From e57aded7c217486ad6e49e4e7781897736c796db Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 11:35:57 -0400
Subject: [PATCH 01/18] Add documentation for 'make setup'.

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index af181a5..e7c1a81 100644
--- a/README.md
+++ b/README.md
@@ -35,6 +35,7 @@ Benchmarks are run with the `make` command.
 * `make memory`     -- Get memory profiling information.
 * `make reports`    -- Create the reports.
 * `make test`       -- Test the configuration file. Check for correct syntax and then try to open files referred in the configuration file.
+* `make setup`      -- Download and set up all of the libraries to compare against.
 * `make scripts`    -- Make additional scripts.
 
 

From 6a1e7cce801801fc0926eb58a66456321e716b50 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:32:40 -0400
Subject: [PATCH 02/18] Use local installations of packages.

Also remove some unnecessary previous variables.
---
 Makefile | 71 ++++++++++++++++++--------------------------------------
 1 file changed, 22 insertions(+), 49 deletions(-)

diff --git a/Makefile b/Makefile
index 3a5ca13..ff7776f 100644
--- a/Makefile
+++ b/Makefile
@@ -1,3 +1,13 @@
+# These are the directories that contain everything we need after 'make setup'
+# is completed.  We assume that 'matlab' is available on the PATH.
+export INCLUDEPATH := $(shell pwd)/libraries/include/
+export LIBPATH := $(shell pwd)/libraries/lib/
+export BINPATH := $(shell pwd)/libraries/bin/
+export JAVAPATH := $(shell pwd)/libraries/share/
+export DEBUGBINPATH := $(shell pwd)/libraries/debug/bin/
+export DEBUGINCLUDEPATH := $(shell pwd)/libraries/debug/include/
+export DEBUGLIBPATH := $(shell pwd)/libraries/debug/lib/
+
 # Locate the python bin.
 PYTHON_BIN := $(shell which python3.3)
 ifndef PYTHON_BIN
@@ -38,52 +48,10 @@ COPY := False
 USER := ""
 PASSWORD := ""
 
-################################################################################################
-# How to use:                                                                                  #
-# Specify the environment variables in this file or set these variables from the command line. #
-# All environment path variables should end with a slash.                                      #
-# Note that four settings need to be changed for this to work.                                 #
-# 1) SHOGUN_PATH                                                                               #
-# 2) PYTHONPATH                                                                                #
-# 3) WEKA_CLASSPATH                                                                            #
-# 4) MATLAB_BIN                                                                                #
-################################################################################################
-
-# Set the environment variable for the mlpack executables.
-
-ifdef $(shell which mlpack_knn)
-	export MLPACK_BIN=$(shell dirname $(firstword $(shell which mlpack_knn)))/
-else
-	export MLPACK_BIN=""
-endif
-
-# Set the environment variable for the mlpack executables.
-export MLPACK_BIN_DEBUG=$(MLPACK_BIN)
-
-# Export the MLPACK_PATH environment variable.
-export MLPACK_PATH=$(shell dirname $(MLPACK_BIN))/
+# Set the environment variable for the compiled mlpack executables.
 export MLPACK_BIN_SRC=methods/mlpack/src/build/
 export MLPACK_BIN_DEBUG_SRC=methods/mlpack/src/build/
 
-# Set the environment variable for the matlab executable.
-# You can use the following command to search the 'matlab' file everytime:
-# export MATLAB_BIN=$(shell find / -name matlab  -print 2>/dev/null -quit)
-export MATLAB_BIN=""
-
-# Export the MATLABPATH environment variable.
-export MATLABPATH=$(shell pwd)/methods/matlab/
-
-# Export the WEKA_CLASSPATH environment variable.
-# You can use the following command to search the 'weka.jar' file everytime:
-# export WEKA_CLASSPATH=".:$(shell find / -name weka.jar  -print 2>/dev/null -quit)"
-export WEKA_CLASSPATH=".:/Users/marcus/Downloads/weka-3-6-11/weka.jar"
-
-# Export the SHOGUN_PATH environment variable.
-export SHOGUN_PATH=""
-
-# Export the PYTHONPATH environment variable.
-export PYTHONPATH=""
-
 # Set the environment variable for the the ms_print executable.
 export MS_PRINT_BIN=$(shell which ms_print)
 
@@ -92,12 +60,14 @@ export VALGRIND_BIN=$(shell which valgrind)
 
 # Export the path to the FLANN library.
 export FLANN_PATH=methods/flann/
-
 # Export the path to the ANN library.
 export ANN_PATH=methods/ann/
 
-# Export the path to the HLearn library.
-export HLEARN_PATH=""
+# Set LD_LIBRARY_PATH correctly.
+export LD_LIBRARY_PATH=$(shell echo $(LIBPATH))
+# Set PYTHONPATH correctly.
+PYVERSION=$(shell python3 -c 'import sys; print("python" + sys.version[0:3])')
+export PYTHONPATH=$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/dist-packages:$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/site-packages
 
 # Color settings.
 NO_COLOR=\033[0m
@@ -200,11 +170,14 @@ endif
 
 .scripts:
 	# Compile the java files for the weka methods.
-	javac -cp $(shell echo $(WEKA_CLASSPATH)) -d methods/weka methods/weka/src/*.java
+	javac -cp $(shell echo $(JAVAPATH)/weka.jar) -d methods/weka methods/weka/src/*.java
 	# Compile the ann scripts.
-	g++ -O0 -std=c++11 methods/ann/src/allknn.cpp -o methods/ann/allknn -I$(MLPACK_PATH)/include -I$(ANN_PATH)/include -L$(MLPACK_PATH)/lib -L$(ANN_PATH)/lib -lANN -lmlpack -lboost_program_options
+	g++ -O0 -std=c++11 methods/ann/src/allknn.cpp -o methods/ann/allknn -I$(INCLUDEPATH) -L$(LIBPATH) -lANN -lmlpack -lboost_program_options
 	# Compile the FLANN scripts.
-	g++ -O0 -std=c++11 methods/flann/src/allknn.cpp -o methods/flann/allknn -I$(MLPACK_PATH)/include -I$(FLANN_PATH)/include -L$(MLPACK_PATH)/lib -L$(FLANN_PATH)/lib -lmlpack -lboost_program_options
+	g++ -O0 -std=c++11 methods/flann/src/allknn.cpp -o methods/flann/allknn -I$(INCLUDEPATH) -L$(LIBPATH) -lmlpack -lboost_program_options -llz4
+	# Compile the mlpack scripts.  (Can't do this until ANN is released or a
+	# git version of mlpack is used.)
+	#cd methods/mlpack/src/ && ./build_scripts.sh
 
 .setup:
 	cd libraries/ && ./download_packages.sh && ./install_all.sh

From 3915c2772be1860815103dbda322c39bb6a144a2 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:33:56 -0400
Subject: [PATCH 03/18] Update mlpack location.

