Implement CI

21 files changed, 222 insertions, 13 deletions

diff --git a/packages/base/src/Internal/Algorithms.hs b/packages/base/src/Internal/Algorithms.hs
index 99c9e34..cea06ce 100644
--- a/packages/base/src/Internal/Algorithms.hs
+++ b/packages/base/src/Internal/Algorithms.hs
@@ -4,6 +4,8 @@
 {-# LANGUAGE UndecidableInstances #-}
 {-# LANGUAGE TypeFamilies #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 -----------------------------------------------------------------------------
 {- |
 Module      :  Internal.Algorithms
diff --git a/packages/base/src/Internal/CG.hs b/packages/base/src/Internal/CG.hs
index cc10ad8..29edd35 100644
--- a/packages/base/src/Internal/CG.hs
+++ b/packages/base/src/Internal/CG.hs
@@ -1,6 +1,8 @@
 {-# LANGUAGE FlexibleContexts, FlexibleInstances #-}
 {-# LANGUAGE RecordWildCards #-}
 
+{-# OPTIONS_GHC -fno-warn-orphans #-}
+
 module Internal.CG(
     cgSolve, cgSolve',
     CGState(..), R, V
diff --git a/packages/base/src/Internal/Chain.hs b/packages/base/src/Internal/Chain.hs
index f87eb02..4000c2b 100644
--- a/packages/base/src/Internal/Chain.hs
+++ b/packages/base/src/Internal/Chain.hs
@@ -1,5 +1,7 @@
 {-# LANGUAGE FlexibleContexts #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Internal.Chain
diff --git a/packages/base/src/Internal/Devel.hs b/packages/base/src/Internal/Devel.hs
index 3887663..f72d8aa 100644
--- a/packages/base/src/Internal/Devel.hs
+++ b/packages/base/src/Internal/Devel.hs
@@ -54,6 +54,7 @@ check msg f = do
 
 -- | postfix error code check
 infixl 0 #|
+(#|) :: IO CInt -> String -> IO ()
 (#|) = flip check
 
 -- | Error capture and conversion to Maybe
diff --git a/packages/base/src/Internal/Element.hs b/packages/base/src/Internal/Element.hs
index eb3a25b..2e330ee 100644
--- a/packages/base/src/Internal/Element.hs
+++ b/packages/base/src/Internal/Element.hs
@@ -4,6 +4,8 @@
 {-# LANGUAGE UndecidableInstances #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
 
+{-# OPTIONS_GHC -fno-warn-orphans #-}
+
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Data.Packed.Matrix
@@ -31,6 +33,7 @@ import Data.List.Split(chunksOf)
 import Foreign.Storable(Storable)
 import System.IO.Unsafe(unsafePerformIO)
 import Control.Monad(liftM)
+import Foreign.C.Types(CInt)
 
 -------------------------------------------------------------------
 
@@ -53,8 +56,10 @@ instance (Show a, Element a) => (Show (Matrix a)) where
     show m | rows m == 0 || cols m == 0 = sizes m ++" []"
     show m = (sizes m++) . dsp . map (map show) . toLists $ m
 
+sizes :: Matrix t -> [Char]
 sizes m = "("++show (rows m)++"><"++show (cols m)++")\n"
 
+dsp :: [[[Char]]] -> [Char]
 dsp as = (++" ]") . (" ["++) . init . drop 2 . unlines . map (" , "++) . map unwords' $ transpose mtp
     where
         mt = transpose as
@@ -73,6 +78,7 @@ instance (Element a, Read a) => Read (Matrix a) where
               rs = read . snd . breakAt '(' .init . fst . breakAt '>' $ dims
 
 
+breakAt :: Eq a => a -> [a] -> ([a], [a])
 breakAt c l = (a++[c],tail b) where
     (a,b) = break (==c) l
 
@@ -88,7 +94,8 @@ data Extractor
     | Drop Int
     | DropLast Int
   deriving Show
-  
+
+ppext :: Extractor -> [Char]
 ppext All = ":"
 ppext (Range a 1 c) = printf "%d:%d" a c
 ppext (Range a b c) = printf "%d:%d:%d" a b c
@@ -128,10 +135,14 @@ ppext (DropLast n) = printf "DropLast %d" n
 infixl 9 ??
 (??)  :: Element t => Matrix t -> (Extractor,Extractor) -> Matrix t
 
+minEl :: Vector CInt -> CInt
 minEl = toScalarI Min
+maxEl :: Vector CInt -> CInt
 maxEl = toScalarI Max
+cmodi :: Foreign.C.Types.CInt -> Vector Foreign.C.Types.CInt -> Vector Foreign.C.Types.CInt
 cmodi = vectorMapValI ModVS
 
+extractError :: Matrix t1 -> (Extractor, Extractor) -> t
 extractError m (e1,e2)= error $ printf "can't extract (%s,%s) from matrix %dx%d" (ppext e1::String) (ppext e2::String) (rows m) (cols m)
 
 m ?? (Range a s b,e) | s /= 1 = m ?? (Pos (idxs [a,a+s .. b]), e)
@@ -232,8 +243,10 @@ disp = putStr . dispf 2
 fromBlocks :: Element t => [[Matrix t]] -> Matrix t
 fromBlocks = fromBlocksRaw . adaptBlocks
 
+fromBlocksRaw :: Element t => [[Matrix t]] -> Matrix t
 fromBlocksRaw mms = joinVert . map joinHoriz $ mms
 
+adaptBlocks :: Element t => [[Matrix t]] -> [[Matrix t]]
 adaptBlocks ms = ms' where
     bc = case common length ms of
           Just c -> c
@@ -486,6 +499,9 @@ liftMatrix2Auto f m1 m2
     m2' = conformMTo (r,c) m2
 
