diff --git a/CHANGELOG.md b/CHANGELOG.md --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # Change Log +## 1.0.1 - 2023-05-22 +* Populate `R_LIBS` environment variable when starting R (#393) +* Map backslashes to forwardslashes in temp file names under Windows (#399) +* Relax upper bounds for GHC 9.6 +* Fix imports for compatibility with mtl-2.3 (#414) + ## 1.0.0 - 2022-11-11 * Support for R >= 4.2. * Support for GHC 9 and GHC 9.2. diff --git a/inline-r.cabal b/inline-r.cabal --- a/inline-r.cabal +++ b/inline-r.cabal @@ -1,225 +1,252 @@ -name: inline-r -version: 1.0.0 -license: BSD3 -license-file: LICENSE -copyright: Copyright (c) 2013-2015 Amgen, Inc. - Copyright (c) 2015-2020 Tweag I/O Limited. -author: Mathieu Boespflug, Facundo Dominguez, Alexander Vershilov -maintainer: Mathieu Boespflug -build-type: Simple -Category: FFI -Synopsis: Seamlessly call R from Haskell and vice versa. No FFI required. +cabal-version: 2.2 +name: inline-r +version: 1.0.1 +license: BSD-3-Clause +license-file: LICENSE +author: Mathieu Boespflug, Facundo Dominguez, Alexander Vershilov +maintainer: Mathieu Boespflug +build-type: Simple +Category: FFI +Synopsis: Seamlessly call R from Haskell and vice versa. No FFI required. description: - For up to date Haddock documentation, please see . - -homepage: https://tweag.github.io/HaskellR -cabal-version: >=1.10 +homepage: https://tweag.github.io/HaskellR -extra-source-files: CHANGELOG.md - cbits/missing_r.h - tests/shootout/binarytrees.R - tests/shootout/fasta.R - tests/shootout/knucleotide.R - tests/shootout/fastaredux.R - tests/shootout/mandelbrot.R - tests/shootout/mandelbrot-noout.R - tests/shootout/nbody.R - tests/shootout/pidigits.R - tests/shootout/regexdna.R - tests/shootout/reversecomplement.R - tests/shootout/spectralnorm.R - tests/shootout/spectralnorm-math.R - tests/shootout/fannkuchredux.R - tests/R/fib.R - tests/R/fib-benchmark.R - ./R/collectAntis.R -extra-tmp-files: inline-r.buildinfo +extra-source-files: + CHANGELOG.md + cbits/missing_r.h + tests/shootout/binarytrees.R + tests/shootout/fasta.R + tests/shootout/knucleotide.R + tests/shootout/fastaredux.R + tests/shootout/mandelbrot.R + tests/shootout/mandelbrot-noout.R + tests/shootout/nbody.R + tests/shootout/pidigits.R + tests/shootout/regexdna.R + tests/shootout/reversecomplement.R + tests/shootout/spectralnorm.R + tests/shootout/spectralnorm-math.R + tests/shootout/fannkuchredux.R + tests/R/fib.R + tests/R/fib-benchmark.R + ./R/collectAntis.R +extra-tmp-files: inline-r.buildinfo source-repository head - type: git + type: git location: git://github.com/tweag/HaskellR.git subdir: inline-r library - exposed-modules: Control.Memory.Region - Data.Vector.SEXP - Data.Vector.SEXP.Base - Data.Vector.SEXP.Mutable - Foreign.R - Foreign.R.Constraints - Foreign.R.Context - Foreign.R.Embedded - Foreign.R.Encoding - Foreign.R.Error - Foreign.R.Internal - Foreign.R.Parse - Foreign.R.Type - H.Prelude - H.Prelude.Interactive - Language.R - Language.R.Debug - Language.R.GC - Language.R.Globals - Language.R.HExp - Language.R.Instance - Language.R.Internal - Language.R.Internal.FunWrappers - Language.R.Internal.FunWrappers.TH - Language.R.Literal - Language.R.Matcher - Language.R.QQ + exposed-modules: + Control.Memory.Region + Data.Vector.SEXP + Data.Vector.SEXP.Base + Data.Vector.SEXP.Mutable + Foreign.R + Foreign.R.Constraints + Foreign.R.Context + Foreign.R.Embedded + Foreign.R.Encoding + Foreign.R.Error + Foreign.R.Internal + Foreign.R.Parse + Foreign.R.Type + H.Prelude + H.Prelude.Interactive + Language.R + Language.R.Debug + Language.R.GC + Language.R.Globals + Language.R.HExp + Language.R.Instance + Language.R.Internal + Language.R.Internal.FunWrappers + Language.R.Internal.FunWrappers.TH + Language.R.Literal + Language.R.Matcher + Language.R.QQ if !os(windows) - exposed-modules: Foreign.R.EventLoop - Language.R.Event - other-modules: Control.Monad.R.Class - Control.Monad.R.Internal - Data.Vector.SEXP.Mutable.Internal - Internal.Error - build-depends: base >=4.7 && <5 - , aeson >=0.6 && <2.2 - , bytestring >=0.10 && <0.12 - , containers >=0.5 && <0.7 - , data-default-class >=0.1.2.0 && <0.2 - , deepseq >=1.3 && <1.5 - , exceptions >=0.6 && <1.1 - , heredoc >=0.2 && <0.3 - , mtl >=2.1 && <2.3 - , pretty >=1.1 && <1.2 - , primitive >=0.5 && <0.8 - , process >=1.2 && <1.7 - , reflection >=2 && <2.2 - , setenv >=0.1.1 && <0.2 - , template-haskell >=2.8 && <2.20 - , temporary >=1.2 && <1.4 - , text >=0.11 && <2.1 - , th-lift >=0.6 && <0.9 - , th-orphans >=0.8 && <0.14 - , transformers >=0.3 && <0.6 - , vector >=0.10 && <0.14 - if impl(ghc < 8.2.1) + exposed-modules: + Foreign.R.EventLoop + Language.R.Event + other-modules: + Control.Monad.R.Class + Control.Monad.R.Internal + Data.Vector.SEXP.Mutable.Internal + Internal.Error + build-depends: + base >=4.7 && <5, + aeson >=0.6 && <2.2, + bytestring >=0.10 && <0.12, + containers >=0.5 && <0.7, + data-default-class >=0.1.2.0 && <0.2, + deepseq >=1.3 && <1.5, + exceptions >=0.6 && <1.1, + heredoc >=0.2 && <0.3, + inline-c >=0.6 && <0.10, + mtl >=2.1 && <2.4, + pretty >=1.1 && <1.2, + primitive >=0.5 && <0.9, + process >=1.2 && <1.7, + reflection >=2 && <2.2, + setenv >=0.1.1 && <0.2, + template-haskell >=2.8 && <2.21, + temporary >=1.2 && <1.4, + text >=0.11 && <2.1, + th-lift >=0.6 && <0.9, + th-orphans >=0.8 && <0.14, + transformers >=0.3 && <0.7, + vector >=0.10 && <0.14, + if impl(ghc <9) build-depends: - inline-c >=0.5.6.1 && <0.6 + singletons >=2.7 && <3, else build-depends: - inline-c >=0.6 && <0.10 - if impl(ghc <9) - build-depends: singletons >=2.7 && <3 - else - build-depends: - singletons >=3 && <3.1, - singletons-th >=3 && <3.2 - hs-source-dirs: src - includes: cbits/missing_r.h - c-sources: cbits/missing_r.c - include-dirs: cbits - default-language: Haskell2010 - other-extensions: CPP - ForeignFunctionInterface - build-tools: hsc2hs + singletons >=3 && <3.1, + singletons-th >=3 && <3.3, + hs-source-dirs: src + includes: cbits/missing_r.h + c-sources: cbits/missing_r.c + include-dirs: cbits + default-language: Haskell2010 + other-extensions: + CPP + ForeignFunctionInterface if os(windows) - extra-libraries: R + extra-libraries: R else - build-depends: unix >= 2.6 && <2.8 + build-depends: unix >= 2.6 && <2.9 pkgconfig-depends: libR >= 3.0 -- XXX -fcontext-stack=32 required on GHC >= 7.8 to allow foreign -- export function -wrappers of high arities. - ghc-options: -freduction-depth=32 + ghc-options: -freduction-depth=32 --- We don't use ticks for promoted constructors, because we use --- promoted constructors heavily and because they confuse hsc2hs. - ghc-options: -Wall -fno-warn-unticked-promoted-constructors + ghc-options: -Wall -fno-warn-unticked-promoted-constructors test-suite tests - main-is: tests.hs - type: exitcode-stdio-1.0 - build-depends: inline-r - , base >=4.6 && <5 - , bytestring >=0.10 && <0.12 - , directory >=1.2 && <1.4 - , filepath >=1.3 && <1.5 - , heredoc >=0.2 && <0.3 - , ieee754 >=0.7 && <0.9 - , mtl >=2.0 && <2.3 - , process >=1.2 && <1.7 - , quickcheck-assertions >=0.1.1 && <0.4 - , singletons >=0.10 && <3.1 - , strict >=0.3.2 && <0.5 - , tasty >=0.11 && <1.5 - , tasty-expected-failure >=0.11 && <0.13 - , tasty-golden >=2.3 && <2.4 - , tasty-hunit >=0.4.1 && <0.11 - , tasty-quickcheck >=0.4.1 && <0.11 - , temporary >=1.2 && <1.4 - , text >=0.11 && <2.1 - , vector >=0.12.3.1 && <0.14 + main-is: tests.hs + type: exitcode-stdio-1.0 + build-depends: + inline-r, + base >=4.6 && <5, + bytestring >=0.10 && <0.12, + directory >=1.2 && <1.4, + filepath >=1.3 && <1.5, + heredoc >=0.2 && <0.3, + ieee754 >=0.7 && <0.9, + mtl >=2.0 && <2.4, + process >=1.2 && <1.7, + quickcheck-assertions >=0.1.1 && <0.4, + singletons >=0.10 && <3.1, + strict >=0.3.2 && <0.6, + tasty >=0.11 && <1.5, + tasty-expected-failure >=0.11 && <0.13, + tasty-golden >=2.3 && <2.4, + tasty-hunit >=0.4.1 && <0.11, + tasty-quickcheck >=0.4.1 && <0.11, + temporary >=1.2 && <1.4, + text >=0.11 && <2.1, + vector >=0.12.3.1 && <0.14, if !os(windows) - build-depends: unix >=2.5 && <2.8 - other-modules: Test.GC - Test.FunPtr - Test.Constraints - Test.Event - Test.Regions - Test.Vector - Test.Matcher - ghc-options: -Wall -threaded - hs-source-dirs: tests - default-language: Haskell2010 + build-depends: unix >=2.5 && <2.9, + other-modules: + Test.GC + Test.FunPtr + Test.Constraints + Test.Event + Test.Regions + Test.Vector + Test.Matcher + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 test-suite test-qq - main-is: test-qq.hs - type: exitcode-stdio-1.0 - build-depends: inline-r - , base >=4.6 && <5 - , mtl >=2.0 && <2.3 - , process >=1.2 && <1.7 - , tasty-hunit >=0.4.1 && <0.11 - , singletons >=0.9 && <3.1 - , text >=0.11 && <2.1 - ghc-options: -Wall -threaded - hs-source-dirs: tests - default-language: Haskell2010 + main-is: test-qq.hs + type: exitcode-stdio-1.0 + build-depends: + inline-r, + base >=4.6 && <5, + mtl >=2.0 && <2.4, + process >=1.2 && <1.7, + tasty-hunit >=0.4.1 && <0.11, + singletons >=0.9 && <3.1, + text >=0.11 && <2.1, + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 test-suite test-shootout - main-is: test-shootout.hs - type: exitcode-stdio-1.0 - other-modules: Test.Scripts - build-depends: inline-r - , base >=4.6 && <5 - , filepath >=1.3 && <1.5 - , process >=1.2 && <1.7 - , silently >=1.2 && <1.3 - , tasty >=0.3 && <1.5 - , tasty-hunit >=0.4.1 && <0.11 - , template-haskell >=2.8 && <2.20 - ghc-options: -Wall -threaded - hs-source-dirs: tests - default-language: Haskell2010 + main-is: test-shootout.hs + type: exitcode-stdio-1.0 + other-modules: Test.Scripts + build-depends: + inline-r, + base >=4.6 && <5, + filepath >=1.3 && <1.5, + process >=1.2 && <1.7, + silently >=1.2 && <1.3, + tasty >=0.3 && <1.5, + tasty-hunit >=0.4.1 && <0.11, + template-haskell >=2.8 && <2.21, + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 if os(windows) - buildable: False + buildable: False +test-suite test-env1 + main-is: test-env1.hs + type: exitcode-stdio-1.0 + build-depends: + inline-r, + base >=4.6 && <5, + tasty >=0.3 && <1.5, + tasty-hunit >=0.4.1 && <0.11, + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 + +test-suite test-env2 + main-is: test-env2.hs + type: exitcode-stdio-1.0 + build-depends: + inline-r, + base >=4.6 && <5, + tasty >=0.3 && <1.5, + tasty-hunit >=0.4.1 && <0.11, + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 + benchmark bench-qq - main-is: bench-qq.hs - type: exitcode-stdio-1.0 - build-depends: inline-r - , base >=4.6 && <5 - , criterion >=0.8 && <1.7 - , filepath >=1.3 && <1.5 - , process >=1.2 && <1.7 - , template-haskell >=2.8 && <2.20 - ghc-options: -Wall -threaded - hs-source-dirs: tests - default-language: Haskell2010 + main-is: bench-qq.hs + type: exitcode-stdio-1.0 + build-depends: + inline-r, + base >=4.6 && <5, + criterion >=0.8 && <1.7, + filepath >=1.3 && <1.5, + process >=1.2 && <1.7, + template-haskell >=2.8 && <2.21, + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 benchmark bench-hexp - main-is: bench-hexp.hs - type: exitcode-stdio-1.0 - build-depends: inline-r - , base >=4.6 && <5 - , criterion >=0.8 && <1.7 - , primitive >=0.5 && <0.8 - , vector >=0.10 && <0.14 - , singletons >=2.7 && <3.1 - ghc-options: -Wall -threaded - hs-source-dirs: tests - default-language: Haskell2010 + main-is: bench-hexp.hs + type: exitcode-stdio-1.0 + build-depends: + inline-r, + base >=4.6 && <5, + criterion >=0.8 && <1.7, + primitive >=0.5 && <0.9, + vector >=0.10 && <0.14, + singletons >=2.7 && <3.1, + ghc-options: -Wall -threaded + hs-source-dirs: tests + default-language: Haskell2010 diff --git a/src/Language/R/Instance.hs b/src/Language/R/Instance.hs --- a/src/Language/R/Instance.hs +++ b/src/Language/R/Instance.hs @@ -37,6 +37,7 @@ , finalize ) where +import Control.Monad ((<=<), unless, when, zipWithM_) import Control.Monad.Primitive (PrimMonad(..)) import Control.Monad.R.Class import Control.Monad.ST.Unsafe (unsafeSTToIO) @@ -189,12 +190,17 @@ defaultConfig :: Config defaultConfig = Config (Last Nothing) ["--vanilla", "--silent"] (Last (Just False)) --- | Populate environment with @R_HOME@ variable if it does not exist. +-- | Populate environment with @R_HOME@ variable if it does not exist and +-- @R_LIBS@ variable if it doesn't exist either. populateEnv :: IO () populateEnv = do mh <- lookupEnv "R_HOME" when (mh == Nothing) $ setEnv "R_HOME" =<< fmap (head . lines) (readProcess "R" ["-e","cat(R.home())","--quiet","--slave"] "") + + ml <- lookupEnv "R_LIBS" + when (ml == Nothing) $ + setEnv "R_LIBS" =<< fmap (head . lines) (readProcess "R" ["-e","cat(.libPaths(),sep=if (.Platform$OS.type == \"unix\") \":\" else \";\")","--quiet","--slave"] "") -- | A static address that survives GHCi reloadings which indicates -- whether R has been initialized. diff --git a/src/Language/R/QQ.hs b/src/Language/R/QQ.hs --- a/src/Language/R/QQ.hs +++ b/src/Language/R/QQ.hs @@ -108,6 +108,15 @@ chop :: String -> String chop name = take (length name - length antiSuffix) name +-- | Map backwards slashes to forward slashes. +#ifdef mingw32_HOST_OS +fixwinslash :: String -> String +fixwinslash str = let + repl '\\' = '/' + repl c = c + in map repl str +#endif + -- | Find all occurences of antiquotations. -- -- This function works by parsing the user's R code in a separate @@ -130,11 +139,21 @@ Temp.withSystemTempFile "inline-r-.R" $ \input_file input_fh -> do hPutStr input_fh input hClose input_fh - (code, stdout, stderr) <- readProcessWithExitCode "R" ["--slave"] $ + (code, stdout, stderr) <- readProcessWithExitCode "R" ["--slave"] -- Note: --slave was recently renamed to --no-echo. --slave still works -- but is no longer documented. Using the old option name for now just -- in case the user have an older (pre-2020) version of R. - "input_file <- \"" ++ input_file ++ "\"\n" ++ + -- + -- Change backslashes to forward slashes in tempFile names + -- under Windows. Windows is tolerant of this Unixification, but + -- Unix systems (and R) are less tolerant of naked backslashes + -- outside of valid escape sequences. For example, + -- str <- "C:\Users\joe" is invalid in R. +#ifdef mingw32_HOST_OS + $ "input_file <- \"" ++ (fixwinslash input_file) ++ "\"\n" ++ +#else + $ "input_file <- \"" ++ input_file ++ "\"\n" ++ +#endif [Heredoc.there|R/collectAntis.R|] return $ case code of ExitSuccess -> Right $ words stdout diff --git a/tests/test-env1.hs b/tests/test-env1.hs new file mode 100644 --- /dev/null +++ b/tests/test-env1.hs @@ -0,0 +1,17 @@ +module Main where + +import qualified Language.R.Instance as R + +import System.Environment +import Test.Tasty +import Test.Tasty.HUnit + +tests :: TestTree +tests = testCase "initialize respects R_LIBS env" $ do + let somePath = "bogusfasdfassomePath" + setEnv "R_LIBS" somePath + _ <- R.initialize R.defaultConfig + (somePath @=?) =<< getEnv "R_LIBS" + +main :: IO () +main = defaultMain tests diff --git a/tests/test-env2.hs b/tests/test-env2.hs new file mode 100644 --- /dev/null +++ b/tests/test-env2.hs @@ -0,0 +1,20 @@ +{-# LANGUAGE QuasiQuotes #-} +module Main where + +import H.Prelude as H +import qualified Language.R.Instance as R + +import System.Environment.Blank as BlankEnv +import Test.Tasty +import Test.Tasty.HUnit + +tests :: TestTree +tests = testCase "blank R_LIBS does not affect R's stdlib" $ do + -- use an explcitly blank env R_LIBS="", see `System.Environment.setEnv` + BlankEnv.setEnv "R_LIBS" "" True + _ <- R.initialize R.defaultConfig + ("TRUE" @=?) =<< runRegion + (fromSomeSEXP <$> [r| deparse(.libPaths() == normalizePath(.Library,winslash="/")) |] :: R s String) + +main :: IO () +main = defaultMain tests