.028988991 1
+id747852 3.836260637 1
+id711012 0.341281233 0
+id683879 9.297243459 0
+id789575 5.098990324 0
+id650729 7.941450537 0
+id934302 9.134082902 1
+id555013 8.812444844 1
+id82779 7.657743527 0
+id771444 6.664855358 1
+id821562 5.19036265 0
+id292809 9.909691181 1
+id645690 6.515405399 0
+id223901 6.355198262 1
+id41320 0.397540162 1
+id96181 3.155308448 1
+id147900 4.719584771 0
+id702917 7.72554794 0
+id150640 6.511110099 1
+id518391 9.626758766 0
+id879076 7.61506094 0
+id952031 4.87888217 1
+id10055 5.724749579 0
+id727213 5.731963291 1
+id41961 6.818411434 0
+id257209 9.897638239 1
+id995361 3.151184642 0
+id957918 5.30099154 0
+id975370 9.047264812 0
+id889896 9.578142144 1
+id978164 4.726348119 0
+id90359 6.237920077 0
+id307158 5.49680528 0
+id755940 1.683472511 0
+id995582 1.486566562 0
+id363965 7.723182293 1
+id729124 6.861379688 0
+id871963 1.399526332 1
+id475172 2.745065294 0
+id804699 8.378029915 1
+id625843 4.925798265 1
+id595713 3.273883772 0
+id462604 5.541305429 0
+id106141 9.529928524 0
+id689349 9.243194854 0
+id639003 6.594759182 1
+id393896 8.69916317 1
+id450307 7.291170542 1
diff --git a/checks/test_cox_nocovar.sh b/checks/test_cox_nocovar.sh
new file mode 100755
index 0000000..72be69b
--- /dev/null
+++ b/checks/test_cox_nocovar.sh
@@ -0,0 +1,82 @@
+#!/bin/bash
+# This script runs checks on ProbABEL's pacoxph module
+# These are almost identical to the checks in test_cox.sh, but this
+# time without covariate data (see bug #1266).
+
+
+echo "Analysing Cox model without covariates..."
+
+scriptdir=$(dirname $0)
+
+if [ -z ${PA_BINDIR} ]; then
+ PA_BINDIR="${scriptdir}/../src/"
+fi
+if [ -z ${srcdir} ]; then
+ srcdir="."
+ PA_BINDIR=${scriptdir}/../src/
+fi
+
+. ${scriptdir}/run_diff.sh
+
+inputdir=${scriptdir}/inputfiles
+pacoxph=${PA_BINDIR}/pacoxph
+
+# Redirect all output to file descriptor 3 to /dev/null except if
+# the first argument is "verbose" then redirect handle 3 to stdout
+exec 3>/dev/null
+if [ "$1" = "verbose" ]; then
+ echo "Verbose mode ON"
+ exec 3>&1
+fi
+
+$pacoxph \
+ -p ${inputdir}/coxph_data_nocovar.txt \
+ -d ${inputdir}/test.mldose \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o coxph_dose_nocovar \
+ >& 3
+
+$pacoxph \
+ -p ${inputdir}/coxph_data_nocovar.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o coxph_dose_nocovar_fv \
+ >& 3
+
+run_diff coxph_dose_nocovar_add.out.txt coxph_dose_nocovar_fv_add.out.txt \
+ "pacoxph check: dose vs. dose_fv"
+
+
+$pacoxph \
+ -p ${inputdir}/coxph_data_nocovar.txt \
+ -d ${inputdir}/test.mlprob \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o coxph_prob_nocovar \
+ >& 3
+
+run_diff coxph_dose_nocovar_add.out.txt coxph_prob_nocovar_add.out.txt \
+ "pacoxph check: dose vs. prob" -I SNP
+
+
+$pacoxph \
+ -p ${inputdir}/coxph_data_nocovar.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o coxph_prob_nocovar_fv \
+ >& 3
+
+for model in add domin recess over_domin 2df; do
+ run_diff coxph_prob_nocovar_${model}.out.txt \
+ coxph_prob_nocovar_fv_${model}.out.txt \
+ "pacoxph check ($model model): prob vs. prob_fv"
+done
diff --git a/configure b/configure
index bb7b684..85b1232 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for ProbABEL 0.4.3.
+# Generated by GNU Autoconf 2.69 for ProbABEL 0.4.5.
#
# Report bugs to <genabel-devel at r-forge.wu-wien.ac.at>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='ProbABEL'
PACKAGE_TARNAME='probabel'
-PACKAGE_VERSION='0.4.3'
-PACKAGE_STRING='ProbABEL 0.4.3'
+PACKAGE_VERSION='0.4.5'
+PACKAGE_STRING='ProbABEL 0.4.5'
PACKAGE_BUGREPORT='genabel-devel at r-forge.wu-wien.ac.at'
PACKAGE_URL=''
@@ -1305,7 +1305,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures ProbABEL 0.4.3 to adapt to many kinds of systems.
+\`configure' configures ProbABEL 0.4.5 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1371,7 +1371,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of ProbABEL 0.4.3:";;
+ short | recursive ) echo "Configuration of ProbABEL 0.4.5:";;
esac
cat <<\_ACEOF
@@ -1484,7 +1484,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-ProbABEL configure 0.4.3
+ProbABEL configure 0.4.5
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1945,7 +1945,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by ProbABEL $as_me 0.4.3, which was
+It was created by ProbABEL $as_me 0.4.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2293,7 +2293,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-am__api_version='1.13'
+am__api_version='1.14'
ac_aux_dir=
for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
@@ -2808,7 +2808,7 @@ fi
# Define the identity of the package.
PACKAGE='probabel'
- VERSION='0.4.3'
+ VERSION='0.4.5'
cat >>confdefs.h <<_ACEOF
@@ -2859,6 +2859,48 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
+ fi
+fi
+
# Check whether --enable-silent-rules was given.
if test "${enable_silent_rules+set}" = set; then :
enableval=$enable_silent_rules;
@@ -3719,6 +3761,65 @@ 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
+
+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
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
+$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
+if ${am_cv_prog_cc_c_o+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
+ ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
+$as_echo "$am_cv_prog_cc_c_o" >&6; }
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+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
+
DEPDIR="${am__leading_dot}deps"
ac_config_commands="$ac_config_commands depfiles"
@@ -3911,131 +4012,6 @@ else
fi
-if test "x$CC" != xcc; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC and cc understand -c and -o together" >&5
-$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether cc understands -c and -o together" >&5
-$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
-fi
-set dummy $CC; ac_cc=`$as_echo "$2" |
- sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
-if eval \${ac_cv_prog_cc_${ac_cc}_c_o+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-# Make sure it works both with $CC and with simple cc.