 -- FIXME do not flatten if equal order
+lM :: (Storable t, Element t1, Element t2)
+   => (Vector t1 -> Vector t2 -> Vector t)
+   -> Matrix t1 -> Matrix t2 -> Matrix t
 lM f m1 m2 = matrixFromVector
                 RowMajor
                 (max' (rows m1) (rows m2))
@@ -504,6 +520,7 @@ compat' m1 m2 = s1 == (1,1) || s2 == (1,1) || s1 == s2
 
 ------------------------------------------------------------
 
+toBlockRows :: Element t => [Int] -> Matrix t -> [Matrix t]
 toBlockRows [r] m
     | r == rows m = [m]
 toBlockRows rs m
@@ -513,6 +530,7 @@ toBlockRows rs m
     szs = map (* cols m) rs
     g k = (k><0)[]
 
+toBlockCols :: Element t => [Int] -> Matrix t -> [Matrix t]
 toBlockCols [c] m | c == cols m = [m]
 toBlockCols cs m = map trans . toBlockRows cs . trans $ m
 
@@ -576,7 +594,7 @@ Just (3><3)
 mapMatrixWithIndexM
   :: (Element a, Storable b, Monad m) =>
       ((Int, Int) -> a -> m b) -> Matrix a -> m (Matrix b)
-mapMatrixWithIndexM g m = liftM (reshape c) . mapVectorWithIndexM (mk c g) . flatten $ m 
+mapMatrixWithIndexM g m = liftM (reshape c) . mapVectorWithIndexM (mk c g) . flatten $ m
     where
       c = cols m
 
@@ -598,4 +616,3 @@ mapMatrixWithIndex g m = reshape c . mapVectorWithIndex (mk c g) . flatten $ m
 
 mapMatrix :: (Element a, Element b) => (a -> b) -> Matrix a -> Matrix b
 mapMatrix f = liftMatrix (mapVector f)
-
diff --git a/packages/base/src/Internal/IO.hs b/packages/base/src/Internal/IO.hs
index a899cfd..b0f5606 100644
--- a/packages/base/src/Internal/IO.hs
+++ b/packages/base/src/Internal/IO.hs
@@ -20,7 +20,7 @@ import Internal.Devel
 import Internal.Vector
 import Internal.Matrix
 import Internal.Vectorized
-import Text.Printf(printf)
+import Text.Printf(printf, PrintfArg, PrintfType)
 import Data.List(intersperse,transpose)
 import Data.Complex
 
@@ -78,12 +78,18 @@ disps d x = sdims x ++ "  " ++ formatScaled d x
 dispf :: Int -> Matrix Double -> String
 dispf d x = sdims x ++ "\n" ++ formatFixed (if isInt x then 0 else d) x
 
+sdims :: Matrix t -> [Char]
 sdims x = show (rows x) ++ "x" ++ show (cols x)
 
+formatFixed :: (Show a, Text.Printf.PrintfArg t, Element t)
+            => a -> Matrix t -> String
 formatFixed d x = format "  " (printf ("%."++show d++"f")) $ x
 
+isInt :: Matrix Double -> Bool
 isInt = all lookslikeInt . toList . flatten
 
+formatScaled :: (Text.Printf.PrintfArg b, RealFrac b, Floating b, Num t, Element b, Show t)
+             => t -> Matrix b -> [Char]
 formatScaled dec t = "E"++show o++"\n" ++ ss
     where ss = format " " (printf fmt. g) t
           g x | o >= 0    = x/10^(o::Int)
@@ -133,14 +139,18 @@ showComplex d (a:+b)
     s2 = if b<0 then "-" else ""
     s3 = if b<0 then "-" else "+"
 
+shcr :: (Show a, Show t1, Text.Printf.PrintfType t, Text.Printf.PrintfArg t1, RealFrac t1)
+     => a -> t1 -> t
 shcr d a | lookslikeInt a = printf "%.0f" a
          | otherwise      = printf ("%."++show d++"f") a
 
-
+lookslikeInt :: (Show a, RealFrac a) => a -> Bool
 lookslikeInt x = show (round x :: Int) ++".0" == shx || "-0.0" == shx
    where shx = show x
 
+isZero :: Show a => a -> Bool
 isZero x = show x `elem` ["0.0","-0.0"]
+isOne :: Show a => a -> Bool
 isOne  x = show x `elem` ["1.0","-1.0"]
 
 -- | Pretty print a complex matrix with at most n decimal digits.
@@ -168,6 +178,6 @@ loadMatrix f = do
       else
         return (reshape c v)
 
-
+loadMatrix' :: FilePath -> IO (Maybe (Matrix Double))
 loadMatrix' name = mbCatch (loadMatrix name)
 
diff --git a/packages/base/src/Internal/LAPACK.hs b/packages/base/src/Internal/LAPACK.hs
index e306454..64cf2f5 100644
--- a/packages/base/src/Internal/LAPACK.hs
+++ b/packages/base/src/Internal/LAPACK.hs
@@ -1,6 +1,8 @@
 {-# LANGUAGE TypeOperators #-}
 {-# LANGUAGE ViewPatterns #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Numeric.LinearAlgebra.LAPACK
diff --git a/packages/base/src/Internal/Matrix.hs b/packages/base/src/Internal/Matrix.hs
index 4905f61..4bfa13d 100644
--- a/packages/base/src/Internal/Matrix.hs
+++ b/packages/base/src/Internal/Matrix.hs
@@ -57,19 +57,24 @@ cols :: Matrix t -> Int
 cols = icols
 {-# INLINE cols #-}
 
+size :: Matrix t -> (Int, Int)
 size m = (irows m, icols m)
 {-# INLINE size #-}
 
+rowOrder :: Matrix t -> Bool
 rowOrder m = xCol m == 1 || cols m == 1
 {-# INLINE rowOrder #-}
 
+colOrder :: Matrix t -> Bool
 colOrder m = xRow m == 1 || rows m == 1
 {-# INLINE colOrder #-}
 
