diff options
Diffstat (limited to 'gn/packages/statistics.scm')
| -rw-r--r-- | gn/packages/statistics.scm | 133 |
1 files changed, 132 insertions, 1 deletions
diff --git a/gn/packages/statistics.scm b/gn/packages/statistics.scm index e0edd52..8e8483a 100644 --- a/gn/packages/statistics.scm +++ b/gn/packages/statistics.scm @@ -14,7 +14,18 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages statistics) - #:use-module (past packages python27)) + #:use-module (gnu packages cran) + #:use-module (past packages python27) + + ;; for python-rpy2 and dependencies + #:use-module (gnu packages python-build) + #:use-module (guix build-system pyproject); python-rpy2-rinterface + #:use-module (gnu packages libffi); python-rpy2-rinterface + #:use-module (gnu packages check); python-rpy2-rinterface + #:use-module (gnu packages compression); python-rpy2-rinterface + #:use-module (gnu packages icu4c); python-rpy2-rinterface + #:use-module (gnu packages time); python-rpy2-robjects + #:use-module (guix gexp)) (define-public r-hmisc-3 (package @@ -149,3 +160,123 @@ traits (CTL). The additional correlation information obtained can be combined with QTL information to perform de novo reconstruction of interaction networks.") (license license:gpl3))) + + +(define-public python-rpy2-rinterface + (package + (name "python-rpy2-rinterface") + (version "3.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rpy2_rinterface" version)) + (sha256 + (base32 "1hjnc4143dvcrp9m4vnxm4fs2ahiagp5lklsqp1nki341kh0samn")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-cffi + python-packaging + ;;python-backports-zoneinfo ; needed for python_version<3.9 + r-minimal)) + (native-inputs (list zlib + icu4c + libdeflate + python-cffi + python-coverage + python-packaging + python-pytest + python-pytest-cov + python-setuptools + python-wheel + r-survival)) + (home-page "https://rpy2.github.io/") + (synopsis "Low-level interface from Python to the R") + (description "Low-level interface for rpy2. rpy2 is an interface to R + running embedded in a Python process.") + (license license:gpl2))) + + +(define-public python-rpy2-robjects + (package + (name "python-rpy2-robjects") + (version "3.6.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rpy2_robjects" version)) + (sha256 + (base32 "0yn4nq26na9hzlm08vsxr050ls5nmngpyma49fpfwc9mhxc7njlk")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-jinja2 + python-packaging + python-rpy2-rinterface + ;;python-backports-zoneinfo; needed for python_version<3.9 + python-tzlocal)) + (native-inputs (list python-coverage + python-ipython + python-numpy + python-packaging + python-pandas + python-pytest + python-pytest-cov + python-setuptools + python-wheel)) + (home-page #f) + (synopsis "Python interface to the R language (embedded R)") + (description "Python interface to the R language (embedded R).") + (license #f))) + + +(define-public python-rpy2-patched + ;; TODO: Delete this after python-rpy2 is fixed upstream. + (package + (inherit python-rpy2) + (name "python-rpy2") + (version "3.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rpy2" version)) + (sha256 + (base32 "1l3paflfc2wczjms9ghaklg4bxg0c2cqh4anvlskpl4id9vsakhp")))) + (propagated-inputs + (modify-inputs (package-propagated-inputs python-rpy2) + (prepend r-minimal) + (prepend python-rpy2-rinterface) + (prepend python-rpy2-robjects))) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'fix-license-metadata + (lambda* _ + ;; Remove one field + (substitute* "./pyproject.toml" + (("license = \"GPL-2.0-or-later\"\n") + "") + ;; update remaining field to acceptable PEP 621 format + (("^license-files = .*$") + "license = {file = \"LICENSE\"}\n")))) + (delete 'check)))))) + + +(define-public r-thor + (package + (name "r-thor") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "thor" version)) + (sha256 + (base32 "1g9204n6khm1k9ifwlmhbycfp996k5c2zpcmk2aqd95iqafpaw4g")))) + (build-system r-build-system) + (propagated-inputs `(("r-r6" ,r-r6) + ("r-storr" ,r-storr))) + (native-inputs (list r-testthat r-knitr)) + (home-page "https://github.com/richfitz/thor") + (synopsis "R binding for the ‘Lightning’ database (LMDB) ") + (description + "This package is an R interface to LMDB. + LMDB is an embedded transactional key-value store and this package provides R mappings to it. + It wraps the entire LMDB interface, except for support for duplicated keys.") + (license license:openldap2.8))) |