-# We do the test twice because some compilers refuse to overwrite an
-# existing .o file with -o, though they will create one.
-ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
-rm -f conftest2.*
-if { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; } &&
- test -f conftest2.$ac_objext && { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; };
-then
- eval ac_cv_prog_cc_${ac_cc}_c_o=yes
- if test "x$CC" != xcc; then
- # Test first that cc exists at all.
- if { ac_try='cc -c conftest.$ac_ext >&5'
- { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; }; then
- ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
- rm -f conftest2.*
- if { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; } &&
- test -f conftest2.$ac_objext && { { case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; };
- then
- # cc works too.
- :
- else
- # cc exists but doesn't like -o.
- eval ac_cv_prog_cc_${ac_cc}_c_o=no
- fi
- fi
- fi
-else
- eval ac_cv_prog_cc_${ac_cc}_c_o=no
-fi
-rm -f core conftest*
-
-fi
-if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-
-$as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h
-
-fi
-
-# FIXME: we rely on the cache variable name because
-# there is no other way.
-set dummy $CC
-am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
-eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
-if test "$am_t" != yes; then
- # Losing compiler, so override with the script.
- # FIXME: It is wrong to rewrite CC.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__CC in this case,
- # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
- CC="$am_aux_dir/compile $CC"
-fi
-
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
@@ -4055,7 +4031,7 @@ if test -z "$CXXFLAGS"; then
fi
if test -z "$CPPFLAGS"; then
# User did not set CPPFLAGS, so we can put in our own defaults
- CPPFLAGS="-Wall"
+ CPPFLAGS="-Wall -DNDEBUG"
fi
# If CXXFLAGS/CPPFLAGS are already set AC_PROG_CXX will not overwrite them
# with its own defaults
@@ -4447,7 +4423,8 @@ fi
#Tell compiler to build not R version of filevector
-CXXFLAGS+=" -D_NOT_R_FILEVECTOR"
+CPPFLAGS="$CPPFLAGS -D_NOT_R_FILEVECTOR"
+
# Since most of our code is in C++, set that language as the default
@@ -5086,11 +5063,9 @@ $as_echo "$as_me: building using the Eigen headers enabled" >&6;}
# Check whether --with-eigen-include-path was given.
if test "${with_eigen_include_path+set}" = set; then :
- withval=$with_eigen_include_path; CXXFLAGS+=" -I${withval}"
- CPPFLAGS+=" -I${withval}"
+ withval=$with_eigen_include_path; CPPFLAGS+=" -I${withval}"
else
- CXXFLAGS+=' -I/usr/include/eigen3'
- CPPFLAGS+=' -I/usr/include/eigen3'
+ CPPFLAGS+=' -I/usr/include/eigen3'
fi
@@ -5364,7 +5339,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5410,7 +5385,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5434,7 +5409,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5479,7 +5454,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -5503,7 +5478,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -6491,7 +6466,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by ProbABEL $as_me 0.4.3, which was
+This file was extended by ProbABEL $as_me 0.4.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -6557,7 +6532,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-ProbABEL config.status 0.4.3
+ProbABEL config.status 0.4.5
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index 3a59486..4dc2e8e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.4.3, genabel-devel at r-forge.wu-wien.ac.at)
+AC_INIT(ProbABEL, 0.4.5, genabel-devel at r-forge.wu-wien.ac.at)
AM_INIT_AUTOMAKE([silent-rules subdir-objects])
AM_SILENT_RULES([yes])
AC_CONFIG_SRCDIR([src/data.h])
@@ -25,7 +25,7 @@ if test -z "$CXXFLAGS"; then
fi
if test -z "$CPPFLAGS"; then
# User did not set CPPFLAGS, so we can put in our own defaults
- CPPFLAGS="-Wall"
+ CPPFLAGS="-Wall -DNDEBUG"
fi
# If CXXFLAGS/CPPFLAGS are already set AC_PROG_CXX will not overwrite them
# with its own defaults
@@ -33,7 +33,7 @@ AC_PROG_CXX
#Tell compiler to build not R version of filevector
-CXXFLAGS+=" -D_NOT_R_FILEVECTOR"
+AC_SUBST(CPPFLAGS, "$CPPFLAGS -D_NOT_R_FILEVECTOR")
# Since most of our code is in C++, set that language as the default
@@ -65,10 +65,8 @@ if test "x$with_eigen" != "xno"; then
AC_ARG_WITH([eigen-include-path],
[AS_HELP_STRING([--with-eigen-include-path],
[location of the Eigen headers, defaults to /usr/include/eigen3])],
- [CXXFLAGS+=" -I${withval}"
- CPPFLAGS+=" -I${withval}"],
- [CXXFLAGS+=' -I/usr/include/eigen3'
- CPPFLAGS+=' -I/usr/include/eigen3'])
+ [CPPFLAGS+=" -I${withval}"],
+ [CPPFLAGS+=' -I/usr/include/eigen3'])
# Check for the EIGEN header files
AC_CHECK_HEADERS([Eigen/Dense Eigen/LU])
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 22ff7ed..657a279 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,3 +1,34 @@
+***** v.0.4.5 (2015.05.26)
+* Fixed bug #6054: "Not all ProbABEL's short command line options are
+ correctly parsed."
+* Fixed bug #6041: "ProbABEL's Cox module reports too many errors (beta
+ may be infinite, setting beta and se to 'NaN')". Thanks to Anne
+ Grotenhuis from the Radboud Medical Centre Nijmegen and forum user
+ quentin300 for their extensive bug reports and help in testing the fix.