+is1d :: Matrix t -> Bool
 is1d (size->(r,c)) = r==1 || c==1
 {-# INLINE is1d #-}
 
 -- data is not contiguous
+isSlice :: Storable t => Matrix t -> Bool
 isSlice m@(size->(r,c)) = r*c < dim (xdat m)
 {-# INLINE isSlice #-}
 
@@ -136,16 +141,20 @@ instance Storable t => TransArray (Matrix t)
     {-# INLINE applyRaw #-}
 
 infixr 1 #
+(#) :: TransArray c => c -> (b -> IO r) -> Trans c b -> IO r
 a # b = apply a b
 {-# INLINE (#) #-}
 
+(#!) :: (TransArray c, TransArray c1) => c1 -> c -> Trans c1 (Trans c (IO r)) -> IO r
 a #! b = a # b # id
 {-# INLINE (#!) #-}
 
 --------------------------------------------------------------------------------
 
+copy :: Element t => MatrixOrder -> Matrix t -> IO (Matrix t)
 copy ord m = extractR ord m 0 (idxs[0,rows m-1]) 0 (idxs[0,cols m-1])
 
+extractAll :: Element t => MatrixOrder -> Matrix t -> Matrix t
 extractAll ord m = unsafePerformIO (copy ord m)
 
 {- | Creates a vector by concatenation of rows. If the matrix is ColumnMajor, this operation requires a transpose.
@@ -223,11 +232,13 @@ m@Matrix {irows = r, icols = c} @@> (i,j)
 {-# INLINE (@@>) #-}
 
 --  Unsafe matrix access without range checking
+atM' :: Storable t => Matrix t -> Int -> Int -> t
 atM' m i j = xdat m `at'` (i * (xRow m) + j * (xCol m))
 {-# INLINE atM' #-}
 
 ------------------------------------------------------------------
 
+matrixFromVector :: Storable t => MatrixOrder -> Int -> Int -> Vector t -> Matrix t
 matrixFromVector _ 1 _ v@(dim->d) = Matrix { irows = 1, icols = d, xdat = v, xRow = d, xCol = 1 }
 matrixFromVector _ _ 1 v@(dim->d) = Matrix { irows = d, icols = 1, xdat = v, xRow = 1, xCol = d }
 matrixFromVector o r c v
@@ -387,18 +398,21 @@ subMatrix (r0,c0) (rt,ct) m
 
 --------------------------------------------------------------------------
 
+maxZ :: (Num t1, Ord t1, Foldable t) => t t1 -> t1
 maxZ xs = if minimum xs == 0 then 0 else maximum xs
 
+conformMs :: Element t => [Matrix t] -> [Matrix t]
 conformMs ms = map (conformMTo (r,c)) ms
   where
     r = maxZ (map rows ms)
     c = maxZ (map cols ms)
 
-
+conformVs :: Element t => [Vector t] -> [Vector t]
 conformVs vs = map (conformVTo n) vs
   where
     n = maxZ (map dim vs)
 
+conformMTo :: Element t => (Int, Int) -> Matrix t -> Matrix t
 conformMTo (r,c) m
     | size m == (r,c) = m
     | size m == (1,1) = matrixFromVector RowMajor r c (constantD (m@@>(0,0)) (r*c))
@@ -406,18 +420,24 @@ conformMTo (r,c) m
     | size m == (1,c) = repRows r m
     | otherwise = error $ "matrix " ++ shSize m ++ " cannot be expanded to " ++ shDim (r,c)
 
+conformVTo :: Element t => Int -> Vector t -> Vector t
 conformVTo n v
     | dim v == n = v
     | dim v == 1 = constantD (v@>0) n
     | otherwise = error $ "vector of dim=" ++ show (dim v) ++ " cannot be expanded to dim=" ++ show n
 
+repRows :: Element t => Int -> Matrix t -> Matrix t
 repRows n x = fromRows (replicate n (flatten x))
+repCols :: Element t => Int -> Matrix t -> Matrix t
 repCols n x = fromColumns (replicate n (flatten x))
 
+shSize :: Matrix t -> [Char]
 shSize = shDim . size
 
+shDim :: (Show a, Show a1) => (a1, a) -> [Char]
 shDim (r,c) = "(" ++ show r ++"x"++ show c ++")"
 
+emptyM :: Storable t => Int -> Int -> Matrix t
 emptyM r c = matrixFromVector RowMajor r c (fromList[])
 
 ----------------------------------------------------------------------
@@ -432,6 +452,11 @@ instance (Storable t, NFData t) => NFData (Matrix t)
 
 ---------------------------------------------------------------
 
+extractAux :: (Eq t3, Eq t2, TransArray c, Storable a, Storable t1,
+                Storable t, Num t3, Num t2, Integral t1, Integral t)
+           => (t3 -> t2 -> CInt -> Ptr t1 -> CInt -> Ptr t
+                  -> Trans c (CInt -> CInt -> CInt -> CInt -> Ptr a -> IO CInt))
+           -> MatrixOrder -> c -> t3 -> Vector t1 -> t2 -> Vector t -> IO (Matrix a)
 extractAux f ord m moder vr modec vc = do
     let nr = if moder == 0 then fromIntegral $ vr@>1 - vr@>0 + 1 else dim vr
         nc = if modec == 0 then fromIntegral $ vc@>1 - vc@>0 + 1 else dim vc
@@ -451,6 +476,9 @@ foreign import ccall unsafe "extractL" c_extractL :: Extr Z
 
 ---------------------------------------------------------------
 
+setRectAux :: (TransArray c1, TransArray c)
+           => (CInt -> CInt -> Trans c1 (Trans c (IO CInt)))
+           -> Int -> Int -> c1 -> c -> IO ()
 setRectAux f i j m r = (m #! r) (f (fi i) (fi j)) #|"setRect"
 
 type SetRect x = I -> I -> x ::> x::> Ok
@@ -464,19 +492,29 @@ foreign import ccall unsafe "setRectL" c_setRectL :: SetRect Z
 
