[Genabel-commits] r847 - in pkg/ProbABEL: . doc src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2012-03-04 21:31:40 +0100 (Sun, 04 Mar 2012)
New Revision: 847

Modified:
   pkg/ProbABEL/configure.ac
   pkg/ProbABEL/doc/CHANGES.LOG
   pkg/ProbABEL/doc/packaging.txt
   pkg/ProbABEL/src/Makefile.am
Log:
- Changed configure.ac and src/Makefile.am in ProbABEL so that pacoxph won't get built by default. I consider it too buggy to release. Use ./configure --enable-pacoxph to build it anyway. 
- Updated CHANGES.LOG to represent this change. 
- Minor update to doc/packaging.txt



Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac	2012-02-22 10:01:52 UTC (rev 846)
+++ pkg/ProbABEL/configure.ac	2012-03-04 20:31:40 UTC (rev 847)
@@ -44,12 +44,23 @@
 # Check for presence of pdfLaTeX
 AC_CHECK_PROG(PDFLATEX, pdflatex, pdflatex)
 if test -z "$PDFLATEX"; then
-  AC_MSG_WARN([Unable to create PDF version of the user manual.])
+  AC_MSG_WARN([Unable to create PDF version of the user manual])
 fi
 
 AM_CONDITIONAL([HAVE_PDFLATEX], test -n "$PDFLATEX")
 
+# Since pacoxph is buggy it needs to be enabled explixitly
+AC_ARG_ENABLE([pacoxph],
+ [  --enable-pacoxph    build the pacoxph binary (still contains lots of bugs)],
+ [pacoxph=${enableval}],
+ [pacoxph=no])
 
+if test "x$pacoxph" = "xyes"; then
+   AC_MSG_NOTICE([building of pacoxph is enabled])
+fi
+
+AM_CONDITIONAL([BUILD_pacoxph], test "x$pacoxph" = "xyes")
+
 # Files to be generated by autotools
 AC_CONFIG_FILES([
 	Makefile

Modified: pkg/ProbABEL/doc/CHANGES.LOG
===================================================================
--- pkg/ProbABEL/doc/CHANGES.LOG	2012-02-22 10:01:52 UTC (rev 846)
+++ pkg/ProbABEL/doc/CHANGES.LOG	2012-03-04 20:31:40 UTC (rev 847)
@@ -1,13 +1,16 @@
-***** v.0.2-0 (2011.08.23)
+***** v.0.2-0 (2012.03.04)
 
+* pacoxph will not be built by default, because it is quite buggy. See
+  ./configure notes below on how to enable building it anyway.
+
+
 * ProbABEL can now (experimentally!) analyze binary traits accounting
 for relationship structure (thanks to Yurii and Nicola Pirastu). This
-adds '--mmscore' option for logistic regression. Important: on the
-contrast to the 'palinear' the matrix which should be supplied to
-palogist with --mmscore should contain an inverse of the correlation
-matrix (not the inverse of var-cov matrix, as is the case for
-'palinear' with --mmscore). This matrix can be obtained through
-(GenABEL notation):
+adds '--mmscore' option for logistic regression. Important: compared
+to 'palinear' the matrix which should be supplied to palogist with
+--mmscore should contain an inverse of the correlation matrix (not the
+inverse of var-cov matrix, as is the case for 'palinear' with
+--mmscore). This matrix can be obtained through (GenABEL notation):
 
 h2.object$InvSigma * h2.object$h2an$estimate[length(h2.object$h2an$estimate)]
 
@@ -15,6 +18,7 @@
 explains this procedure in more details; a wrapper function to prepare
 and export correct objects for ProbABEL is planned. (thanks to Yurii)
 
+* Small changes (thanks to Lennart).
 - in probabel.pl the location for the probabel config file is now set
   to /etc/, the default location it will end up. Before it still
   pointed to the location the probabel.pl file was in. However, a
@@ -61,6 +65,10 @@
   to install ProbABEL in that subdirectory. Instead of using
   /usr/local/ as install root, it installs in /some/subdirectory.
 
+  The second important option is
+./configure --enable-pacoxph
+  this enables the building of the pacoxph binary.
+
   To generate a .tar.gz package for distribution run:
 ./configure
 make dist

Modified: pkg/ProbABEL/doc/packaging.txt
===================================================================
--- pkg/ProbABEL/doc/packaging.txt	2012-02-22 10:01:52 UTC (rev 846)
+++ pkg/ProbABEL/doc/packaging.txt	2012-03-04 20:31:40 UTC (rev 847)
@@ -8,7 +8,7 @@
    - dh-make
    - fakeroot
    - lintian
-** Building the package
+** Building the package for the first time
    First check to see if everything compiles and all files are included
    in the automake files:
     ./configure
@@ -28,7 +28,7 @@
      --packagename probabel
 
    Hit the enter key to confirm the settings. Several files need to be
-   edited (or at least checked to see if they are still up to date).
+   edited.
    - debian/control
    - debian/changelog
    - debian/copyright

Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am	2012-02-22 10:01:52 UTC (rev 846)
+++ pkg/ProbABEL/src/Makefile.am	2012-03-04 20:31:40 UTC (rev 847)
@@ -24,13 +24,15 @@
  include/R_ext/Print.h include/R_ext/Random.h include/R_ext/Utils.h	\
  include/R_ext/RS.h
 
+bin_PROGRAMS = palinear palogist
+if BUILD_pacoxph
 ## Extra files for pacoxph
 COXBASE = coxfit2 chinv2 cholesky2 chsolve2 dmatrix
 COXSRC = $(COXBASE:=.c)
 
+bin_PROGRAMS += pacoxph
+endif
 
-bin_PROGRAMS = palinear palogist pacoxph
-
 palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
 palinear_CXXFLAGS = -DLINEAR