+* Fixed bug #1266: "pacoxph with no covariates"; ProbABEL now also works
+ when no covariates have been provided. Thanks to Aaron Joon for
+ reporting this bug back in 2011 and to Anne Grotenhuis and to forum user
+ quentin300 for pushing this bug to my attention and their help in beta
+ testing.
+* pacoxph now displays the regression equation correctly.
+* Minor fix to the manual: the Rsq values in the info file should be >
+ 1e-16 (and not > 0 as mentioned before) otherwise the output will be set
+ to 'nan'.
+* Minor fix to the man-pages: according to the man-pages palogist,
+ palinear and pacoxph all did regression using a linear model.
+
+
+***** v.0.4.4 (2014.11.07)
+* Fixed bug #5729 in the Cox PH module. Some checks for problems with the
+ regression were incorrectly implemented. Thanks to Matthias Wuttke from
+ the University Medical Centre Freiburg, Anne Grotenhuis from the Radboud
+ Medical Centre Nijmegen, and Luba Pardo and Joris Verkouteren from the
+ Erasmus Medical Centre Rotterdam for their time and effort in reporting
+ the bug, helping to identify the problem and testing the fix.
+* Backported fix of bug #5982: ProbABEL's make install fails on MacOS X
+ and FreeBSD with sed error. Thanks to forum user mmold for reporting the bug.
+
+
***** v.0.4.3 (2014.04.01)
* Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when
using filevector input files.
diff --git a/doc/Makefile.in b/doc/Makefile.in
index b93b8c0..19fd069 100644
--- a/doc/Makefile.in
+++ b/doc/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -102,18 +102,6 @@ AM_V_at = $(am__v_at_ at AM_V@)
am__v_at_ = $(am__v_at_ at AM_DEFAULT_V@)
am__v_at_0 = @
am__v_at_1 =
-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-AM_V_CC = $(am__v_CC_ at AM_V@)
-am__v_CC_ = $(am__v_CC_ at AM_DEFAULT_V@)
-am__v_CC_0 = @echo " CC " $@;
-am__v_CC_1 =
-CCLD = $(CC)
-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-AM_V_CCLD = $(am__v_CCLD_ at AM_V@)
-am__v_CCLD_ = $(am__v_CCLD_ at AM_DEFAULT_V@)
-am__v_CCLD_0 = @echo " CCLD " $@;
-am__v_CCLD_1 =
SOURCES =
DIST_SOURCES =
am__can_run_installinfo = \
@@ -283,9 +271,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign doc/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu doc/Makefile
+ $(AUTOMAKE) --foreign doc/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
diff --git a/doc/ProbABEL_manual.tex b/doc/ProbABEL_manual.tex
index aeba9cd..5b6d630 100644
--- a/doc/ProbABEL_manual.tex
+++ b/doc/ProbABEL_manual.tex
@@ -1,17 +1,17 @@
\documentclass[12pt,a4paper]{article}
-\title{Manual for ProbABEL v0.4.3}
+\title{Manual for ProbABEL v0.4.5}
\author{\emph{Current Programmers:} Lennart Karssen$^{1,2}$, Maarten
Kooyman$^2$, \\
Yurii Aulchenko$^{1,3}$ \\
\emph{Former Programmers:} Maksim Struchalin
\\
\\
- $^{1}${\small YuriiA Consulting} \\
- $^{2}${\small Erasmus MC, Rotterdam}\\
+ $^{1}${\small PolyOmica, Groningen, The Netherlands} \\
+ $^{2}${\small Erasmus MC, Rotterdam, The Netherlands}\\
$^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
}
-\date{April 1, 2014}
+\date{May 26, 2015}
\usepackage[utf8]{inputenc}
@@ -223,22 +223,22 @@ of the EIGEN library\footnote{EIGEN is a library for fast matrix
it will speed up your analyses considerably. Moreover, we plan to
remove the non-EIGEN part of the code in a future release. So, go to
\url{http://eigen.tuxfamily.org} and download the \texttt{tar.gz} file
-of the latest version of EIGEN (3.2.1 at the time of writing). Extract
+of the latest version of EIGEN (3.2.4 at the time of writing). Extract
the files:
\begin{lstlisting}
-user at server:~$ tar -xzf 3.2.1.tar.gz
+user at server:~$ tar -xzf 3.2.4.tar.gz
\end{lstlisting}
This will create a directory called \texttt{eigen-eigen} followed by a
series of letters and digits. For simplicity we rename it to EIGEN
\begin{lstlisting}
-user at server:~$ mv eigen-eigen-6b38706d90a9 EIGEN
+user at server:~$ mv eigen-eigen-10219c95fe65 EIGEN
\end{lstlisting}
Now it's time to extract the \PA{} source code and move into the
directory that is created:
\begin{lstlisting}
-user at server:~$ tar -xzf probabel-0.4.3.tar.gz
-user at server:~$ cd probabel-0.4.3
+user at server:~$ tar -xzf probabel-0.4.5.tar.gz
+user at server:~$ cd probabel-0.4.5
\end{lstlisting}
With the following command we will indicate where the EIGEN files can
be found and where we want to install \PA{}. Let's install in a
@@ -306,12 +306,13 @@ metrics (``Quality'', the average maximum posterior probability and
Actually, for \PA{}, it (almost) does not matter what is written in
this file -- this information is simply copied to the output. However,
\textbf{it is critical} that the number of columns is
-seven\footnote{This means that for \texttt{minimac} output files the number of
- columns needs to be reduced. This can be done using e.g.~GAWK or
- \texttt{cut}.} and the number of lines in the file is equal to the
-number of SNPs in the corresponding DOSE file (plus one for the header
-line). Also make sure that the ``Rsq'' column contains values $>0$,
-otherwise you will end up with $\beta$'s set to \texttt{nan}.
+seven\footnote{This means that for \texttt{minimac} output files the
+ number of columns needs to be reduced. This can be done using
+ e.g.~GAWK or \texttt{cut}.} and the number of lines in the file is
+equal to the number of SNPs in the corresponding DOSE file (plus one
+for the header line). Also make sure that the ``Rsq'' column contains
+values $>1 \cdot 10^{-16}$, otherwise you will end up with $\beta$'s
+set to \texttt{nan}.