---
 methods/mlpack/allkfn.py                  | 4 ++--
 methods/mlpack/allknn.py                  | 4 ++--
 methods/mlpack/allkrann.py                | 4 ++--
 methods/mlpack/decision_stump.py          | 4 ++--
 methods/mlpack/det.py                     | 4 ++--
 methods/mlpack/emst.py                    | 4 ++--
 methods/mlpack/fastmks.py                 | 4 ++--
 methods/mlpack/hmm_generate.py            | 4 ++--
 methods/mlpack/hmm_loglik.py              | 4 ++--
 methods/mlpack/hmm_train.py               | 4 ++--
 methods/mlpack/hmm_viterbi.py             | 4 ++--
 methods/mlpack/ica.py                     | 4 ++--
 methods/mlpack/kernel_pca.py              | 4 ++--
 methods/mlpack/kmeans.py                  | 4 ++--
 methods/mlpack/lars.py                    | 4 ++--
 methods/mlpack/linear_regression.py       | 4 ++--
 methods/mlpack/local_coordinate_coding.py | 4 ++--
 methods/mlpack/logistic_regression.py     | 4 ++--
 methods/mlpack/lsh.py                     | 4 ++--
 methods/mlpack/mlp_backward.py            | 2 +-
 methods/mlpack/nbc.py                     | 4 ++--
 methods/mlpack/nca.py                     | 4 ++--
 methods/mlpack/nmf.py                     | 4 ++--
 methods/mlpack/pca.py                     | 4 ++--
 methods/mlpack/perceptron.py              | 4 ++--
 methods/mlpack/range_search.py            | 4 ++--
 methods/mlpack/sparse_coding.py           | 4 ++--
 27 files changed, 53 insertions(+), 53 deletions(-)

diff --git a/methods/mlpack/allkfn.py b/methods/mlpack/allkfn.py
index 34991b3..566c161 100644
--- a/methods/mlpack/allkfn.py
+++ b/methods/mlpack/allkfn.py
@@ -43,8 +43,8 @@ class ALLKFN(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/allknn.py b/methods/mlpack/allknn.py
index 35b6be0..9c3a7f4 100644
--- a/methods/mlpack/allknn.py
+++ b/methods/mlpack/allknn.py
@@ -43,8 +43,8 @@ class ALLKNN(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-    verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+    verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/allkrann.py b/methods/mlpack/allkrann.py
index 39c1b60..0360116 100644
--- a/methods/mlpack/allkrann.py
+++ b/methods/mlpack/allkrann.py
@@ -43,8 +43,8 @@ class ALLKRANN(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/decision_stump.py b/methods/mlpack/decision_stump.py
index 615c07d..76e3359 100644
--- a/methods/mlpack/decision_stump.py
+++ b/methods/mlpack/decision_stump.py
@@ -51,8 +51,8 @@ class DecisionStump(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/det.py b/methods/mlpack/det.py
index 07a14d7..c7735c0 100644
--- a/methods/mlpack/det.py
+++ b/methods/mlpack/det.py
@@ -45,8 +45,8 @@ class DET(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/emst.py b/methods/mlpack/emst.py
index 381ffc9..33b074c 100644
--- a/methods/mlpack/emst.py
+++ b/methods/mlpack/emst.py
@@ -43,8 +43,8 @@ class EMST(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/fastmks.py b/methods/mlpack/fastmks.py
index baf070b..e393906 100644
--- a/methods/mlpack/fastmks.py
+++ b/methods/mlpack/fastmks.py
@@ -43,8 +43,8 @@ class FastMKS(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/hmm_generate.py b/methods/mlpack/hmm_generate.py
index ccdef13..a95bcb0 100644
--- a/methods/mlpack/hmm_generate.py
+++ b/methods/mlpack/hmm_generate.py
@@ -43,8 +43,8 @@ class HMMGENERATE(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/hmm_loglik.py b/methods/mlpack/hmm_loglik.py
index dda57b5..2832932 100644
--- a/methods/mlpack/hmm_loglik.py
+++ b/methods/mlpack/hmm_loglik.py
@@ -44,8 +44,8 @@ class HMMLOGLIK(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/hmm_train.py b/methods/mlpack/hmm_train.py
index 5a80b36..9acc9a8 100644
--- a/methods/mlpack/hmm_train.py
+++ b/methods/mlpack/hmm_train.py
@@ -43,8 +43,8 @@ class HMMTRAIN(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/hmm_viterbi.py b/methods/mlpack/hmm_viterbi.py
index fb8376d..0c3b1dd 100644
--- a/methods/mlpack/hmm_viterbi.py
+++ b/methods/mlpack/hmm_viterbi.py
@@ -45,8 +45,8 @@ class HMMVITERBI(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/ica.py b/methods/mlpack/ica.py
index 955cf30..cb749f4 100644
--- a/methods/mlpack/ica.py
+++ b/methods/mlpack/ica.py
@@ -43,8 +43,8 @@ class ICA(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/kernel_pca.py b/methods/mlpack/kernel_pca.py
index a1ac03a..927b652 100644
--- a/methods/mlpack/kernel_pca.py
+++ b/methods/mlpack/kernel_pca.py
@@ -43,8 +43,8 @@ class KPCA(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/kmeans.py b/methods/mlpack/kmeans.py
index 2e8b95c..52438b8 100644
--- a/methods/mlpack/kmeans.py
+++ b/methods/mlpack/kmeans.py
@@ -43,8 +43,8 @@ class KMEANS(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/lars.py b/methods/mlpack/lars.py
index a3a057c..3373399 100644
--- a/methods/mlpack/lars.py
+++ b/methods/mlpack/lars.py
@@ -43,8 +43,8 @@ class LARS(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-    verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+    verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/linear_regression.py b/methods/mlpack/linear_regression.py
index 5a36b41..a53d4d6 100644
--- a/methods/mlpack/linear_regression.py
+++ b/methods/mlpack/linear_regression.py
@@ -50,8 +50,8 @@ class LinearRegression(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/local_coordinate_coding.py b/methods/mlpack/local_coordinate_coding.py
index 1097614..a36403d 100644
--- a/methods/mlpack/local_coordinate_coding.py
+++ b/methods/mlpack/local_coordinate_coding.py
@@ -43,8 +43,8 @@ class LocalCoordinateCoding(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/logistic_regression.py b/methods/mlpack/logistic_regression.py
index 9932f03..de02f9e 100644
--- a/methods/mlpack/logistic_regression.py
+++ b/methods/mlpack/logistic_regression.py
@@ -51,8 +51,8 @@ class LogisticRegression(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/lsh.py b/methods/mlpack/lsh.py
index 2f1d293..8785ba4 100644
--- a/methods/mlpack/lsh.py
+++ b/methods/mlpack/lsh.py
@@ -44,8 +44,8 @@ class LSH(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/mlp_backward.py b/methods/mlpack/mlp_backward.py
index 6726f6a..9c86742 100644
--- a/methods/mlpack/mlp_backward.py
+++ b/methods/mlpack/mlp_backward.py
@@ -80,7 +80,7 @@ def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN_SRC"],
   successful.
   '''
   def RunMetrics(self, options):
-    Log.Info("Perform MLP Backard.", self.verbose)
+    Log.Info("Perform MLP Backward.", self.verbose)
 
