gnu: r-rhdf5lib: Use G-expressions and fix test instead of disabling it.

* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Use G-expressions;
fix library version check instead of disabling the test.

Change-Id: I78e8cfd9d2588517b0911dde5fc8aa53d4f67892

1 files changed, 57 insertions, 52 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 651b81d911..9ccd609721 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -25662,59 +25662,64 @@ block processing.")
         . ("r-mockery"))))
     (build-system r-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'do-not-use-bundled-hdf5
-           (lambda* (#:key inputs #:allow-other-keys)
-             (for-each delete-file '("configure" "configure.ac"))
-             (substitute* "R/zzz.R"
-               (("return\\(links\\)") "return(\" -lz\")"))
-             (with-directory-excursion "src"
-               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
-               (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
-                            "hdf5")
-               ;; Remove timestamp and host system information to make
-               ;; the build reproducible.
-               (substitute* "hdf5/src/libhdf5.settings.in"
-                 (("Configured on: @CONFIG_DATE@")
-                  "Configured on: Guix")
-                 (("Uname information:.*")
-                  "Uname information: Linux\n")
-                 ;; Remove unnecessary store reference.
-                 (("C Compiler:.*")
-                  "C Compiler: GCC\n"))
-               (rename-file "hdf5/src/libhdf5.settings.in"
-                            "hdf5/src/libhdf5.settings")
-               (rename-file "Makevars.in" "Makevars")
-               (substitute* "Makevars"
-                 (("@BUILD_HDF5@") "")
-                 (("@COPY_SZIP@") "")
-                 (("HDF5_CXX_LIB=.*")
-                  (string-append "HDF5_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
-                 (("HDF5_LIB=.*")
-                  (string-append "HDF5_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
-                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
-                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
-                 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
-                 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
-                 (("HDF5_HL_LIB=.*")
-                  (string-append "HDF5_HL_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
-                 (("HDF5_HL_CXX_LIB=.*")
-                  (string-append "HDF5_HL_CXX_LIB="
-                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
-                 (("@ZLIB_LIB_PATH@") "-lz")
-                 (("@ZLIB_INCLUDE_PATH@") "")
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'do-not-use-bundled-hdf5
+            (lambda* (#:key inputs #:allow-other-keys)
+              (for-each delete-file '("configure" "configure.ac"))
+              (substitute* "R/zzz.R"
+                (("return\\(links\\)") "return(\" -lz\")"))
+              (with-directory-excursion "src"
+                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+                (rename-file (string-append "hdf5-" #$(package-version hdf5-1.10))
+                             "hdf5")
+                ;; Remove timestamp and host system information to make
+                ;; the build reproducible.
+                (substitute* "hdf5/src/libhdf5.settings.in"
+                  (("Configured on: @CONFIG_DATE@")
+                   "Configured on: Guix")
+                  (("Uname information:.*")
+                   "Uname information: Linux\n")
+                  ;; Remove unnecessary store reference.
+                  (("C Compiler:.*")
+                   "C Compiler: GCC\n"))
+                (rename-file "hdf5/src/libhdf5.settings.in"
+                             "hdf5/src/libhdf5.settings")
+                (rename-file "Makevars.in" "Makevars")
+                (substitute* "Makevars"
+                  (("@BUILD_HDF5@") "")
+                  (("@COPY_SZIP@") "")
+                  (("HDF5_CXX_LIB=.*")
+                   (string-append "HDF5_CXX_LIB="
+                                  #$(this-package-input "hdf5") "/lib/libhdf5_cpp.a\n"))
+                  (("HDF5_LIB=.*")
+                   (string-append "HDF5_LIB="
+                                  #$(this-package-input "hdf5") "/lib/libhdf5.a\n"))
+                  (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                  (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                  (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
+                  (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
+                  (("HDF5_HL_LIB=.*")
+                   (string-append "HDF5_HL_LIB="
+                                  #$(this-package-input "hdf5")
+                                  "/lib/libhdf5_hl.a\n"))
+                  (("HDF5_HL_CXX_LIB=.*")
+                   (string-append "HDF5_HL_CXX_LIB="
+                                  #$(this-package-input "hdf5")
+                                  "/lib/libhdf5_hl_cpp.a\n"))
+                  (("@ZLIB_LIB_PATH@") "-lz")
+                  (("@ZLIB_INCLUDE_PATH@") "")
 
-                 ;; szip is non-free software
-                 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
-                 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))
-         (add-after 'unpack 'disable-bad-test
-           (lambda _
-             ;; This tests for a specific minor version of HDF5.
-             (delete-file "inst/tinytest/test_library_version.R"))))))
+                  ;; szip is non-free software
+                  (("cp \"\\$\\{SZIP_LIB\\}.*") "")
+                  (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))
+          (add-after 'unpack 'fix-bad-test
+            (lambda _
+              ;; This tests for a specific minor version of HDF5.
+              (substitute* "inst/tinytest/test_library_version.R"
+                (("1.10.7")
+                 #$(package-version (this-package-input "hdf5")))))))))
     (propagated-inputs
      (list hdf5-1.10 zlib))
     (native-inputs