The example of SNP information file content follows here (also
to be found in \texttt{ProbABEL/examples/test.mlinfo})
@@ -463,7 +464,7 @@ you run either program with the \texttt{--help} option, you will get a
short explanation to the command line options:
\begin{verbatim}
user at server:~$ palogist --help
-probabel v. 0.4.3
+probabel v. 0.4.5
(C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
Using EIGEN version 3.1.2 for matrix operations
@@ -877,20 +878,20 @@ developed in the works of Aulchenko \emph{et al}. (2007) and Chen and
Abecasis (2007). The general analysis model is a linear mixed model
where the expectation of the trait is defined as
$$
-E[\mathbf{Y}] = \mathbf{X} \mathbf{\beta},
+E[\mathbf{Y}] = \mathbf{X} \boldsymbol{\beta},
$$
identical to that defined for a linear model
(cf.~Eq.~\ref{eq:expectation}). To account for correlations between
the phenotypes of relatives which may be induced by family relations
the variance-covariance matrix is defined to be proportional to the
linear combination of the identity matrix $\mathbf{I}$ and the
-relationship matrix $\mathbf{\Phi}$:
+relationship matrix $\boldsymbol{\Phi}$:
$$
-\mathbf{V}_{\sigma^2,h^2} = \sigma^2 \left( 2 h^2 \mathbf{\Phi} + (1-h^2)
+\mathbf{V}_{\sigma^2,h^2} = \sigma^2 \left( 2 h^2 \boldsymbol{\Phi} + (1-h^2)
\mathbf{I} \right),
$$
where $h^2$ is the heritability of the trait. The relationship matrix
-$\mathbf{\Phi}$ is twice the matrix containing the coefficients of
+$\boldsymbol{\Phi}$ is twice the matrix containing the coefficients of
kinship between all pairs of individuals under consideration; its
estimation is discussed separately in section \ref{kinship}.
@@ -909,19 +910,19 @@ $\mathbf{X}_x$, which includes all terms not changing across all SNP
models fit in GWAS (e.g.\ effects of sex, age, etc.), and the part
including SNP information, $\mathbf{X_g}$:
$$
-E[\mathbf{Y}] = \mathbf{X}_x \mathbf{\beta}_x +
-\mathbf{X}_g \mathbf{\beta}_g.
+E[\mathbf{Y}] = \mathbf{X}_x \boldsymbol{\beta}_x +
+\mathbf{X}_g \boldsymbol{\beta}_g.
$$
Note that the latter design matrix may include not only the main SNP
effect, but e.g.\ SNP by environment interaction terms.
In the first step, a linear mixed model not including SNP effects
$$
-E[\mathbf{Y}] = \mathbf{X}_x \mathbf{\beta}_x
+E[\mathbf{Y}] = \mathbf{X}_x \boldsymbol{\beta}_x
$$
is fitted. The maximum likelihood estimates (MLEs) of the model
parameters (regression coefficients for the fixed effects
-$\hat{\mathbf{\beta}}_x$, the residual variance $\hat{\sigma}^2_x$ and
+$\hat{\boldsymbol{\beta}}_x$, the residual variance $\hat{\sigma}^2_x$ and
the heritability $\hat{h}^2_x$) can be obtained by numerical
maximization of the likelihood function
$$
@@ -977,7 +978,7 @@ asymptotically follows $\chi^2_1$.
\subsubsection{Estimation of the kinship matrix}
\label{kinship}
-The relationship matrix $\mathbf{\Phi}$ used in estimation of the
+The relationship matrix $\boldsymbol{\Phi}$ used in estimation of the
linear mixed model for pedigree data is twice the matrix containing
the coefficients of kinship between all pairs of individuals under consideration.
This coefficient is defined as the probability that two gametes randomly sampled
@@ -1028,7 +1029,7 @@ BMC Bioinformatics. 2010, 11:134.
\end{quote}
A proper reference may look like
\begin{quote}
-For the analysis of imputed data, we used \PA{} v.0.4.3
+For the analysis of imputed data, we used \PA{} v.0.4.5
from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
\end{quote}
@@ -1073,3 +1074,8 @@ as implemented by T. Lumley.