     # Split the command using shell-like syntax.
     cmd = shlex.split(self.path + "mlp_backward -v " + options)
diff --git a/methods/mlpack/nbc.py b/methods/mlpack/nbc.py
index 1e6c91a..cc374fb 100644
--- a/methods/mlpack/nbc.py
+++ b/methods/mlpack/nbc.py
@@ -51,8 +51,8 @@ class NBC(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/nca.py b/methods/mlpack/nca.py
index f84d8b1..867466e 100644
--- a/methods/mlpack/nca.py
+++ b/methods/mlpack/nca.py
@@ -43,8 +43,8 @@ class NCA(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/nmf.py b/methods/mlpack/nmf.py
index 77e869e..8de22e5 100644
--- a/methods/mlpack/nmf.py
+++ b/methods/mlpack/nmf.py
@@ -43,8 +43,8 @@ class NMF(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/pca.py b/methods/mlpack/pca.py
index 9358b75..4f61169 100644
--- a/methods/mlpack/pca.py
+++ b/methods/mlpack/pca.py
@@ -42,8 +42,8 @@ class PCA(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/perceptron.py b/methods/mlpack/perceptron.py
index 4884e26..306cafe 100644
--- a/methods/mlpack/perceptron.py
+++ b/methods/mlpack/perceptron.py
@@ -51,8 +51,8 @@ class PERCEPTRON(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/range_search.py b/methods/mlpack/range_search.py
index ffbd387..17225e5 100644
--- a/methods/mlpack/range_search.py
+++ b/methods/mlpack/range_search.py
@@ -43,8 +43,8 @@ class RANGESEARCH(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path
diff --git a/methods/mlpack/sparse_coding.py b/methods/mlpack/sparse_coding.py
index fca1168..86a7647 100644
--- a/methods/mlpack/sparse_coding.py
+++ b/methods/mlpack/sparse_coding.py
@@ -43,8 +43,8 @@ class SparseCoding(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["MLPACK_BIN"],
-      verbose=True, debug=os.environ["MLPACK_BIN_DEBUG"]):
+  def __init__(self, dataset, timeout=0, path=os.environ["BINPATH"],
+      verbose=True, debug=os.environ["DEBUGBINPATH"]):
     self.verbose = verbose
     self.dataset = dataset
     self.path = path

From 59c29263b25dc382c93a3f14b44e20ee40bdb464 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:34:51 -0400
Subject: [PATCH 04/18] Fix config file.  (Should these datasets have been
 removed?)

---
 config.yaml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/config.yaml b/config.yaml
index 38ef3f1..8d3377d 100644
--- a/config.yaml
+++ b/config.yaml
@@ -969,13 +969,13 @@ methods:
                            ['datasets/scene_train.csv', 'datasets/scene_test.csv', 'datasets/scene_labels.csv'],
                            ['datasets/webpage_train.csv', 'datasets/webpage_test.csv', 'datasets/webpage_labels.csv'], 
                            ['datasets/isolet_train.csv', 'datasets/isolet_test.csv', 'datasets/isolet_labels.csv'],
- -                         ['datasets/mammography_train.csv', 'datasets/mammography_test.csv', 'datasets/mammography_labels.csv'],
- -                         ['datasets/reuters_train.csv', 'datasets/reuters_test.csv', 'datasets/reuters_labels.csv'],
- -                         ['datasets/abalone19_train.csv', 'datasets/abalone19_test.csv', 'datasets/abalone19_labels.csv'],
- -                         ['datasets/sickEuthyroid_train.csv', 'datasets/sickEuthyroid_test.csv', 'datasets/sickEuthyroid_labels.csv'],
- -                         ['datasets/abalone7_train.csv', 'datasets/abalone7_test.csv', 'datasets/abalone7_labels.csv'],
- -                         ['datasets/satellite_train.csv', 'datasets/satellite_test.csv', 'datasets/satellite_labels.csv'],
- -                         ['datasets/ecoli_train.csv', 'datasets/ecoli_test.csv', 'datasets/ecoli_labels.csv'] ]
+                           ['datasets/mammography_train.csv', 'datasets/mammography_test.csv', 'datasets/mammography_labels.csv'],
+                           ['datasets/reuters_train.csv', 'datasets/reuters_test.csv', 'datasets/reuters_labels.csv'],
+                           ['datasets/abalone19_train.csv', 'datasets/abalone19_test.csv', 'datasets/abalone19_labels.csv'],
+                           ['datasets/sickEuthyroid_train.csv', 'datasets/sickEuthyroid_test.csv', 'datasets/sickEuthyroid_labels.csv'],
+                           ['datasets/abalone7_train.csv', 'datasets/abalone7_test.csv', 'datasets/abalone7_labels.csv'],
+                           ['datasets/satellite_train.csv', 'datasets/satellite_test.csv', 'datasets/satellite_labels.csv'],
+                           ['datasets/ecoli_train.csv', 'datasets/ecoli_test.csv', 'datasets/ecoli_labels.csv'] ]
                   options: '-e 50 -c entropy -d 10 --min_samples_split 4 --min_samples_leaf 2 --n_jobs 2'
     SVM:
             run: ['metric']

From 220c405ca4018f8a80af9fd848a15ca0102cd9bc Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:35:14 -0400
Subject: [PATCH 05/18] For MATLAB we should check that it's on the PATH.