 --------------------------------------------------------------------------------
 
+sortG :: (Storable t, Storable a)
+      => (CInt -> Ptr t -> CInt -> Ptr a -> IO CInt) -> Vector t -> Vector a
 sortG f v = unsafePerformIO $ do
     r <- createVector (dim v)
     (v #! r) f #|"sortG"
     return r
 
+sortIdxD :: Vector Double -> Vector CInt
 sortIdxD = sortG c_sort_indexD
+sortIdxF :: Vector Float -> Vector CInt
 sortIdxF = sortG c_sort_indexF
+sortIdxI :: Vector CInt -> Vector CInt
 sortIdxI = sortG c_sort_indexI
+sortIdxL :: Vector Z -> Vector I
 sortIdxL = sortG c_sort_indexL
 
+sortValD :: Vector Double -> Vector Double
 sortValD = sortG c_sort_valD
+sortValF :: Vector Float -> Vector Float
 sortValF = sortG c_sort_valF
+sortValI :: Vector CInt -> Vector CInt
 sortValI = sortG c_sort_valI
+sortValL :: Vector Z -> Vector Z
 sortValL = sortG c_sort_valL
 
 foreign import ccall unsafe "sort_indexD" c_sort_indexD :: CV Double (CV CInt (IO CInt))
@@ -491,14 +529,21 @@ foreign import ccall unsafe "sort_valuesL" c_sort_valL :: Z :> Z :> Ok
 
 --------------------------------------------------------------------------------
 
+compareG :: (TransArray c, Storable t, Storable a)
+         => Trans c (CInt -> Ptr t -> CInt -> Ptr a -> IO CInt)
+         -> c -> Vector t -> Vector a
 compareG f u v = unsafePerformIO $ do
     r <- createVector (dim v)
     (u # v #! r) f #|"compareG"
     return r
 
+compareD :: Vector Double -> Vector Double -> Vector CInt
 compareD = compareG c_compareD
+compareF :: Vector Float -> Vector Float -> Vector CInt
 compareF = compareG c_compareF
+compareI :: Vector CInt -> Vector CInt -> Vector CInt
 compareI = compareG c_compareI
+compareL :: Vector Z -> Vector Z -> Vector CInt
 compareL = compareG c_compareL
 
 foreign import ccall unsafe "compareD" c_compareD :: CV Double (CV Double (CV CInt (IO CInt)))
@@ -508,16 +553,33 @@ foreign import ccall unsafe "compareL" c_compareL :: Z :> Z :> I :> Ok
 
 --------------------------------------------------------------------------------
 
+selectG :: (TransArray c, TransArray c1, TransArray c2, Storable t, Storable a)
+        => Trans c2 (Trans c1 (CInt -> Ptr t -> Trans c (CInt -> Ptr a -> IO CInt)))
+        -> c2 -> c1 -> Vector t -> c -> Vector a
 selectG f c u v w = unsafePerformIO $ do
     r <- createVector (dim v)
     (c # u # v # w #! r) f #|"selectG"
     return r
 
+selectD :: Vector CInt -> Vector Double -> Vector Double -> Vector Double -> Vector Double
 selectD = selectG c_selectD
+selectF :: Vector CInt -> Vector Float -> Vector Float -> Vector Float -> Vector Float
 selectF = selectG c_selectF
+selectI :: Vector CInt -> Vector CInt -> Vector CInt -> Vector CInt -> Vector CInt
 selectI = selectG c_selectI
+selectL :: Vector CInt -> Vector Z -> Vector Z -> Vector Z -> Vector Z
 selectL = selectG c_selectL
+selectC :: Vector CInt
+        -> Vector (Complex Double)
+        -> Vector (Complex Double)
+        -> Vector (Complex Double)
+        -> Vector (Complex Double)
 selectC = selectG c_selectC
+selectQ :: Vector CInt
+        -> Vector (Complex Float)
+        -> Vector (Complex Float)
+        -> Vector (Complex Float)
+        -> Vector (Complex Float)
 selectQ = selectG c_selectQ
 
 type Sel x = CV CInt (CV x (CV x (CV x (CV x (IO CInt)))))
@@ -531,16 +593,29 @@ foreign import ccall unsafe "chooseL" c_selectL :: Sel Z
 
 ---------------------------------------------------------------------------
 
+remapG :: (TransArray c, TransArray c1, Storable t, Storable a)
+       => (CInt -> CInt -> CInt -> CInt -> Ptr t
+                -> Trans c1 (Trans c (CInt -> CInt -> CInt -> CInt -> Ptr a -> IO CInt)))
+       -> Matrix t -> c1 -> c -> Matrix a
 remapG f i j m = unsafePerformIO $ do
     r <- createMatrix RowMajor (rows i) (cols i)
     (i # j # m #! r) f #|"remapG"
     return r
 
+remapD :: Matrix CInt -> Matrix CInt -> Matrix Double -> Matrix Double
 remapD = remapG c_remapD
+remapF :: Matrix CInt -> Matrix CInt -> Matrix Float -> Matrix Float
 remapF = remapG c_remapF
+remapI :: Matrix CInt -> Matrix CInt -> Matrix CInt -> Matrix CInt
 remapI = remapG c_remapI
+remapL :: Matrix CInt -> Matrix CInt -> Matrix Z -> Matrix Z
 remapL = remapG c_remapL
+remapC :: Matrix CInt
+       -> Matrix CInt
+       -> Matrix (Complex Double)
+       -> Matrix (Complex Double)
 remapC = remapG c_remapC
+remapQ :: Matrix CInt -> Matrix CInt -> Matrix (Complex Float) -> Matrix (Complex Float)
 remapQ = remapG c_remapQ
 
 type Rem x = OM CInt (OM CInt (OM x (OM x (IO CInt))))
@@ -554,6 +629,9 @@ foreign import ccall unsafe "remapL" c_remapL :: Rem Z
 