\printindex
\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
diff --git a/doc/pacoxph.1 b/doc/pacoxph.1
index 4fe3121..ce87781 100644
--- a/doc/pacoxph.1
+++ b/doc/pacoxph.1
@@ -1,6 +1,7 @@
-.TH pacoxph 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH pacoxph 1 "26 May 2015" "ProbABEL 0.4.5"
.SH NAME
-pacoxph \- Perform Genome-Wide Association Analysis using a linear model
+pacoxph \- Perform Genome-Wide Association Analysis using Cox' Proportional
+hazards model
.SH SYNOPSIS
.B pacoxph
.RI "[ " "command-line options" " ]"
diff --git a/doc/palinear.1 b/doc/palinear.1
index ecdf295..3105ece 100644
--- a/doc/palinear.1
+++ b/doc/palinear.1
@@ -1,4 +1,4 @@
-.TH palinear 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH palinear 1 "26 May 2015" "ProbABEL 0.4.5"
.SH NAME
palinear \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/palogist.1 b/doc/palogist.1
index e950026..867ae27 100644
--- a/doc/palogist.1
+++ b/doc/palogist.1
@@ -1,6 +1,6 @@
-.TH palogist 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH palogist 1 "26 May 2015" "ProbABEL 0.4.5"
.SH NAME
-palogist \- Perform Genome-Wide Association Analysis using a linear model
+palogist \- Perform Genome-Wide Association Analysis using a logistic model
.SH SYNOPSIS
.B palogist
.RI "[ " "command-line options" " ]"
diff --git a/doc/probabel.1 b/doc/probabel.1
index bd37640..4c2d77d 100644
--- a/doc/probabel.1
+++ b/doc/probabel.1
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH ProbABEL 1 "26 May 2015" "ProbABEL 0.4.5"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
diff --git a/doc/probabel.pl.1 b/doc/probabel.pl.1
index bd37640..4c2d77d 100644
--- a/doc/probabel.pl.1
+++ b/doc/probabel.pl.1
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
+.TH ProbABEL 1 "26 May 2015" "ProbABEL 0.4.5"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
diff --git a/examples/Makefile.in b/examples/Makefile.in
index 4d6d1bf..2c12be8 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
diff --git a/src/Makefile.am b/src/Makefile.am
index 2d1ceaf..f239de3 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -52,29 +52,27 @@ endif
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS)
-palinear_CPPFLAGS = $(AM_CPPFLAGS)
+palinear_CPPFLAGS = -DLINEAR $(AM_CPPFLAGS)
if WITH_EIGEN
palinear_SOURCES += $(EIGENFILES)
-palinear_CXXFLAGS += -DEIGEN
+palinear_CPPFLAGS += -DEIGEN
endif
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS)
-palogist_CPPFLAGS = $(AM_CPPFLAGS)
+palogist_CPPFLAGS = -DLOGISTIC $(AM_CPPFLAGS)
if WITH_EIGEN
palogist_SOURCES += $(EIGENFILES)
-palogist_CXXFLAGS += -DEIGEN
+palogist_CPPFLAGS += -DEIGEN
endif
pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS) \
$(RHEADERS) survS.h survproto.h coxph_data.h coxph_data.cpp
-pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
-pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
-pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
+pacoxph_CXXFLAGS = -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
+pacoxph_CPPFLAGS = -DCOXPH $(AM_CPPFLAGS)
+pacoxph_CFLAGS = -I $(top_srcdir)/src/include $(AM_CFLAGS)
if WITH_EIGEN
pacoxph_SOURCES += $(EIGENFILES)
-pacoxph_CXXFLAGS += -DEIGEN
+pacoxph_CPPFLAGS += -DEIGEN
endif
extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
@@ -92,10 +90,10 @@ dist_sysconf_DATA = probabel_config.cfg.example
## Insert the correct values of several variables in the installed
## probabel script
install-exec-hook:
- $(SED) -i "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
+ $(SED) -i -e "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
$(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
ln -s $(DESTDIR)$(bindir)/probabel $(DESTDIR)$(bindir)/probabel.pl
## Make the script executable
diff --git a/src/Makefile.in b/src/Makefile.in
index 7093c49..0115de9 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -1,4 +1,4 @@
-# Makefile.in generated by automake 1.13.3 from Makefile.am.
+# Makefile.in generated by automake 1.14.1 from Makefile.am.
# @configure_input@
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
@@ -215,8 +215,6 @@ am_palinear_OBJECTS = $(am__objects_9) $(am__objects_10) \
$(am__objects_2) $(am__objects_12)
palinear_OBJECTS = $(am_palinear_OBJECTS)
palinear_LDADD = $(LDADD)
-palinear_LINK = $(CXXLD) $(palinear_CXXFLAGS) $(CXXFLAGS) \
- $(AM_LDFLAGS) $(LDFLAGS) -o $@
am__palogist_SOURCES_DIST = data.h data.cpp gendata.h gendata.cpp \
mematrix.h mematri1.h command_line_settings.h \
command_line_settings.cpp reg1.h usage.h usage.cpp main.cpp \
@@ -256,8 +254,6 @@ am_palogist_OBJECTS = $(am__objects_13) $(am__objects_14) \
$(am__objects_2) $(am__objects_16)
palogist_OBJECTS = $(am_palogist_OBJECTS)
palogist_LDADD = $(LDADD)
-palogist_LINK = $(CXXLD) $(palogist_CXXFLAGS) $(CXXFLAGS) \
- $(AM_LDFLAGS) $(LDFLAGS) -o $@
am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
am__vpath_adj = case $$p in \
$(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
@@ -487,18 +483,15 @@ RHEADERS = include/R.h include/Rmath.h include/R_ext/Arith.h \
@BUILD_pacoxph_TRUE at COXBASE = coxfit2 chinv2 cholesky2 chsolve2 dmatrix
@BUILD_pacoxph_TRUE at COXSRC = $(COXBASE:=.c)
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(am__append_5)
-palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS) $(am__append_6)
-palinear_CPPFLAGS = $(AM_CPPFLAGS)
+palinear_CPPFLAGS = -DLINEAR $(AM_CPPFLAGS) $(am__append_6)
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(am__append_7)
-palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS) $(am__append_8)
-palogist_CPPFLAGS = $(AM_CPPFLAGS)
+palogist_CPPFLAGS = -DLOGISTIC $(AM_CPPFLAGS) $(am__append_8)
pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS) \
$(RHEADERS) survS.h survproto.h coxph_data.h coxph_data.cpp \
$(am__append_9)
-pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS) \
- $(am__append_10)
-pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
-pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
+pacoxph_CXXFLAGS = -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
+pacoxph_CPPFLAGS = -DCOXPH $(AM_CPPFLAGS) $(am__append_10)
+pacoxph_CFLAGS = -I $(top_srcdir)/src/include $(AM_CFLAGS)
extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
dist_bin_SCRIPTS = probabel
scriptdir = $(pkgdatadir)/scripts
@@ -518,9 +511,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --gnu src/Makefile
+ $(AUTOMAKE) --foreign src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -541,8 +534,8 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
- @if test ! -f $@; then rm -f stamp-h1; else :; fi
- @if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
+ @test -f $@ || rm -f stamp-h1
+ @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
@@ -673,7 +666,7 @@ fvlib/palinear-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
palinear$(EXEEXT): $(palinear_OBJECTS) $(palinear_DEPENDENCIES) $(EXTRA_palinear_DEPENDENCIES)
@rm -f palinear$(EXEEXT)
- $(AM_V_CXXLD)$(palinear_LINK) $(palinear_OBJECTS) $(palinear_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(palinear_OBJECTS) $(palinear_LDADD) $(LIBS)
