Just added some print statements to debug an issue with LMM code

Also added some to notes

3 files changed, 6 insertions, 1 deletions

diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index 91fe1781..6329586f 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -320,4 +320,9 @@ Run web server:
 Run server:
 python runserver.py
 
+===========================================
+
+To do full upgrade (as opposed to apt-get upgrade)
+sudo aptitude full-upgrade
+
 ===========================================
\ No newline at end of file
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 188a94a2..ffc77299 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -400,7 +400,6 @@ class DataSet(object):
     #    return self._group
 
 
-
     def retrieve_other_names(self):
         """
         If the data set name parameter is not found in the 'Name' field of the data set table,
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 446683a4..bca90486 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -462,6 +462,7 @@ class LMM:
        x = True - np.isnan(Y)
        #pdb.set_trace()
        if not x.sum() == len(Y):
+          print("Removing %d missing values from Y\n" % ((True - x).sum()))
           if self.verbose: sys.stderr.write("Removing %d missing values from Y\n" % ((True - x).sum()))
           Y = Y[x]
           K = K[x,:][:,x]