gnu: r-maldiquant: Move to (gnu packages cran).

[jackhill/guix/guix.git] / gnu / packages / databases.scm

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index ca320f2..fe99785 100644 (file)
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -43,6 +43,7 @@
 ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
+;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -613,14 +614,13 @@ RDBMS systems (which are deep in functionality).")
 (define-public mycli
   (package
     (name "mycli")
-    (version "1.21.1")
+    (version "1.22.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "mycli" version))
         (sha256
-          (base32
-            "1q9p0yik9cpvpxjs048anvhicfcna84mpl7axv9bwgr48w40lqwg"))))
+          (base32 "1lq2x95553vdmhw13cxcgsd2g2i32izhsb7hxd4m1iwf9b3msbpv"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f))                    ; tests expect a running MySQL
@@ -1973,14 +1973,14 @@ sets, bitmaps and hyperloglogs.")
 (define-public kyotocabinet
   (package
     (name "kyotocabinet")
-    (version "1.2.77")
+    (version "1.2.78")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://fallabs.com/kyotocabinet/pkg/"
                                   "kyotocabinet-" version ".tar.gz"))
               (sha256
                (base32
-                "1rlx4307adbzd842b4npq6cwlw8h010ingxaz3qz1ijc70lr72an"))))
+                "1bxkf9kmcavq9rqridb8mvmrk3hj4447ffi24m2admsbm61n6k29"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -2149,7 +2149,7 @@ database.")
 (define-public lmdb
   (package
     (name "lmdb")
-    (version "0.9.25")
+    (version "0.9.26")
     (source
      (origin
        (method git-fetch)
@@ -2158,7 +2158,7 @@ database.")
              (commit (string-append "LMDB_" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0i60zlca8r6fib23gdgl4c80gxpx24772ggpvz94yr7zaai4k11w"))))
+        (base32 "0323xwb2rqyrr9vr6gbxc2kl89drhqw0ifmyh9pg9qgqmymyhxdx"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -2450,13 +2450,13 @@ etc., and an SQL engine for performing simple SQL queries.")
 (define-public python-lmdb
   (package
     (name "python-lmdb")
-    (version "0.98")
+    (version "0.99")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lmdb" version))
               (sha256
                (base32
-                "027pgbdhhdcbwj53vrzr6a60gjhmz4s75gl3180fd4q8pwlbq986"))
+                "12fwlzfd82471ss9xzbqwcqc6f5miy51y72y2yya9j5cm9589szr"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled lmdb source files.
@@ -2549,7 +2549,19 @@ implementation for Python.")
        ;; TODO: Removing the libsrc/zlib source directory breaks the build.
        ;; This indicates that the internal zlib code may still be used.
        #:configure-flags '("--without-internal-zlib"
-                           "--with-readline")))
+                           "--with-readline"
+                           "--enable-static=no")
+       #:phases
+       (modify-phases %standard-phases
+         ;; Even with "--enable-static=no", "libvirtuoso-t.a" is left in
+         ;; the build output.  The following phase removes it.
+         (add-after 'install 'remove-static-libs
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+               (for-each (lambda (file)
+                           (delete-file (string-append lib "/" file)))
+                         '("libvirtuoso-t.a"
+                           "libvirtuoso-t.la"))))))))
     (inputs
      `(("openssl" ,openssl-1.0)
        ("net-tools" ,net-tools)
@@ -2703,15 +2715,13 @@ You might also want to install the following optional dependencies:
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
-       (patches (search-patches "python-alembic-exceptions-cause.patch"))
        (sha256
-        (base32
-         "0a4hzn76csgbf1px4f5vfm256byvjrqkgi9869nkcjrwjn35c6kr"))))
+        (base32 "1gsdrzx9h7wfva200qvvsc9sn4w79mk2vs0bbnzjhxi1jw2b0nh3"))))
     (build-system python-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
@@ -2887,13 +2897,13 @@ designed to be easy and intuitive to use.")
 (define-public python-psycopg2
   (package
     (name "python-psycopg2")
-    (version "2.8.4")
+    (version "2.8.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psycopg2" version))
        (sha256
-        (base32 "1djvh98pi4hjd8rxbq8qzc63bg8v78k33yg6pl99wak61b6fb67q"))))
+        (base32 "06081jk9srkd4ra9j8b93x9ld3a2yxsbsf5bbbcivbm1yx065m7p"))))
     (build-system python-build-system)
     (arguments
      ;; Tests would require a postgresql database "psycopg2_test"
@@ -3106,13 +3116,13 @@ is designed to have a low barrier to entry.")
 (define-public python-sqlparse
   (package
     (name "python-sqlparse")
-    (version "0.2.4")
+    (version "0.3.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "sqlparse" version))
               (sha256
                (base32
-                "1v3xh0bkfhb262dbndgzhivpnhdwavdzz8jjhx9vx0xbrx2880nf"))))
+                "0j652a6z7bdf6c77aczfn8m8b2nsr1bcqq48wzghf8vi6wvj0qp1"))))
     (build-system python-build-system)
     (arguments
      `(#:phases