fvlib/palogist-AbstractMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
fvlib/$(DEPDIR)/$(am__dirstamp)
fvlib/palogist-CastUtils.$(OBJEXT): fvlib/$(am__dirstamp) \
@@ -697,7 +690,7 @@ fvlib/palogist-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
palogist$(EXEEXT): $(palogist_OBJECTS) $(palogist_DEPENDENCIES) $(EXTRA_palogist_DEPENDENCIES)
@rm -f palogist$(EXEEXT)
- $(AM_V_CXXLD)$(palogist_LINK) $(palogist_OBJECTS) $(palogist_LDADD) $(LIBS)
+ $(AM_V_CXXLD)$(CXXLINK) $(palogist_OBJECTS) $(palogist_LDADD) $(LIBS)
install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
@$(NORMAL_INSTALL)
@list='$(dist_bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
@@ -1267,648 +1260,648 @@ pacoxph-eigen_mematrix.obj: eigen_mematrix.cpp
@am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(pacoxph_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CXXFLAGS) $(CXXFLAGS) -c -o pacoxph-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
palinear-data.o: data.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.o -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.o -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-data.Tpo $(DEPDIR)/palinear-data.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='data.cpp' object='palinear-data.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.o `test -f 'data.cpp' || echo '$(srcdir)/'`data.cpp
palinear-data.obj: data.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.obj -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-data.obj -MD -MP -MF $(DEPDIR)/palinear-data.Tpo -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-data.Tpo $(DEPDIR)/palinear-data.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='data.cpp' object='palinear-data.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-data.obj `if test -f 'data.cpp'; then $(CYGPATH_W) 'data.cpp'; else $(CYGPATH_W) '$(srcdir)/data.cpp'; fi`
palinear-gendata.o: gendata.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.o -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.o -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-gendata.Tpo $(DEPDIR)/palinear-gendata.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='gendata.cpp' object='palinear-gendata.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.o `test -f 'gendata.cpp' || echo '$(srcdir)/'`gendata.cpp
palinear-gendata.obj: gendata.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.obj -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-gendata.obj -MD -MP -MF $(DEPDIR)/palinear-gendata.Tpo -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-gendata.Tpo $(DEPDIR)/palinear-gendata.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='gendata.cpp' object='palinear-gendata.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palinear-gendata.obj `if test -f 'gendata.cpp'; then $(CYGPATH_W) 'gendata.cpp'; else $(CYGPATH_W) '$(srcdir)/gendata.cpp'; fi`
palinear-command_line_settings.o: command_line_settings.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-command_line_settings.o -MD -MP -MF $(DEPDIR)/palinear-command_line_settings.Tpo -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palinear-command_line_settings.o -MD -MP -MF $(DEPDIR)/palinear-command_line_settings.Tpo -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palinear-command_line_settings.Tpo $(DEPDIR)/palinear-command_line_settings.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='command_line_settings.cpp' object='palinear-command_line_settings.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-command_line_settings.o `test -f 'command_line_settings.cpp' || echo '$(srcdir)/'`command_line_settings.cpp
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palinear-command_line_settings.obj: command_line_settings.cpp
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fvlib/palinear-FileVector.o: fvlib/FileVector.cpp
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fvlib/palinear-FilteredMatrix.o: fvlib/FilteredMatrix.cpp
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fvlib/palinear-frutil.o: fvlib/frutil.cpp
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fvlib/palinear-Logger.o: fvlib/Logger.cpp
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- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Logger.obj `if test -f 'fvlib/Logger.cpp'; then $(CYGPATH_W) 'fvlib/Logger.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Logger.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Logger.obj `if test -f 'fvlib/Logger.cpp'; then $(CYGPATH_W) 'fvlib/Logger.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Logger.cpp'; fi`
fvlib/palogist-RealHandlerWrapper.o: fvlib/RealHandlerWrapper.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-RealHandlerWrapper.o -MD -MP -MF fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Tpo -c -o fvlib/palogist-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo '$(srcdir)/'`fvlib/RealHandlerWrapper.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-RealHandlerWrapper.o -MD -MP -MF fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Tpo -c -o fvlib/palogist-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo '$(srcdir)/'`fvlib/RealHandlerWrapper.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Tpo fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-RealHandlerWrapper.o `test -f 'fvlib/RealHandlerWrapper.cpp' || echo '$(srcdir)/'`fvlib/RealHandlerWrapper.cpp
fvlib/palogist-RealHandlerWrapper.obj: fvlib/RealHandlerWrapper.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-RealHandlerWrapper.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Tpo -c -o fvlib/palogist-RealHandlerWrapper.obj `if test -f 'fvlib/RealHandlerWrapper.cpp'; then $(CYGPATH_W) 'fvlib/RealHandlerWrapper.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/RealHandlerWrapper.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-RealHandlerWrapper.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Tpo -c -o fvlib/palogist-RealHandlerWrapper.obj `if test -f 'fvlib/RealHandlerWrapper.cpp'; then $(CYGPATH_W) 'fvlib/RealHandlerWrapper.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/RealHandlerWrapper.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Tpo fvlib/$(DEPDIR)/palogist-RealHandlerWrapper.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-RealHandlerWrapper.obj `if test -f 'fvlib/RealHandlerWrapper.cpp'; then $(CYGPATH_W) 'fvlib/RealHandlerWrapper.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/RealHandlerWrapper.cpp'; fi`
fvlib/palogist-ReusableFileHandle.o: fvlib/ReusableFileHandle.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-ReusableFileHandle.o -MD -MP -MF fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Tpo -c -o fvlib/palogist-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo '$(srcdir)/'`fvlib/ReusableFileHandle.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-ReusableFileHandle.o -MD -MP -MF fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Tpo -c -o fvlib/palogist-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo '$(srcdir)/'`fvlib/ReusableFileHandle.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Tpo fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-ReusableFileHandle.o `test -f 'fvlib/ReusableFileHandle.cpp' || echo '$(srcdir)/'`fvlib/ReusableFileHandle.cpp