 --------------------------------------------------------------------------------
 
+rowOpAux :: (TransArray c, Storable a) =>
+            (CInt -> Ptr a -> CInt -> CInt -> CInt -> CInt -> Trans c (IO CInt))
+         -> Int -> a -> Int -> Int -> Int -> Int -> c -> IO ()
 rowOpAux f c x i1 i2 j1 j2 m = do
     px <- newArray [x]
     (m # id) (f (fi c) px (fi i1) (fi i2) (fi j1) (fi j2)) #|"rowOp"
@@ -572,6 +650,9 @@ foreign import ccall unsafe "rowop_mod_int64_t" c_rowOpML :: Z -> RowOp Z
 
 --------------------------------------------------------------------------------
 
+gemmg :: (TransArray c1, TransArray c, TransArray c2, TransArray c3)
+      => Trans c3 (Trans c2 (Trans c1 (Trans c (IO CInt))))
+      -> c3 -> c2 -> c1 -> c -> IO ()
 gemmg f v m1 m2 m3 = (v # m1 # m2 #! m3) f #|"gemmg"
 
 type Tgemm x = x :> x ::> x ::> x ::> Ok
@@ -587,6 +668,10 @@ foreign import ccall unsafe "gemm_mod_int64_t" c_gemmML :: Z -> Tgemm Z
 
 --------------------------------------------------------------------------------
 
+reorderAux :: (TransArray c, Storable t, Storable a1, Storable t1, Storable a) =>
+              (CInt -> Ptr a -> CInt -> Ptr t1
+                    -> Trans c (CInt -> Ptr t -> CInt -> Ptr a1 -> IO CInt))
+           -> Vector t1 -> c -> Vector t -> Vector a1
 reorderAux f s d v = unsafePerformIO $ do
     k <- createVector (dim s)
     r <- createVector (dim v)
diff --git a/packages/base/src/Internal/Modular.hs b/packages/base/src/Internal/Modular.hs
index 9d51444..eb0c5a8 100644
--- a/packages/base/src/Internal/Modular.hs
+++ b/packages/base/src/Internal/Modular.hs
@@ -13,6 +13,9 @@
 {-# LANGUAGE TypeFamilies  #-}
 {-# LANGUAGE TypeOperators #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+{-# OPTIONS_GHC -fno-warn-missing-methods #-}
+
 {- |
 Module      :  Internal.Modular
 Copyright   :  (c) Alberto Ruiz 2015
diff --git a/packages/base/src/Internal/Numeric.hs b/packages/base/src/Internal/Numeric.hs
index c9ef0c5..216f142 100644
--- a/packages/base/src/Internal/Numeric.hs
+++ b/packages/base/src/Internal/Numeric.hs
@@ -5,6 +5,8 @@
 {-# LANGUAGE FunctionalDependencies #-}
 {-# LANGUAGE UndecidableInstances #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Data.Packed.Internal.Numeric
diff --git a/packages/base/src/Internal/ST.hs b/packages/base/src/Internal/ST.hs
index 544c9e4..7d54e6d 100644
--- a/packages/base/src/Internal/ST.hs
+++ b/packages/base/src/Internal/ST.hs
@@ -81,6 +81,8 @@ unsafeFreezeVector :: (Storable t) => STVector s t -> ST s (Vector t)
 unsafeFreezeVector (STVector x) = unsafeIOToST . return $ x
 
 {-# INLINE safeIndexV #-}
+safeIndexV :: Storable t2
+           => (STVector s t2 -> Int -> t) -> STVector t1 t2 -> Int -> t
 safeIndexV f (STVector v) k
     | k < 0 || k>= dim v = error $ "out of range error in vector (dim="
                                    ++show (dim v)++", pos="++show k++")"
@@ -150,9 +152,12 @@ unsafeFreezeMatrix (STMatrix x) = unsafeIOToST . return $ x
 freezeMatrix :: (Element t) => STMatrix s t -> ST s (Matrix t)
 freezeMatrix m = liftSTMatrix id m
 
+cloneMatrix :: Element t => Matrix t -> IO (Matrix t)
 cloneMatrix m = copy (orderOf m) m
 
 {-# INLINE safeIndexM #-}
+safeIndexM :: (STMatrix s t2 -> Int -> Int -> t)
+           -> STMatrix t1 t2 -> Int -> Int -> t
 safeIndexM f (STMatrix m) r c
     | r<0 || r>=rows m ||
       c<0 || c>=cols m = error $ "out of range error in matrix (size="
@@ -184,6 +189,7 @@ data ColRange = AllCols
               | Col Int
               | FromCol Int
 
+getColRange :: Int -> ColRange -> (Int, Int)
 getColRange c AllCols = (0,c-1)
 getColRange c (ColRange a b) = (a `mod` c, b `mod` c)
 getColRange c (Col a) = (a `mod` c, a `mod` c)
@@ -194,6 +200,7 @@ data RowRange = AllRows
               | Row Int
               | FromRow Int
 
+getRowRange :: Int -> RowRange -> (Int, Int)
 getRowRange r AllRows = (0,r-1)
 getRowRange r (RowRange a b) = (a `mod` r, b `mod` r)
 getRowRange r (Row a) = (a `mod` r, a `mod` r)
@@ -223,6 +230,7 @@ rowOper (SWAP i1 i2 r) (STMatrix m) = unsafeIOToST $ rowOp 2 0 i1' i2' j1 j2 m
     i2' = i2 `mod` (rows m)
 
 
+extractMatrix :: Element a => STMatrix t a -> RowRange -> ColRange -> ST s (Matrix a)
 extractMatrix (STMatrix m) rr rc = unsafeIOToST (extractR (orderOf m) m 0 (idxs[i1,i2]) 0 (idxs[j1,j2]))
   where
     (i1,i2) = getRowRange (rows m) rr
@@ -231,6 +239,7 @@ extractMatrix (STMatrix m) rr rc = unsafeIOToST (extractR (orderOf m) m 0 (idxs[
 -- | r0 c0 height width
 data Slice s t = Slice (STMatrix s t) Int Int Int Int
 
