Merge branch 'master' into core-updates

1 files changed, 25 insertions, 21 deletions

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index aca26edad4..0762037ee3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -639,14 +639,14 @@ curves, Cox models, and parametric accelerated failure time models.")
 (define-public r-bit
   (package
     (name "r-bit")
-    (version "1.1-12")
+    (version "1.1-13")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "bit" version))
        (sha256
         (base32
-         "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
+         "1yhpwvfkxpb773h8khjzyamqxl2jn7pjjmxjfawq626hhds8fsh6"))))
     (build-system r-build-system)
     (home-page "http://ff.r-forge.r-project.org")
     (synopsis "Class for vectors of 1-bit booleans")
@@ -965,13 +965,13 @@ transliteration, concatenation, date-time formatting and parsing, etc.")
 (define-public r-stringr
   (package
     (name "r-stringr")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "stringr" version))
        (sha256
-        (base32 "07dvfbkhv8gk6l32j43jvxpmqlhqp0mdby406h5a3bsc6k94ic13"))))
+        (base32 "0hq3ybz7clnifi5wdm2s6p2i0kzljdkv26blg6yphng472h8x2vs"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-glue" ,r-glue)
@@ -1824,14 +1824,15 @@ building design matrices.")
        (uri (pypi-uri "statsmodels" version))
        (sha256
         (base32
-         "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
-       (patches (search-patches "python-statsmodels-fix-tests.patch"))))
+         "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     `(;; The test suite is very large and rather brittle.  Tests often fail
+       ;; because of minor changes in dependencies that upstream hasn't fixed
+       ;; in a new release.
+       #:tests? #f
+       #:phases
        (modify-phases %standard-phases
-         ;; tests must be run after installation
-         (delete 'check)
          (add-after 'unpack 'set-matplotlib-backend-to-agg
           (lambda _
             ;; Set the matplotlib backend to Agg to avoid problems using the
@@ -1843,14 +1844,17 @@ building design matrices.")
                (string-append "import matplotlib;matplotlib.use('Agg');"
                               line)))
             #t))
-         (add-after 'install 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Make installed package available for running the tests
-             (add-installed-pythonpath inputs outputs)
-             (with-directory-excursion "/tmp"
-               (zero? (system* "nosetests"
-                               "--stop"
-                               "-v" "statsmodels"))))))))
+         ;; FIXME: This is a bug in version 0.8 since the upgrade to scipy 1.0.
+         ;; See https://github.com/statsmodels/statsmodels/issues/3931
+         ;; This has been fixed in version 0.9.
+         (add-after 'unpack 'patch-for-scipy
+           (lambda _
+             (substitute* "statsmodels/discrete/discrete_model.py"
+               (("return stats.chisqprob" match)
+                (string-append
+                 "stats.chisqprob = lambda chisq, df: stats.chi2.sf(chisq, df);"
+                 match)))
+             #t)))))
     (propagated-inputs
      `(("python-numpy" ,python-numpy)
        ("python-scipy" ,python-scipy)
@@ -2423,13 +2427,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
     (name "r-plotrix")
-    (version "3.7")
+    (version "3.7-1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "plotrix" version))
               (sha256
                (base32
-                "0rw81n9p3d2i03b4pgcfj5blryc94f29bm9a4j9bnp5h8qjj6pry"))))
+                "16p6d2dna6dah7rg2xknhyy65jkfn0zzivx1nnfxhd4f5q0v87w2"))))
     (build-system r-build-system)
     (home-page "https://cran.r-project.org/web/packages/plotrix")
     (synopsis "Various plotting functions")
@@ -5195,14 +5199,14 @@ classification and regression models.")
 (define-public r-rcppprogress
   (package
     (name "r-rcppprogress")
-    (version "0.4")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "RcppProgress" version))
        (sha256
         (base32
-         "09ayw6d69i0lplmaj5md25p5hn1nmiyp6a4sh60v93nrrs1cq7iv"))))
+         "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
     (properties `((upstream-name . "RcppProgress")))
     (build-system r-build-system)
     (propagated-inputs