fvlib/palogist-ReusableFileHandle.obj: fvlib/ReusableFileHandle.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-ReusableFileHandle.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Tpo -c -o fvlib/palogist-ReusableFileHandle.obj `if test -f 'fvlib/ReusableFileHandle.cpp'; then $(CYGPATH_W) 'fvlib/ReusableFileHandle.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/ReusableFileHandle.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-ReusableFileHandle.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Tpo -c -o fvlib/palogist-ReusableFileHandle.obj `if test -f 'fvlib/ReusableFileHandle.cpp'; then $(CYGPATH_W) 'fvlib/ReusableFileHandle.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/ReusableFileHandle.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Tpo fvlib/$(DEPDIR)/palogist-ReusableFileHandle.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-ReusableFileHandle.obj `if test -f 'fvlib/ReusableFileHandle.cpp'; then $(CYGPATH_W) 'fvlib/ReusableFileHandle.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/ReusableFileHandle.cpp'; fi`
fvlib/palogist-Transposer.o: fvlib/Transposer.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.o -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo '$(srcdir)/'`fvlib/Transposer.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.o -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo '$(srcdir)/'`fvlib/Transposer.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-Transposer.Tpo fvlib/$(DEPDIR)/palogist-Transposer.Po
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+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo '$(srcdir)/'`fvlib/Transposer.cpp
fvlib/palogist-Transposer.obj: fvlib/Transposer.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-Transposer.Tpo fvlib/$(DEPDIR)/palogist-Transposer.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='fvlib/Transposer.cpp' object='fvlib/palogist-Transposer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
palogist-eigen_mematrix.o: eigen_mematrix.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.o -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.o -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palogist-eigen_mematrix.Tpo $(DEPDIR)/palogist-eigen_mematrix.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='eigen_mematrix.cpp' object='palogist-eigen_mematrix.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
palogist-eigen_mematrix.obj: eigen_mematrix.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.obj -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.obj -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
@am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palogist-eigen_mematrix.Tpo $(DEPDIR)/palogist-eigen_mematrix.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='eigen_mematrix.cpp' object='palogist-eigen_mematrix.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o palogist-eigen_mematrix.obj `if test -f 'eigen_mematrix.cpp'; then $(CYGPATH_W) 'eigen_mematrix.cpp'; else $(CYGPATH_W) '$(srcdir)/eigen_mematrix.cpp'; fi`
install-dist_scriptDATA: $(dist_script_DATA)
@$(NORMAL_INSTALL)
@list='$(dist_script_DATA)'; test -n "$(scriptdir)" || list=; \
@@ -2167,10 +2160,10 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
install-exec-hook:
- $(SED) -i "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
+ $(SED) -i -e "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
$(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
- $(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel
+ $(SED) -i -e "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel
ln -s $(DESTDIR)$(bindir)/probabel $(DESTDIR)$(bindir)/probabel.pl
install-data-hook:
diff --git a/src/command_line_settings.cpp b/src/command_line_settings.cpp
index 34a4103..876c0b3 100644
--- a/src/command_line_settings.cpp
+++ b/src/command_line_settings.cpp
@@ -155,7 +155,7 @@ char* cmdvars::getPhefilename() const
void cmdvars::set_variables(int argc, char * argv[])
{
int next_option;
- const char * const short_options = "p:i:d:m:n:c:o:s:t:g:a:erlhb:vu";
+ const char * const short_options = "p:i:d:m:n:c:o:s:t:g:a:relhb:k:v:u";
// b - interaction parameter
// ADD --fv FLAG (FILEVECTOR), IN WHICH CASE USE ALTERNATIVE
// CONSTRUCTOR FOR GENDATA
diff --git a/src/config.h.in b/src/config.h.in
index 4fc07a4..bcd1c0d 100644
--- a/src/config.h.in
+++ b/src/config.h.in
@@ -96,9 +96,6 @@
/* Define to 1 if the system has the type `_Bool'. */
#undef HAVE__BOOL
-/* Define to 1 if your C compiler doesn't accept -c and -o together. */
-#undef NO_MINUS_C_MINUS_O
-
/* Name of package */
#undef PACKAGE
diff --git a/src/coxph_data.cpp b/src/coxph_data.cpp
index 0d0495d..8518c98 100644
--- a/src/coxph_data.cpp
+++ b/src/coxph_data.cpp
@@ -5,7 +5,7 @@
* Author: mkooyman
*
*
- * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * Copyright (C) 2009--2015 Various members of the GenABEL team. See
* the SVN commit logs for more details.
*
* This program is free software; you can redistribute it and/or
@@ -116,16 +116,16 @@ coxph_data::coxph_data(phedata &phed, gendata &gend, const int snpnum)
exit(1);
}
- X.reinit(nids, ncov);
+ X.reinit(nids, (ncov + 1));
stime.reinit(nids, 1);
sstat.reinit(nids, 1);
weights.reinit(nids, 1);
offset.reinit(nids, 1);
strata.reinit(nids, 1);
order.reinit(nids, 1);
+
for (int i = 0; i < nids; i++)
{
- // X.put(1.,i,0);
stime[i] = (phed.Y).get(i, 0);
sstat[i] = static_cast<int>((phed.Y).get(i, 1));
if (sstat[i] != 1 && sstat[i] != 0)
@@ -137,12 +137,21 @@ coxph_data::coxph_data(phedata &phed, gendata &gend, const int snpnum)
}
}
- for (int j = 0; j < phed.ncov; j++)
+ // Add a column with a constant (=1) to the X matrix (the mean)
+ for (int i = 0; i < nids; i++)
+ {
+ X.put(1., i, 0);
+ }
+
+ for (int j = 1; j <= phed.ncov; j++)
{
for (int i = 0; i < nids; i++)
- X.put((phed.X).get(i, j), i, j);
+ {
+ X.put((phed.X).get(i, j - 1), i, j);
+ }
}
+
if (snpnum > 0)
{
for (int j = 0; j < ngpreds; j++)
@@ -246,7 +255,7 @@ void coxph_data::update_snp(gendata *gend, const int snpnum) {
gend->get_var(snpnum * ngpreds + j, snpdata);
for (int i = 0; i < nids; i++) {
- X.put(snpdata[i], (ncov - j - 1), order[i]);
+ X.put(snpdata[i], (ncov - j), order[i]);
if (std::isnan(snpdata[i])) {
masked_data[order[i]] = 1;
// snp not masked
@@ -398,8 +407,6 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
(cdata.offset).column_mean(0);
mematrix<double> means(X.nrow, 1);
- int maxiterinput = maxiter;
-
for (int i = 0; i < X.nrow; i++)
{
beta[i] = 0.;
@@ -418,6 +425,10 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
// R's coxph()
double sctest = 1.0;
+ // Set the maximum number of iterations that coxfit2() will run to
+ // the default value from the class definition.