---
 libraries/matlab_install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/libraries/matlab_install.sh b/libraries/matlab_install.sh
index e33f880..b519d0d 100755
--- a/libraries/matlab_install.sh
+++ b/libraries/matlab_install.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 # This does not install MATLAB but instead simply checks for its presence.
-if [ ! -f /opt/matlab/bin/matlab ];
+if [ ! -f `which matlab` ];
 then
   echo "MATLAB not found!"
   exit 1

From 8ea39f832b0e388a00c4638f800f1cbda8ef3b5c Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:35:24 -0400
Subject: [PATCH 06/18] Install debug version also.

---
 libraries/mlpack_install.sh | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/libraries/mlpack_install.sh b/libraries/mlpack_install.sh
index 6101da3..dfa1ae8 100755
--- a/libraries/mlpack_install.sh
+++ b/libraries/mlpack_install.sh
@@ -30,3 +30,10 @@ mkdir build/
 cd build/
 cmake -DCMAKE_INSTALL_PREFIX=../../ -DBUILD_TESTS=OFF ../
 make install
+
+# Also install debug version.
+cd ..
+mkdir build-debug/
+cd build-debug/
+cmake -DDEBUG=ON -DCMAKE_INSTALL_PREFIX=../../debug/ -DBUILD_TEST=OFF ../
+make install

From b80d0845db097ce95030a0f0dafb8b1b2fdd32a8 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:35:36 -0400
Subject: [PATCH 07/18] Install Python packages to appropriate directory.

---
 libraries/mlpy_install.sh   | 2 +-
 libraries/scikit_install.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/libraries/mlpy_install.sh b/libraries/mlpy_install.sh
index 0dfdcce..3de1927 100755
--- a/libraries/mlpy_install.sh
+++ b/libraries/mlpy_install.sh
@@ -26,4 +26,4 @@ tar -xzpf mlpy*.tar.gz --strip-components=1 -C mlpy/
 
 cd mlpy/
 python3 setup.py build
-python3 setup.py install --prefix=../../ -O2
+python3 setup.py install --prefix=../ -O2
diff --git a/libraries/scikit_install.sh b/libraries/scikit_install.sh
index 48f3e90..20f32a2 100755
--- a/libraries/scikit_install.sh
+++ b/libraries/scikit_install.sh
@@ -26,4 +26,4 @@ tar -xzpf scikit*.tar.gz --strip-components=1 -C scikit/
 
 cd scikit/
 python3 setup.py build
-python3 setup.py install --prefix=../../ -O2
+python3 setup.py install --prefix=../ -O2

From bb40ca33631381dd79e7dba61ba7a2c44bffeda9 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:35:55 -0400
Subject: [PATCH 08/18] Update Weka location.

---
 methods/weka/allknn.py              | 2 +-
 methods/weka/kmeans.py              | 2 +-
 methods/weka/linear_regression.py   | 2 +-
 methods/weka/logistic_regression.py | 2 +-
 methods/weka/nbc.py                 | 2 +-
 methods/weka/pca.py                 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/methods/weka/allknn.py b/methods/weka/allknn.py
index dc1f43c..bf74f6a 100644
--- a/methods/weka/allknn.py
+++ b/methods/weka/allknn.py
@@ -37,7 +37,7 @@ class ALLKNN(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["WEKA_CLASSPATH"],
+  def __init__(self, dataset, timeout=0, path=os.environ["JAVAPATH"],
       verbose = True):
     self.verbose = verbose
     self.dataset = dataset
diff --git a/methods/weka/kmeans.py b/methods/weka/kmeans.py
index 0c43aed..201547c 100644
--- a/methods/weka/kmeans.py
+++ b/methods/weka/kmeans.py
@@ -37,7 +37,7 @@ class KMEANS(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["WEKA_CLASSPATH"],
+  def __init__(self, dataset, timeout=0, path=os.environ["JAVAPATH"],
       verbose=True):
     self.verbose = verbose
     self.dataset = dataset
diff --git a/methods/weka/linear_regression.py b/methods/weka/linear_regression.py
index d8f49af..e932fcc 100644
--- a/methods/weka/linear_regression.py
+++ b/methods/weka/linear_regression.py
@@ -45,7 +45,7 @@ class LinearRegression(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["WEKA_CLASSPATH"],
+  def __init__(self, dataset, timeout=0, path=os.environ["JAVAPATH"],
       verbose=True):
     self.verbose = verbose
     self.dataset = dataset
diff --git a/methods/weka/logistic_regression.py b/methods/weka/logistic_regression.py
index 8a46030..20e14a9 100644
--- a/methods/weka/logistic_regression.py
+++ b/methods/weka/logistic_regression.py
@@ -45,7 +45,7 @@ class LogisticRegression(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["WEKA_CLASSPATH"],
+  def __init__(self, dataset, timeout=0, path=os.environ["JAVAPATH"],
       verbose=True):
     self.verbose = verbose
     self.dataset = dataset
diff --git a/methods/weka/nbc.py b/methods/weka/nbc.py
index ceff4d2..b93d9f6 100644
--- a/methods/weka/nbc.py
+++ b/methods/weka/nbc.py
@@ -46,7 +46,7 @@ class NBC(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["WEKA_CLASSPATH"],
+  def __init__(self, dataset, timeout=0, path=os.environ["JAVAPATH"],
       verbose=True):
     self.verbose = verbose
     self.dataset = dataset
diff --git a/methods/weka/pca.py b/methods/weka/pca.py
index 383110f..2554525 100644
--- a/methods/weka/pca.py
+++ b/methods/weka/pca.py
@@ -37,7 +37,7 @@ class PCA(object):
   @param path - Path to the mlpack executable.
   @param verbose - Display informational messages.
   '''
-  def __init__(self, dataset, timeout=0, path=os.environ["WEKA_CLASSPATH"],
+  def __init__(self, dataset, timeout=0, path=os.environ["JAVAPATH"],
       verbose=True):
     self.verbose = verbose
     self.dataset = dataset

From c6191f8b11f20465fe7459b991cd39926eed2f39 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:37:11 -0400
Subject: [PATCH 09/18] Fix path of Python install.