+slice :: Element a => Slice t a -> Matrix a
 slice (Slice (STMatrix m) r0 c0 nr nc) = subMatrix (r0,c0) (nr,nc) m
 
 gemmm :: Element t => t -> Slice s t -> t -> Slice s t -> Slice s t -> ST s ()
@@ -238,7 +247,7 @@ gemmm beta (slice->r) alpha (slice->a) (slice->b) = res
   where
     res = unsafeIOToST (gemm v a b r)
     v = fromList [alpha,beta]
-    
+
 
 mutable :: Element t => (forall s . (Int, Int) -> STMatrix s t -> ST s u) -> Matrix t -> (Matrix t,u)
 mutable f a = runST $ do
@@ -246,4 +255,3 @@ mutable f a = runST $ do
    info <- f (rows a, cols a) x
    r <- unsafeFreezeMatrix x
    return (r,info)
-
diff --git a/packages/base/src/Internal/Sparse.hs b/packages/base/src/Internal/Sparse.hs
index 1ff3f57..6233b03 100644
--- a/packages/base/src/Internal/Sparse.hs
+++ b/packages/base/src/Internal/Sparse.hs
@@ -2,6 +2,8 @@
 {-# LANGUAGE MultiParamTypeClasses #-}
 {-# LANGUAGE FlexibleInstances #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 module Internal.Sparse(
     GMatrix(..), CSR(..), mkCSR, fromCSR,
     mkSparse, mkDiagR, mkDense,
diff --git a/packages/base/src/Internal/Static.hs b/packages/base/src/Internal/Static.hs
index f9dfff0..6ef1350 100644
--- a/packages/base/src/Internal/Static.hs
+++ b/packages/base/src/Internal/Static.hs
@@ -15,6 +15,8 @@
 {-# LANGUAGE BangPatterns #-}
 {-# LANGUAGE DeriveGeneric #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 {- |
 Module      :  Internal.Static
 Copyright   :  (c) Alberto Ruiz 2006-14
diff --git a/packages/base/src/Internal/Util.hs b/packages/base/src/Internal/Util.hs
index 8c8a31e..def7cc3 100644
--- a/packages/base/src/Internal/Util.hs
+++ b/packages/base/src/Internal/Util.hs
@@ -6,6 +6,8 @@
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE ViewPatterns #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+{-# OPTIONS_GHC -fno-warn-orphans #-}
 
 -----------------------------------------------------------------------------
 {- |
diff --git a/packages/base/src/Internal/Vector.hs b/packages/base/src/Internal/Vector.hs
index 67d0416..dedb822 100644
--- a/packages/base/src/Internal/Vector.hs
+++ b/packages/base/src/Internal/Vector.hs
@@ -1,6 +1,7 @@
 {-# LANGUAGE MagicHash, UnboxedTuples, BangPatterns, FlexibleContexts #-}
 {-# LANGUAGE TypeSynonymInstances #-}
 
+{-# OPTIONS_GHC -fno-warn-orphans #-}
 
 -- |
 -- Module      :  Internal.Vector
@@ -40,6 +41,7 @@ import qualified Data.Vector.Storable as Vector
 import Data.Vector.Storable(Vector, fromList, unsafeToForeignPtr, unsafeFromForeignPtr, unsafeWith)
 
 import Data.Binary
+import Data.Binary.Put
 import Control.Monad(replicateM)
 import qualified Data.ByteString.Internal as BS
 import Data.Vector.Storable.Internal(updPtr)
@@ -92,6 +94,7 @@ createVector n = do
 
 -}
 
+safeRead :: Storable a => Vector a -> (Ptr a -> IO c) -> c
 safeRead v = inlinePerformIO . unsafeWith v
 {-# INLINE safeRead #-}
 
@@ -283,11 +286,13 @@ foldVectorWithIndex f x v = unsafePerformIO $
         go (dim v -1) x
 {-# INLINE foldVectorWithIndex #-}
 
+foldLoop :: (Int -> t -> t) -> t -> Int -> t
 foldLoop f s0 d = go (d - 1) s0
      where
        go 0 s = f (0::Int) s
        go !j !s = go (j - 1) (f j s)
 
+foldVectorG :: Storable t1 => (Int -> (Int -> t1) -> t -> t) -> t -> Vector t1 -> t
 foldVectorG f s0 v = foldLoop g s0 (dim v)
     where g !k !s = f k (safeRead v . flip peekElemOff) s
           {-# INLINE g #-} -- Thanks to Ryan Ingram (http://permalink.gmane.org/gmane.comp.lang.haskell.cafe/46479)
@@ -390,8 +395,10 @@ chunks d = let c = d `div` chunk
                m = d `mod` chunk
            in if m /= 0 then reverse (m:(replicate c chunk)) else (replicate c chunk)
 
+putVector :: (Storable t, Binary t) => Vector t -> Data.Binary.Put.PutM ()
 putVector v = mapM_ put $! toList v
 
+getVector :: (Storable a, Binary a) => Int -> Get (Vector a)
 getVector d = do
               xs <- replicateM d get
               return $! fromList xs
diff --git a/packages/base/src/Internal/Vectorized.hs b/packages/base/src/Internal/Vectorized.hs
index a410bb2..c00c324 100644
--- a/packages/base/src/Internal/Vectorized.hs
+++ b/packages/base/src/Internal/Vectorized.hs
@@ -28,12 +28,15 @@ import System.IO.Unsafe(unsafePerformIO)
 import Control.Monad(when)
 
 infixr 1 #
+(#) :: TransArray c => c -> (b -> IO r) -> TransRaw c b -> IO r
 a # b = applyRaw a b
 {-# INLINE (#) #-}
 
