gnu: r-genomationdata: Update to 1.10.0. - guix

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author	Ricardo Wurmus <rekado@elephly.net>	2017-11-18 09:52:27 +0100
committer	Ricardo Wurmus <rekado@elephly.net>	2017-11-18 11:18:39 +0100
commit	57dc9b58db6c80581312bf00ad982a82b9f6a407 (patch)
tree	5868533905effebdf5486e77ae16b59eef2c0c2a /gnu/packages/cook.scm
parent	9ef9c6489f805f40dcb2aae8408a7f962b4046a1 (diff)
download	guix-57dc9b58db6c80581312bf00ad982a82b9f6a407.tar.gz guix-57dc9b58db6c80581312bf00ad982a82b9f6a407.zip

gnu: r-genomationdata: Update to 1.10.0.

* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.

Diffstat (limited to 'gnu/packages/cook.scm')

0 files changed, 0 insertions, 0 deletions

put "ncurses"))) (substitute* '("lib_pypy/_dbm.py") ;; Use gdbm compat library, so we don’t need to pull ;; in bdb. (("ctypes.util.find_library\$'db'\$") (format #f "~s" (search-input-file inputs "lib/libgdbm_compat.so")))) (substitute* '("lib_pypy/_sqlite3_build.py") ;; Always use search paths (("sys\\.platform\\.startswith\$'freebsd'\$") "True") ;; Find sqlite3 (("/usr/local") (assoc-ref inputs "sqlite")) (("libname = 'sqlite3'") (format #f "libname = ~s" (search-input-file inputs "lib/libsqlite3.so.0")))) (substitute* '("lib-python/3/subprocess.py") ;; Fix shell path (("/bin/sh") (search-input-file inputs "/bin/sh"))) (substitute* '("lib-python/3/distutils/unixccompiler.py") ;; gcc-toolchain does not provide symlink cc -> gcc (("\"cc\"") "\"gcc\"")))) (add-after 'unpack 'set-source-file-times-to-1980 ;; copied from python package, required by zip testcase (lambda _ (let ((circa-1980 (* 10 366 24 60 60))) (ftw "." (lambda (file stat flag) (utime file circa-1980 circa-1980) #t))))) (replace 'build (lambda _ (with-directory-excursion "pypy/goal" ;; Build with jit optimization. (invoke "python2" "../../rpython/bin/rpython" (string-append "--make-jobs=" (number->string (parallel-job-count))) "-Ojit" "targetpypystandalone" "--allworkingmodules")) ;; Build c modules and package everything, so tests work. (with-directory-excursion "pypy/tool/release" (invoke "python2" "package.py" "--archive-name" "pypy-dist" "--builddir" (getcwd))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (if tests? (begin (setenv "HOME" "/tmp") ; test_with_pip tries to ; access ~/.cache/pip ;; Run library tests only (no interpreter unit tests). ;; This is what Gentoo does. (invoke "python" "pypy/test_all.py" "--pypy=pypy/tool/release/pypy-dist/bin/pypy3" "lib-python")) (format #t "test suite not run~%")))) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((bin-pypy3 (string-append #$output "/bin/pypy3")) (shebang-match-python "#!.+/bin/python") (shebang-pypy3 (string-append "#!" bin-pypy3)) (dist-dir "pypy/tool/release/pypy-dist")) (with-directory-excursion dist-dir ;; Delete test data. (for-each (lambda (x) (delete-file-recursively (string-append "lib/pypy3.10/" x))) '("tkinter/test" "test" "sqlite3/test" "lib2to3/tests" "idlelib/idle_test" "distutils/tests" "ctypes/test" "unittest/test")) ;; Patch shebang referencing python. (substitute* '("lib/pypy3.10/cgi.py" "lib/pypy3.10/encodings/rot_13.py") ((shebang-match-python) shebang-pypy3)) (with-fluids ((%default-port-encoding "ISO-8859-1")) (substitute* '("lib/pypy3.10/_md5.py" "lib/pypy3.10/_sha1.py") ((shebang-match-python) shebang-pypy3)))) (copy-recursively dist-dir #$output))))))) (native-inputs (list gzip nss-certs ; For ssl tests pkg-config python-2 python2-pycparser tar)) ; Required for package.py (inputs (list bzip2 expat gdbm glibc libffi ncurses openssl sqlite tcl tk xz zlib)) (home-page "https://www.pypy.org/") (synopsis "Python implementation with just-in-time compilation") (description "PyPy is a faster, alternative implementation of the Python programming language employing a just-in-time compiler. It supports most Python code natively, including C extensions.") (license (list license:expat ; pypy itself; _pytest/ license:psfl ; python standard library in lib-python/ license:asl2.0 ; dotviewer/font/ and some of lib-python/ license:gpl3+ ; ./rpython/rlib/rvmprof/src/shared/libbacktrace/dwarf2.* license:bsd-3 ; lib_pypy/cffi/_pycparser/ply/ (license:non-copyleft "http://www.unicode.org/copyright.html"))))) (define-public pypy3 (deprecated-package "pypy3" pypy))


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