---
 libraries/annoy_install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/libraries/annoy_install.sh b/libraries/annoy_install.sh
index 115c190..a0614fe 100644
--- a/libraries/annoy_install.sh
+++ b/libraries/annoy_install.sh
@@ -26,4 +26,4 @@ tar -xzpf annoy*.tar.gz --strip-components=1 -C annoy/
 
 cd annoy/
 python3 setup.py build
-python3 setup.py install --prefix=../../ -O2
+python3 setup.py install --prefix=../ -O2

From a1d80e08a0f01123cbb3471d677057acb49d5f25 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Mon, 10 Apr 2017 15:42:33 -0400
Subject: [PATCH 10/18] Fix install path and get around setuptools warning.

---
 libraries/annoy_install.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)
 mode change 100644 => 100755 libraries/annoy_install.sh

diff --git a/libraries/annoy_install.sh b/libraries/annoy_install.sh
old mode 100644
new mode 100755
index a0614fe..63c24e3
--- a/libraries/annoy_install.sh
+++ b/libraries/annoy_install.sh
@@ -26,4 +26,5 @@ tar -xzpf annoy*.tar.gz --strip-components=1 -C annoy/
 
 cd annoy/
 python3 setup.py build
-python3 setup.py install --prefix=../ -O2
+PYVER=`python3 -c 'import sys; print("python" + sys.version[0:3])'`;
+PYTHONPATH=../lib/$PYVER/site-packages/ python3 setup.py install --prefix=../ -O2

From 85b0e57b3fd90b7999a133401a2daf5089ae12d8 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 11 Apr 2017 10:45:59 -0400
Subject: [PATCH 11/18] Fix naming conflicts and force names to
 <library>.tar.gz.

---
 libraries/ann_install.sh    | 14 ++++----------
 libraries/annoy_install.sh  | 14 ++++----------
 libraries/flann_install.sh  | 14 ++++----------
 libraries/hlearn_install.sh | 26 +++++++-------------------
 libraries/mlpack_install.sh | 14 ++++----------
 libraries/mlpy_install.sh   | 14 ++++----------
 libraries/scikit_install.sh | 14 ++++----------
 libraries/shogun_install.sh | 14 ++++----------
 libraries/weka_install.sh   | 14 ++++----------
 9 files changed, 39 insertions(+), 99 deletions(-)

diff --git a/libraries/ann_install.sh b/libraries/ann_install.sh
index 14f2e24..5595b64 100755
--- a/libraries/ann_install.sh
+++ b/libraries/ann_install.sh
@@ -5,25 +5,19 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One ann*.tar.gz file should be located in this directory containing the
+# One ann.tar.gz file should be located in this directory containing the
 # source code of the desired mlpack version.
-tars=`ls ann*.tar.gz | wc -l`;
+tars=`ls ann.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No ann source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one ann source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source ann.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf ann/
 mkdir ann/
-tar -xzpf ann*.tar.gz --strip-components=1 -C ann/
+tar -xzpf ann.tar.gz --strip-components=1 -C ann/
 
 cd ann/
 make linux-g++
diff --git a/libraries/annoy_install.sh b/libraries/annoy_install.sh
index 63c24e3..626eb93 100755
--- a/libraries/annoy_install.sh
+++ b/libraries/annoy_install.sh
@@ -5,24 +5,18 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One annoy*.tar.gz file should be located in this directory.
-tars=`ls annoy*.tar.gz | wc -l`;
+# One annoy.tar.gz file should be located in this directory.
+tars=`ls annoy.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No annoy source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one annoy source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source annoy.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf annoy/
 mkdir annoy/
-tar -xzpf annoy*.tar.gz --strip-components=1 -C annoy/
+tar -xzpf annoy.tar.gz --strip-components=1 -C annoy/
 
 cd annoy/
 python3 setup.py build
diff --git a/libraries/flann_install.sh b/libraries/flann_install.sh
index 4cb017c..ebd8499 100755
--- a/libraries/flann_install.sh
+++ b/libraries/flann_install.sh
@@ -5,25 +5,19 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One flann*.tar.gz file should be located in this directory containing the
+# One flann.tar.gz file should be located in this directory containing the
 # source code of the desired mlpack version.
-tars=`ls flann*.tar.gz | wc -l`;
+tars=`ls flann.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No flann source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one flann source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source flann.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf flann/
 mkdir flann/
-tar -xzpf flann*.tar.gz --strip-components=1 -C flann/
+tar -xzpf flann.tar.gz --strip-components=1 -C flann/
 
 cd flann/
 mkdir build/
diff --git a/libraries/hlearn_install.sh b/libraries/hlearn_install.sh
index c905092..b579d18 100755
--- a/libraries/hlearn_install.sh
+++ b/libraries/hlearn_install.sh
@@ -5,43 +5,31 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One HLearn*.tar.gz file should be located in this directory.  Also since
+# One HLearn.tar.gz file should be located in this directory.  Also since
 # HLearn depends on subhask, a subhask*.tar.gz file should also be located in
 # this directory.
-tars=`ls HLearn*.tar.gz | wc -l`;
+tars=`ls HLearn.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No HLearn source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one HLearn source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source HLearn.tar.gz found in libraries/!"
   exit 1
 fi
 