+(#!) :: (TransArray c, TransArray c1) => c1 -> c -> TransRaw c1 (TransRaw c (IO r)) -> IO r
 a #! b = a # b # id
 {-# INLINE (#!) #-}
 
+fromei :: Enum a => a -> CInt
 fromei x = fromIntegral (fromEnum x) :: CInt
 
 data FunCodeV = Sin
@@ -100,10 +103,20 @@ sumQ = sumg c_sumQ
 sumC :: Vector (Complex Double) -> Complex Double
 sumC = sumg c_sumC
 
+sumI :: ( TransRaw c (CInt -> Ptr a -> IO CInt) ~ (CInt -> Ptr I -> I :> Ok)
+        , TransArray c
+        , Storable a
+        )
+     => I -> c -> a
 sumI m = sumg (c_sumI m)
 
+sumL :: ( TransRaw c (CInt -> Ptr a -> IO CInt) ~ (CInt -> Ptr Z -> Z :> Ok)
+        , TransArray c
+        , Storable a
+        ) => Z -> c -> a
 sumL m = sumg (c_sumL m)
 
+sumg :: (TransArray c, Storable a) => TransRaw c (CInt -> Ptr a -> IO CInt) -> c -> a
 sumg f x = unsafePerformIO $ do
     r <- createVector 1
     (x #! r) f #| "sum"
@@ -140,6 +153,8 @@ prodI = prodg . c_prodI
 prodL :: Z-> Vector Z -> Z
 prodL = prodg . c_prodL
 
+prodg :: (TransArray c, Storable a)
+      => TransRaw c (CInt -> Ptr a -> IO CInt) -> c -> a
 prodg f x = unsafePerformIO $ do
     r <- createVector 1
     (x #! r) f #| "prod"
@@ -155,16 +170,25 @@ foreign import ccall unsafe "prodL" c_prodL :: Z -> TVV Z
 
 ------------------------------------------------------------------
 
+toScalarAux :: (Enum a, TransArray c, Storable a1)
+            => (CInt -> TransRaw c (CInt -> Ptr a1 -> IO CInt)) -> a -> c -> a1
 toScalarAux fun code v = unsafePerformIO $ do
     r <- createVector 1
     (v #! r) (fun (fromei code)) #|"toScalarAux"
     return (r @> 0)
 
+
+vectorMapAux :: (Enum a, Storable t, Storable a1)
+             => (CInt -> CInt -> Ptr t -> CInt -> Ptr a1 -> IO CInt)
+             -> a -> Vector t -> Vector a1
 vectorMapAux fun code v = unsafePerformIO $ do
     r <- createVector (dim v)
     (v #! r) (fun (fromei code)) #|"vectorMapAux"
     return r
 
+vectorMapValAux :: (Enum a, Storable a2, Storable t, Storable a1)
+                => (CInt -> Ptr a2 -> CInt -> Ptr t -> CInt -> Ptr a1 -> IO CInt)
+                -> a -> a2 -> Vector t -> Vector a1
 vectorMapValAux fun code val v = unsafePerformIO $ do
     r <- createVector (dim v)
     pval <- newArray [val]
@@ -172,6 +196,9 @@ vectorMapValAux fun code val v = unsafePerformIO $ do
     free pval
     return r
 
+vectorZipAux :: (Enum a, TransArray c, Storable t, Storable a1)
+             => (CInt -> CInt -> Ptr t -> TransRaw c (CInt -> Ptr a1 -> IO CInt))
+             -> a -> Vector t -> c -> Vector a1
 vectorZipAux fun code u v = unsafePerformIO $ do
     r <- createVector (dim u)
     (u # v #! r) (fun (fromei code)) #|"vectorZipAux"
@@ -378,6 +405,7 @@ foreign import ccall unsafe "random_vector" c_random_vector :: CInt -> CInt -> D
 
 --------------------------------------------------------------------------------
 
+roundVector :: Vector Double -> Vector Double
 roundVector v = unsafePerformIO $ do
     r <- createVector (dim v)
     (v #! r) c_round_vector #|"roundVector"
@@ -432,6 +460,8 @@ long2intV :: Vector Z -> Vector I
 long2intV = tog c_long2int
 
 
+tog :: (Storable t, Storable a)
+    => (CInt -> Ptr t -> CInt -> Ptr a -> IO CInt) -> Vector t -> Vector a
 tog f v = unsafePerformIO $ do
     r <- createVector (dim v)
     (v #! r) f #|"tog"
@@ -451,6 +481,8 @@ foreign import ccall unsafe "long2int"    c_long2int    :: Z :> I :> Ok
 
 ---------------------------------------------------------------
 
+stepg :: (Storable t, Storable a)
+      => (CInt -> Ptr t -> CInt -> Ptr a -> IO CInt) -> Vector t -> Vector a
 stepg f v = unsafePerformIO $ do
     r <- createVector (dim v)
     (v #! r) f #|"step"
@@ -476,6 +508,8 @@ foreign import ccall unsafe "stepL" c_stepL :: TVV Z
 
 --------------------------------------------------------------------------------
 
+conjugateAux :: (Storable t, Storable a)
+             => (CInt -> Ptr t -> CInt -> Ptr a -> IO CInt) -> Vector t -> Vector a
 conjugateAux fun x = unsafePerformIO $ do
     v <- createVector (dim x)
     (x #! v) fun #|"conjugateAux"
@@ -501,6 +535,8 @@ cloneVector v = do
 