+ int maxiterinput = maxiter;
+
// When using Eigen coxfit2 needs to be called in a slightly
// different way (i.e. the .data()-part needs to be added).
#if EIGEN
@@ -438,22 +449,50 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
niter = maxiter;
+
// Check the results of the Cox fit; mirrored from the same checks
- // in coxph_fit.S from the R survival package
+ // in coxph.fit.S and coxph.R from the R survival package.
- bool setToZero = false;
+ bool setToNAN = false;
- if (flag < X.nrow && maxiter > 0) {
- cerr << "Warning for " << snpinfo.name[cursnp]
- << ": X matrix deemed to be singular,"
- << " setting beta and se to 'nan'\n";
- setToZero = true;
+ // Based on coxph.fit.S lines with 'which.sing' and coxph.R line
+ // with if(any(is.NA(coefficients))). These lines set coefficients
+ // to NA if flag < nvar (with nvar = ncol(x)) and maxiter >
+ // 0. coxph.R then checks for any NAs in the coefficients and
+ // outputs the warning message if NAs were found.
+
+ if (flag < X.nrow)
+ {
+#if EIGEN
+ int which_sing = 0;
+ MatrixXd imateigen = imat.data;
+ VectorXd imatdiag = imateigen.diagonal();
+
+ // Start at i=1 to exclude the beta coefficient for the
+ // (constant) mean from the check.
+ for (int i=1; i < imatdiag.size(); i++)
+ {
+ if (imatdiag[i] == 0)
+ {
+ which_sing = i;
+ setToNAN = true;
+ std::cerr << "Warning for " << snpinfo.name[cursnp]
+ << ": X matrix deemed to be singular (variable "
+ << which_sing + 1 << ")" << std::endl;
+ }
+ }
+#else
+ std::cerr << "Warning for " << snpinfo.name[cursnp]
+ << ": can't check for singular X matrix."
+ << " Please compile ProbABEL with Eigen support to fix this."
+ << std::endl;
+#endif
}
if (niter >= maxiterinput)
{
cerr << "Warning for " << snpinfo.name[cursnp]
- << ": nr of iterations > MAXITER (" << maxiterinput << "): "
+ << ": nr of iterations >= MAXITER (" << maxiterinput << "): "
<< niter << endl;
}
@@ -461,22 +500,35 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
{
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": Cox regression ran out of iterations and did not converge,"
- << " setting beta and se to 'nan'\n";
- setToZero = true;
+ << " setting beta and se to 'NaN'\n";
+ setToNAN = true;
} else {
#if EIGEN
VectorXd ueigen = u.data;
MatrixXd imateigen = imat.data;
VectorXd infs = ueigen.transpose() * imateigen;
+ infs = infs.cwiseAbs();
VectorXd betaeigen = beta.data;
- if ( infs.norm() > eps ||
- infs.norm() > sqrt(eps) * betaeigen.norm() )
- {
+ bool problems = false;
+
+ assert(betaeigen.size() == infs.size());
+
+ // We check the beta's for all coefficients
+ // (incl. covariates), maybe stick to only checking the SNP
+ // coefficient?
+ for (int i = 0; i < infs.size(); i++) {
+ if (infs[i] > eps &&
+ infs[i] > sqrt(eps) * abs(betaeigen[i])) {
+ problems = true;
+ }
+ }
+
+ if (problems) {
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": beta may be infinite,"
- << " setting beta and se to 'nan'\n";
+ << " setting beta and se to 'NaN'\n";
- setToZero = true;
+ setToNAN = true;
}
#else
cerr << "Warning for " << snpinfo.name[cursnp]
@@ -488,7 +540,7 @@ void coxph_reg::estimate(coxph_data &cdatain, const int verbose,
for (int i = 0; i < X.nrow; i++)
{
- if (setToZero)
+ if (setToNAN)
{
// Cox regression failed
sebeta[i] = NAN;
diff --git a/src/fvlib/CastUtils.h b/src/fvlib/CastUtils.h
index 751f2a0..b109f4d 100644
--- a/src/fvlib/CastUtils.h
+++ b/src/fvlib/CastUtils.h
@@ -1,6 +1,9 @@
#ifndef __CastUtils__
#define __CastUtils__
+#include "const.h"
+
+
// these copy-pastes are for template support
void setNan(unsigned short int &i);
void setNan(short int &i);
diff --git a/src/main.cpp b/src/main.cpp
index 5543c90..71b1729 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -83,7 +83,7 @@
/// Maximum number of iterations we allow the regression to run
#define MAXITER 20
/// Tolerance for convergence
-#define EPS 1.e-8
+#define EPS 1.e-9
/// Precision for the Cholesky decomposition
#define CHOLTOL 1.5e-12
diff --git a/src/phedata.cpp b/src/phedata.cpp
index 9f7426b..c3f53de 100644
--- a/src/phedata.cpp
+++ b/src/phedata.cpp
@@ -135,17 +135,14 @@ void phedata::setphedata(char * fname, int noutc, int npeople, int interaction,
model = model + tmp;
}
n_model_terms = 0;
-#if COXPH
- model = model + " ) ~ ";
-#else
- model = model + " ) ~ mu + ";
+
+ model = model + " ) ~ mu";
model_terms[n_model_terms++] = "mu";
-#endif
if (nphenocols > noutcomes + 1)
{
infile >> tmp;
- model = model + tmp;
+ model = model + " + " + tmp;
model_terms[n_model_terms++] = tmp;
for (int i = (2 + noutcomes); i < nphenocols; i++)
{
--
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