-subhasktars=`ls subhask*.tar.gz | wc -l`;
+subhasktars=`ls subhask.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No subhask source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one subhask source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source subhask.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf hlearn/
 mkdir hlearn/
-tar -xzpf HLearn*.tar.gz --strip-components=1 -C hlearn/
+tar -xzpf HLearn.tar.gz --strip-components=1 -C hlearn/
 
 rm -rf subhask/
 mkdir subhask/
-tar -xvzpf subhask*.tar.gz --strip-components=1 -C subhask/
+tar -xvzpf subhask.tar.gz --strip-components=1 -C subhask/
 
 cd hlearn/
 cabal sandbox init
diff --git a/libraries/mlpack_install.sh b/libraries/mlpack_install.sh
index dfa1ae8..0fa38dc 100755
--- a/libraries/mlpack_install.sh
+++ b/libraries/mlpack_install.sh
@@ -5,25 +5,19 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One mlpack*.tar.gz file should be located in this directory containing the
+# One mlpack.tar.gz file should be located in this directory containing the
 # source code of the desired mlpack version.
-tars=`ls mlpack*.tar.gz | wc -l`;
+tars=`ls mlpack.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No mlpack source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one mlpack source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source mlpack.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf mlpack/
 mkdir mlpack/
-tar -xzpf mlpack*.tar.gz --strip-components=1 -C mlpack/
+tar -xzpf mlpack.tar.gz --strip-components=1 -C mlpack/
 
 cd mlpack/
 mkdir build/
diff --git a/libraries/mlpy_install.sh b/libraries/mlpy_install.sh
index 3de1927..fae4c06 100755
--- a/libraries/mlpy_install.sh
+++ b/libraries/mlpy_install.sh
@@ -5,24 +5,18 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One mlpy*.tar.gz file should be located in this directory.
-tars=`ls mlpy*.tar.gz | wc -l`;
+# One mlpy.tar.gz file should be located in this directory.
+tars=`ls mlpy.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No mlpy source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one mlpy source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source mlpy.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf mlpy/
 mkdir mlpy/
-tar -xzpf mlpy*.tar.gz --strip-components=1 -C mlpy/
+tar -xzpf mlpy.tar.gz --strip-components=1 -C mlpy/
 
 cd mlpy/
 python3 setup.py build
diff --git a/libraries/scikit_install.sh b/libraries/scikit_install.sh
index 20f32a2..903af98 100755
--- a/libraries/scikit_install.sh
+++ b/libraries/scikit_install.sh
@@ -5,24 +5,18 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One scikit*.tar.gz file should be located in this directory.
-tars=`ls scikit*.tar.gz | wc -l`;
+# One scikit.tar.gz file should be located in this directory.
+tars=`ls scikit.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No scikit source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one scikit source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source scikit.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf scikit/
 mkdir scikit/
-tar -xzpf scikit*.tar.gz --strip-components=1 -C scikit/
+tar -xzpf scikit.tar.gz --strip-components=1 -C scikit/
 
 cd scikit/
 python3 setup.py build
diff --git a/libraries/shogun_install.sh b/libraries/shogun_install.sh
index 649ef4e..67e0eba 100755
--- a/libraries/shogun_install.sh
+++ b/libraries/shogun_install.sh
@@ -5,24 +5,18 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One shogun*.tar.gz file should be located in this directory.
-tars=`ls shogun*.tar.gz | wc -l`;
+# One shogun.tar.gz file should be located in this directory.
+tars=`ls shogun.tar.gz | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No shogun source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one shogun source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source shogun.tar.gz found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf shogun/
 mkdir shogun/
-tar -xzpf shogun*.tar.gz --strip-components=1 -C shogun/
+tar -xzpf shogun.tar.gz --strip-components=1 -C shogun/
 
 cd shogun/
 mkdir build/
diff --git a/libraries/weka_install.sh b/libraries/weka_install.sh
index 3e5c986..e112ff9 100755
--- a/libraries/weka_install.sh
+++ b/libraries/weka_install.sh
@@ -5,23 +5,17 @@
 # Include files will be installed to ../include/.
 # Library files will be installed to ../lib/.
 #
-# One weka*.tar.gz file should be located in this directory.
-tars=`ls scikit*.tar.gz | wc -l`;
+# One weka.zip file should be located in this directory.
+tars=`ls weka.zip | wc -l`;
 if [ "$tars" -eq "0" ];
 then
-  echo "No weka source .tar.gz found in libraries/!"
-  exit 1
-fi
-if [ "$tars" -ne "1" ];
-then
-  echo "More than one weka source .tar.gz found."
-  echo "Ensure only one is present in libraries/!"
+  echo "No source weka.zip found in libraries/!"
   exit 1
 fi
 
 # Remove any old directory.
 rm -rf weka/
-unzip weka*.zip
+unzip weka.zip
 mv weka-[0-9]-[0-9]-[0-9]/ weka/
 
 cd weka/

From bff5a5515f30d6b8cbe37b4130ed6615c9498594 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Tue, 11 Apr 2017 10:46:31 -0400
Subject: [PATCH 12/18] Preserve existing PYTHONPATH.

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index ff7776f..28eca4e 100644
--- a/Makefile
+++ b/Makefile
@@ -67,7 +67,7 @@ export ANN_PATH=methods/ann/
 export LD_LIBRARY_PATH=$(shell echo $(LIBPATH))
 # Set PYTHONPATH correctly.
 PYVERSION=$(shell python3 -c 'import sys; print("python" + sys.version[0:3])')
-export PYTHONPATH=$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/dist-packages:$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/site-packages
+export PYTHONPATH=$(shell printenv PYTHONPATH):$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/dist-packages:$(shell pwd)/libraries/lib/$(shell echo $(PYVERSION))/site-packages
 
 # Color settings.
 NO_COLOR=\033[0m

From 0334f9628d464c36ffa251c61581601b0f3fa32f Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 20 Apr 2017 16:03:34 -0400
Subject: [PATCH 13/18] Better handling of JAVAPATH with Weka jar.

---
 methods/weka/allknn.py              | 7 ++++---
 methods/weka/kmeans.py              | 2 +-
 methods/weka/linear_regression.py   | 6 +++---
 methods/weka/logistic_regression.py | 6 +++---
 methods/weka/nbc.py                 | 5 +++--
 methods/weka/pca.py                 | 4 ++--
 6 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/methods/weka/allknn.py b/methods/weka/allknn.py
index bf74f6a..0b19c21 100644
--- a/methods/weka/allknn.py
+++ b/methods/weka/allknn.py
@@ -58,13 +58,14 @@ def RunMetrics(self, options):
     # If the dataset contains two files then the second file is the query file.
     # In this case we add this to the command line.
     if len(self.dataset) == 2:
-      inputCmd = "-r " + self.dataset[0] + " -q " + self.dataset[1] + " " + options
+      inputCmd = "-r " + self.dataset[0] + " -q " + self.dataset[1] + " " +
+          options
     else:
       inputCmd = "-r " + self.dataset + " " + options
 
     # Split the command using shell-like syntax.
-    cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
-      " AllKnn " + inputCmd + " " + options)
+    cmd = shlex.split("java -classpath " + self.path + "/weka.jar" +
+        ":methods/weka" + " AllKnn " + inputCmd + " " + options)
 