 --------------------------------------------------------------------------------
 
+constantAux :: (Storable a1, Storable a)
+            => (Ptr a1 -> CInt -> Ptr a -> IO CInt) -> a1 -> Int -> Vector a
 constantAux fun x n = unsafePerformIO $ do
     v <- createVector n
     px <- newArray [x]
diff --git a/packages/base/src/Numeric/LinearAlgebra.hs b/packages/base/src/Numeric/LinearAlgebra.hs
index 73d4a13..970c77e 100644
--- a/packages/base/src/Numeric/LinearAlgebra.hs
+++ b/packages/base/src/Numeric/LinearAlgebra.hs
@@ -1,6 +1,8 @@
 {-# LANGUAGE CPP #-}
 {-# LANGUAGE FlexibleContexts #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+
 -----------------------------------------------------------------------------
 {- |
 Module      :  Numeric.LinearAlgebra
diff --git a/packages/base/src/Numeric/LinearAlgebra/HMatrix.hs b/packages/base/src/Numeric/LinearAlgebra/HMatrix.hs
index 3a84645..57e5cf1 100644
--- a/packages/base/src/Numeric/LinearAlgebra/HMatrix.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/HMatrix.hs
@@ -28,7 +28,9 @@ infixr 8 <·>
 (<·>) :: Numeric t => Vector t -> Vector t -> t
 (<·>) = dot
 
+app :: Numeric t => Matrix t -> Vector t -> Vector t
 app m v = m #> v
 
+mul :: Numeric t => Matrix t -> Matrix t -> Matrix t
 mul a b = a <> b
 
diff --git a/packages/base/src/Numeric/LinearAlgebra/Static.hs b/packages/base/src/Numeric/LinearAlgebra/Static.hs
index e328904..2e05c90 100644
--- a/packages/base/src/Numeric/LinearAlgebra/Static.hs
+++ b/packages/base/src/Numeric/LinearAlgebra/Static.hs
@@ -14,6 +14,8 @@
 {-# LANGUAGE GADTs #-}
 {-# LANGUAGE TypeFamilies #-}
 
+{-# OPTIONS_GHC -fno-warn-missing-signatures #-}
+{-# OPTIONS_GHC -fno-warn-orphans #-}
 
 {- |
 Module      :  Numeric.LinearAlgebra.Static
diff --git a/packages/base/src/Numeric/Matrix.hs b/packages/base/src/Numeric/Matrix.hs
index 06da150..6e3db61 100644
--- a/packages/base/src/Numeric/Matrix.hs
+++ b/packages/base/src/Numeric/Matrix.hs
@@ -4,6 +4,8 @@
 {-# LANGUAGE UndecidableInstances #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
 
+{-# OPTIONS_GHC -fno-warn-orphans #-}
+
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Numeric.Matrix
@@ -35,6 +37,7 @@ import Data.List(partition)
 import qualified Data.Foldable as F
 import qualified Data.Semigroup as S
 import Internal.Chain
+import Foreign.Storable(Storable)
 
 
 -------------------------------------------------------------------
@@ -80,8 +83,16 @@ instance (Floating a, Container Vector a, Floating (Vector a), Fractional (Matri
 
 --------------------------------------------------------------------------------
 
+isScalar :: Matrix t -> Bool
 isScalar m = rows m == 1 && cols m == 1
 
+adaptScalarM :: (Foreign.Storable.Storable t1, Foreign.Storable.Storable t2)
+             => (t1 -> Matrix t2 -> t)
+             -> (Matrix t1 -> Matrix t2 -> t)
+             -> (Matrix t1 -> t2 -> t)
+             -> Matrix t1
+             -> Matrix t2
+             -> t
 adaptScalarM f1 f2 f3 x y
     | isScalar x = f1   (x @@>(0,0) ) y
     | isScalar y = f3 x (y @@>(0,0) )
@@ -96,7 +107,7 @@ instance (Container Vector t, Eq t, Num (Vector t), Product t) => M.Monoid (Matr
   where
     mempty = 1
     mappend = adaptScalarM scale mXm (flip scale)
-    
+
     mconcat xs = work (partition isScalar xs)
       where
         work (ss,[]) = product ss
@@ -106,4 +117,3 @@ instance (Container Vector t, Eq t, Num (Vector t), Product t) => M.Monoid (Matr
             | otherwise              = scale x00 m
           where
             x00 = x @@> (0,0)
-
diff --git a/packages/base/src/Numeric/Vector.hs b/packages/base/src/Numeric/Vector.hs
index 017196c..1e5877d 100644
--- a/packages/base/src/Numeric/Vector.hs
+++ b/packages/base/src/Numeric/Vector.hs
@@ -3,6 +3,9 @@
 {-# LANGUAGE FlexibleInstances #-}
 {-# LANGUAGE UndecidableInstances #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
+
+{-# OPTIONS_GHC -fno-warn-orphans #-}
+
 -----------------------------------------------------------------------------
 -- |
 -- Module      :  Numeric.Vector
@@ -14,7 +17,7 @@
 --
 -- Provides instances of standard classes 'Show', 'Read', 'Eq',
 -- 'Num', 'Fractional',  and 'Floating' for 'Vector'.
--- 
+--
 -----------------------------------------------------------------------------
 
 module Numeric.Vector () where
@@ -23,9 +26,17 @@ import Internal.Vectorized
 import Internal.Vector
 import Internal.Numeric
 import Internal.Conversion
+import Foreign.Storable(Storable)
 
 -------------------------------------------------------------------
 
+adaptScalar :: (Foreign.Storable.Storable t1, Foreign.Storable.Storable t2)
+            => (t1 -> Vector t2 -> t)
+            -> (Vector t1 -> Vector t2 -> t)
+            -> (Vector t1 -> t2 -> t)
+            -> Vector t1
+            -> Vector t2
+            -> t
 adaptScalar f1 f2 f3 x y
     | dim x == 1 = f1   (x@>0) y
     | dim y == 1 = f3 x (y@>0)
@@ -172,4 +183,3 @@ instance Floating (Vector (Complex Float)) where
     sqrt  = vectorMapQ Sqrt
     (**)  = adaptScalar (vectorMapValQ PowSV) (vectorZipQ Pow) (flip (vectorMapValQ PowVS))
     pi    = fromList [pi]
-