     # Run command with the nessecary arguments and return its output as a byte
     # string. We have untrusted input so we disable all shell based features.
diff --git a/methods/weka/kmeans.py b/methods/weka/kmeans.py
index 201547c..b9302ed 100644
--- a/methods/weka/kmeans.py
+++ b/methods/weka/kmeans.py
@@ -56,7 +56,7 @@ def RunMetrics(self, options):
     Log.Info("Perform K-Means.", self.verbose)
 
     # Split the command using shell-like syntax.
-    cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
+    cmd = shlex.split("java -classpath " + self.path + "/weka.jar:methods/weka" +
       " KMeans -i " + self.dataset[0] + " " + options)
 
     # Run command with the nessecary arguments and return its output as a byte
diff --git a/methods/weka/linear_regression.py b/methods/weka/linear_regression.py
index e932fcc..0e3118e 100644
--- a/methods/weka/linear_regression.py
+++ b/methods/weka/linear_regression.py
@@ -79,9 +79,9 @@ def RunMetrics(self, options):
     # If the dataset contains two files then the second file is the responses
     # file. In this case we add this to the command line.
     if len(self.dataset) >= 2:
-      cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
-        " LinearRegression -i " + self.dataset[0] + " -t " + self.dataset[1]
-        + " " + options)
+      cmd = shlex.split("java -classpath " + self.path + "/weka.jar" +
+        ":methods/weka" + " LinearRegression -i " + self.dataset[0] + " -t " +
+        self.dataset[1] + " " + options)
     else:
       cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
         " LinearRegression -i " + self.dataset[0] + " " + options)
diff --git a/methods/weka/logistic_regression.py b/methods/weka/logistic_regression.py
index 20e14a9..c9eb824 100644
--- a/methods/weka/logistic_regression.py
+++ b/methods/weka/logistic_regression.py
@@ -79,9 +79,9 @@ def RunMetrics(self, options):
     # If the dataset contains two files then the second file is the responses
     # file. In this case we add this to the command line.
     if len(self.dataset) >= 2:
-      cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
-        " LogisticRegression -i " + self.dataset[0] + " -t " + self.dataset[1]
-        + " " + options)
+      cmd = shlex.split("java -classpath " + self.path + "/weka.jar" +
+        ":methods/weka LogisticRegression -i " + self.dataset[0] + " -t " +
+        self.dataset[1] + " " + options)
     else:
       cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
         " LogisticRegression -i " + self.dataset[0] + " " + options)
diff --git a/methods/weka/nbc.py b/methods/weka/nbc.py
index b93d9f6..05b6a6b 100644
--- a/methods/weka/nbc.py
+++ b/methods/weka/nbc.py
@@ -69,8 +69,9 @@ def RunMetrics(self, options):
       return -1
 
     # Split the command using shell-like syntax.
-    cmd = shlex.split("java -classpath " + self.path + ":methods/weka" +
-      " NBC -t " + self.dataset[0] + " -T " + self.dataset[1] + " " + options)
+    cmd = shlex.split("java -classpath " + self.path + "/weka.jar" +
+        ":methods/weka" + " NBC -t " + self.dataset[0] + " -T " +
+        self.dataset[1] + " " + options)
 
     # Run command with the nessecary arguments and return its output as a byte
     # string. We have untrusted input so we disable all shell based features.
diff --git a/methods/weka/pca.py b/methods/weka/pca.py
index 2554525..fd935e4 100644
--- a/methods/weka/pca.py
+++ b/methods/weka/pca.py
@@ -56,8 +56,8 @@ def RunMetrics(self, options):
     Log.Info("Perform PCA.", self.verbose)
 
     # Split the command using shell-like syntax.
-    cmd = shlex.split("java -classpath " + self.path + ":methods/weka" + 
-      " PCA -i " + self.dataset + " " + options)
+    cmd = shlex.split("java -classpath " + self.path + "/weka.jar" +
+        ":methods/weka" + " PCA -i " + self.dataset + " " + options)
 
     # Run command with the nessecary arguments and return its output as a byte
     # string. We have untrusted input so we disable all shell based features.

From f67b78f473f0c7c11a8bf410e808f6899e7fadce Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 20 Apr 2017 17:20:53 -0400
Subject: [PATCH 14/18] Use -fPIC for compilation.

---
 libraries/ann_install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/libraries/ann_install.sh b/libraries/ann_install.sh
index 5595b64..7efd68e 100755
--- a/libraries/ann_install.sh
+++ b/libraries/ann_install.sh
@@ -20,7 +20,7 @@ mkdir ann/
 tar -xzpf ann.tar.gz --strip-components=1 -C ann/
 
 cd ann/
-make linux-g++
+CXXFLAGS=-fPIC make linux-g++
 cp -r include/* ../include/
 cp -r bin/* ../bin/
 cp -r lib/* ../lib/

From 59d05dec89755e2b3afc29ca263759be5a8b1ef3 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Thu, 11 May 2017 15:48:07 -0400
Subject: [PATCH 15/18] Remove HLearn install and configuration; doesn't work
 with ghc 8.

---
 config.yaml                 | 22 ---------------
 libraries/hlearn_install.sh | 53 ++++++++++++++++++++-----------------
 2 files changed, 28 insertions(+), 47 deletions(-)

diff --git a/config.yaml b/config.yaml
index f0dfde2..87beffe 100644
--- a/config.yaml
+++ b/config.yaml
@@ -1967,28 +1967,6 @@ methods:
                         'datasets/Twitter.csv', 'datasets/tinyImages100k.csv']
                 options: '-k 3 -s 42 -e 0.25'
 ---
-# HLearn: Homomorphic machine learning
-library: hlearn
-methods:
-    ALLKNN:
-          run: ['metric']
-          script: methods/hlearn/allknn.py
-          format: [csv, txt]
-          datasets:
-              - files: ['datasets/wine.csv', 'datasets/cloud.csv',
-                        'datasets/wine_qual.csv', 'datasets/isolet.csv',
-                        'datasets/corel-histogram.csv', 'datasets/covtype.csv',
-                        'datasets/1000000-10-randu.csv', 'datasets/mnist_all.csv',
-                        'datasets/Twitter.csv', 'datasets/tinyImages100k.csv']
-                options: '-k 3'
-
-              - files: ['datasets/wine.csv', 'datasets/cloud.csv',
-                        'datasets/wine_qual.csv', 'datasets/isolet.csv',
-                        'datasets/corel-histogram.csv', 'datasets/covtype.csv',
-                        'datasets/1000000-10-randu.csv', 'datasets/mnist_all.csv',
-                        'datasets/Twitter.csv', 'datasets/tinyImages100k.csv']
-                options: '-k 4'
----
 # MRPT: fast nearest neighbor search with random projection
 library: mrpt
 methods:
diff --git a/libraries/hlearn_install.sh b/libraries/hlearn_install.sh
index b579d18..4b70a69 100755
--- a/libraries/hlearn_install.sh
+++ b/libraries/hlearn_install.sh
@@ -8,33 +8,36 @@
 # One HLearn.tar.gz file should be located in this directory.  Also since
 # HLearn depends on subhask, a subhask*.tar.gz file should also be located in
 # this directory.
-tars=`ls HLearn.tar.gz | wc -l`;
-if [ "$tars" -eq "0" ];
-then
-  echo "No source HLearn.tar.gz found in libraries/!"
-  exit 1
-fi
+#
+# HLearn doesn't work with ghc 8, so this installation is commented out.
+
+#tars=`ls HLearn.tar.gz | wc -l`;
+#if [ "$tars" -eq "0" ];
+#then
+#  echo "No source HLearn.tar.gz found in libraries/!"
+#  exit 1
+#fi
 
-subhasktars=`ls subhask.tar.gz | wc -l`;
-if [ "$tars" -eq "0" ];
-then
-  echo "No source subhask.tar.gz found in libraries/!"
-  exit 1
-fi
+#subhasktars=`ls subhask.tar.gz | wc -l`;
+#if [ "$tars" -eq "0" ];
+#then
+#  echo "No source subhask.tar.gz found in libraries/!"
+#  exit 1
+#fi
 
 # Remove any old directory.
-rm -rf hlearn/
-mkdir hlearn/
-tar -xzpf HLearn.tar.gz --strip-components=1 -C hlearn/
+#rm -rf hlearn/
+#mkdir hlearn/
+#tar -xzpf HLearn.tar.gz --strip-components=1 -C hlearn/
 
-rm -rf subhask/
-mkdir subhask/
-tar -xvzpf subhask.tar.gz --strip-components=1 -C subhask/
+#rm -rf subhask/
+#mkdir subhask/
+#tar -xvzpf subhask.tar.gz --strip-components=1 -C subhask/
 
-cd hlearn/
-cabal sandbox init
-cabal sandbox add-source ../subhask
-cabal update
-cabal install --only-dependencies --force-reinstalls
-cabal build
-cabal install
+#cd hlearn/
+#cabal sandbox init
+#cabal sandbox add-source ../subhask
+#cabal update
+#cabal install --only-dependencies --force-reinstalls
+#cabal build
+#cabal install

From 86d9ab3866f9665bf53bc0760edbb673674bf520 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Fri, 12 May 2017 10:23:30 -0400
Subject: [PATCH 16/18] Work around 2.2.0 and 2.2.1 bug.

---
 libraries/mlpack_install.sh | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/libraries/mlpack_install.sh b/libraries/mlpack_install.sh
index 0fa38dc..4ab3e80 100755
--- a/libraries/mlpack_install.sh
+++ b/libraries/mlpack_install.sh
@@ -31,3 +31,13 @@ mkdir build-debug/
 cd build-debug/
 cmake -DDEBUG=ON -DCMAKE_INSTALL_PREFIX=../../debug/ -DBUILD_TEST=OFF ../
 make install
+
+# Work around bug in 2.2.0 and 2.2.1.
+cd ../../bin/
+ln -s mlpack_knn mlpack_allknn
+ln -s mlpack_kfn mlpack_allkfn
+ln -s mlpack_krann mlpack_allkrann
+cd ../debug/bin/
+ln -s mlpack_knn mlpack_allknn
+ln -s mlpack_kfn mlpack_allkfn
+ln -s mlpack_krann mlpack_allkrann

From 9b7b7b9c7144f5a45a0034e67f7760a644c70bc3 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Fri, 12 May 2017 11:00:05 -0400
Subject: [PATCH 17/18] Fix line wrap.

---
 methods/weka/allknn.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/methods/weka/allknn.py b/methods/weka/allknn.py
index 0b19c21..d377a54 100644
--- a/methods/weka/allknn.py
+++ b/methods/weka/allknn.py
@@ -58,7 +58,7 @@ def RunMetrics(self, options):
     # If the dataset contains two files then the second file is the query file.
     # In this case we add this to the command line.
     if len(self.dataset) == 2:
-      inputCmd = "-r " + self.dataset[0] + " -q " + self.dataset[1] + " " +
+      inputCmd = "-r " + self.dataset[0] + " -q " + self.dataset[1] + " " + \
           options
     else:
       inputCmd = "-r " + self.dataset + " " + options

From 8c6cde9e03d03572e5b3d0a1d9a918dd693a0cb8 Mon Sep 17 00:00:00 2001
From: Ryan Curtin <ryan@ratml.org>
Date: Fri, 12 May 2017 11:00:40 -0400
Subject: [PATCH 18/18] Don't change directory when loading module.

---
 util/loader.py | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/util/loader.py b/util/loader.py
index 7d3c80a..0305512 100644
--- a/util/loader.py
+++ b/util/loader.py
@@ -21,12 +21,6 @@ class Loader(object):
   '''
   @staticmethod
   def ImportModuleFromPath(path):
-    if hasattr(os, "getcwdu"):
-      # Returns a unicode object represantation.
-      realPath = os.path.realpath(os.getcwdu())
-    else:
-      realPath = os.path.realpath(os.path.curdir)
-
     destinationPath = os.path.dirname(path)
 
     if destinationPath == "":
@@ -40,16 +34,14 @@ def ImportModuleFromPath(path):
     else:
       modName = scriptName
 
-    os.chdir(destinationPath)
     fileHandle = None
     try:
-      tup = imp.find_module(modName, ['.'])
+      tup = imp.find_module(modName, [destinationPath])
       module = imp.load_module(modName, *tup)
       fileHandle = tup[0]
     finally:
-      os.chdir(realPath)
       if fileHandle is not None:
         fileHandle.close()
 
     # Return the name of the module.
-    return module
\ No newline at end of file
+    return module