diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/base.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/databases.scm | 94 | ||||
| -rw-r--r-- | gnu/packages/linux.scm | 16 | ||||
| -rw-r--r-- | gnu/packages/package-management.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch | 55 |
6 files changed, 168 insertions, 19 deletions
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 972ffeeecb..bc745351af 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -883,12 +883,12 @@ the 'share/locale' sub-directory of this package.") ,@(package-arguments glibc)))) (substitute-keyword-arguments args ((#:phases phases) - `(alist-replace - 'build - (lambda* (#:key outputs #:allow-other-keys) - (zero? (system* "make" "localedata/install-locales" - "-j" (number->string (parallel-job-count))))) - (alist-delete 'install ,phases))) + `(modify-phases ,phases + (replace 'build + (lambda _ + (zero? (system* "make" "localedata/install-locales" + "-j" (number->string (parallel-job-count)))))) + (delete 'install))) ((#:configure-flags flags) `(append ,flags ;; Use $(libdir)/locale/X.Y as is the case by default. diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 95632e2f9c..f2f3b807c3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6161,7 +6161,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.4.4") + (version "2.5.0") (source (origin (method url-fetch) @@ -6171,7 +6171,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1d8a4gjwaqdv57krlr80x18mg5py1bbdiqs5m0jdn38filc9z40k")) + "1k8wf3qns4mqrsizywbkqcasqjw000m4drxsag3qd7390pwvf9kz")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 2afc94c965..ae138796ff 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -69,8 +69,10 @@ #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) + #:use-module (gnu packages serialization) #:use-module (gnu packages tcl) #:use-module (gnu packages tls) + #:use-module (gnu packages valgrind) #:use-module (gnu packages xml) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -355,6 +357,98 @@ and generic API, and was originally intended for use with dynamic web applications.") (license license:bsd-3))) +(define-public mongodb + (package + (name "mongodb") + (version "3.4.9") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mongodb/mongo/archive/r" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0gidwyvh3bdwmk2pccgkqkaln4ysgn8iwa7ihjzllsq0rdg95045")) + (patches + (list + (search-patch "mongodb-support-unknown-linux-distributions.patch"))))) + (build-system gnu-build-system) + (inputs + `(("openssl" ,openssl) + ("pcre" ,pcre) + ("yaml-cpp" ,yaml-cpp) + ("zlib" ,zlib) + ("snappy" ,snappy) + ("boost" ,boost))) + (native-inputs + `(("scons" ,scons) + ("python" ,python-2) + ("valgrind" ,valgrind) + ("perl" ,perl))) + (arguments + `(#:phases + (let ((common-options + `(;; "--use-system-tcmalloc" TODO: Missing gperftools + "--use-system-pcre" + ;; TODO + ;; build/opt/mongo/db/fts/unicode/string.o failed: Error 1 + ;; --use-system-boost + "--use-system-snappy" + "--use-system-zlib" + "--use-system-valgrind" + ;; "--use-system-stemmer" TODO: Missing relevant package + "--use-system-yaml" + "--disable-warnings-as-errors" + ,(format #f "--jobs=~a" (parallel-job-count)) + "--ssl"))) + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase + (add-after 'unpack 'scons-propagate-environment + (lambda _ + ;; Modify the SConstruct file to arrange for + ;; environment variables to be propagated. + (substitute* "SConstruct" + (("^env = Environment\\(") + "env = Environment(ENV=os.environ, ")) + #t)) + (add-after 'unpack 'create-version-file + (lambda _ + (call-with-output-file "version.json" + (lambda (port) + (display ,(simple-format #f "{ + \"version\": \"~A\" +}" version) port))) + #t)) + (replace 'build + (lambda _ + (zero? (apply system* + `("scons" + ,@common-options + "mongod" "mongo" "mongos"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (or (not tests?) + (zero? (apply system* + `("scons" + ,@common-options + "dbtest" "unittests")))))) + (replace 'install + (lambda _ + (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))) + (install-file "mongod" bin) + (install-file "mongos" bin) + (install-file "mongo" bin)) + #t)))))) + (home-page "https://www.mongodb.org/") + (synopsis "High performance and high availability document database") + (description + "Mongo is a high-performance, high availability, schema-free +document-oriented database. A key goal of MongoDB is to bridge the gap +between key/value stores (which are fast and highly scalable) and traditional +RDBMS systems (which are deep in functionality).") + (license (list license:agpl3 + ;; Some parts are licensed under the Apache License + license:asl2.0)))) + (define-public mysql (package (name "mysql") diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 585b41a376..1445089a58 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -367,8 +367,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) -(define %linux-libre-version "4.13.4") -(define %linux-libre-hash "028dww9c6x22mvd0jd87bmibqiz5lrsyynrbzka18gh39sk0v8j7") +(define %linux-libre-version "4.13.5") +(define %linux-libre-hash "1crw61x7qrijhpw0azxf9b3fra0cxq87ncni2419p0s23jfdpc4m") (define-public linux-libre (make-linux-libre %linux-libre-version @@ -377,14 +377,14 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.52" - "0zl1z13r4gg6r2sbx8mrif2cnjkjlfrswiap7wzb22jyfnlyj5nb" + (make-linux-libre "4.9.53" + "174i53cd090akbjq34dj4z00h1nyfmy3sl3fk6svcmbx6h34381h" %intel-compatible-systems #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.89" - "1bw1cma8hxcj6wi8znc4nvw1p6dlc1lgciqak6n6ijn53xdd242h" + (make-linux-libre "4.4.90" + "1sqzvz8yrcf99vhphkxp1wm2agq6q9nshxb1mkypspm8rhm11vhw" %intel-compatible-systems #:configuration-file kernel-config)) @@ -3163,7 +3163,7 @@ and copy/paste text in the console and in xterm.") (define-public btrfs-progs (package (name "btrfs-progs") - (version "4.13.1") + (version "4.13.2") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/kernel/" @@ -3171,7 +3171,7 @@ and copy/paste text in the console and in xterm.") "btrfs-progs-v" version ".tar.xz")) (sha256 (base32 - "1clavvrlkswgicqsm2yfsxqw04lsn8dra0db84jqm6j2apz80kz0")))) + "1ga8jk2hkaxpm17z3gdfrpq0i62kqpv2wm5yzbzmsj862cgk7ivm")))) (build-system gnu-build-system) (outputs '("out" "static")) ; static versions of the binaries in "out" diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 197a7a0142..91e44ec6fe 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -78,8 +78,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "0.13.0") - (commit "a9468b422b6df2349a3f4d1451c9302c3d77011b") - (revision 6)) + (commit "8b920d707ed07a3251227f77526cf875d86a4417") + (revision 7)) (package (name "guix") @@ -95,7 +95,7 @@ (commit commit))) (sha256 (base32 - "0bv323yp657x0a2aa2z5pp5541hjqmn908kh9jqlbdw5gpx9vg3d")) + "15phwcadkw44mr4hnv1dxzzw9an6x7sbdfzwy4iciqw6y2wckncd")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments diff --git a/gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch b/gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch new file mode 100644 index 0000000000..6057ebeb08 --- /dev/null +++ b/gnu/packages/patches/mongodb-support-unknown-linux-distributions.patch @@ -0,0 +1,55 @@ +From e724bb7018a482640c4f194f88b554af2c59d76e Mon Sep 17 00:00:00 2001 +From: Mark Benvenuto <mark.benvenuto@mongodb.com> +Date: Wed, 20 Sep 2017 11:50:02 -0400 +Subject: [PATCH] SERVER-30857 Support unknown Linux distributions + +--- + src/mongo/rpc/metadata/client_metadata.cpp | 6 ------ + src/mongo/util/processinfo_linux.cpp | 9 ++++++--- + 2 files changed, 6 insertions(+), 9 deletions(-) + +diff --git a/src/mongo/rpc/metadata/client_metadata.cpp b/src/mongo/rpc/metadata/client_metadata.cpp +index 845a315dd74..a959a4e31e9 100644 +--- a/src/mongo/rpc/metadata/client_metadata.cpp ++++ b/src/mongo/rpc/metadata/client_metadata.cpp +@@ -302,9 +302,6 @@ void ClientMetadata::serializePrivate(StringData driverName, + StringData osArchitecture, + StringData osVersion, + BSONObjBuilder* builder) { +- invariant(!driverName.empty() && !driverVersion.empty() && !osType.empty() && !osName.empty() && +- !osArchitecture.empty() && !osVersion.empty()); +- + BSONObjBuilder metaObjBuilder(builder->subobjStart(kMetadataDocumentName)); + + { +@@ -347,9 +344,6 @@ Status ClientMetadata::serializePrivate(StringData driverName, + StringData osVersion, + StringData appName, + BSONObjBuilder* builder) { +- invariant(!driverName.empty() && !driverVersion.empty() && !osType.empty() && !osName.empty() && +- !osArchitecture.empty() && !osVersion.empty()); +- + if (appName.size() > kMaxApplicationNameByteLength) { + return Status(ErrorCodes::ClientMetadataAppNameTooLarge, + str::stream() << "The '" << kApplication << "." << kName +diff --git a/src/mongo/util/processinfo_linux.cpp b/src/mongo/util/processinfo_linux.cpp +index c3debf377bd..c2813b026b0 100644 +--- a/src/mongo/util/processinfo_linux.cpp ++++ b/src/mongo/util/processinfo_linux.cpp +@@ -376,10 +376,13 @@ class LinuxSysHelper { + if ((nl = name.find('\n', nl)) != string::npos) + // stop at first newline + name.erase(nl); +- // no standard format for name and version. use kernel version +- version = "Kernel "; +- version += LinuxSysHelper::readLineFromFile("/proc/sys/kernel/osrelease"); ++ } else { ++ name = "unknown"; + } ++ ++ // There is no standard format for name and version so use the kernel version. ++ version = "Kernel "; ++ version += LinuxSysHelper::readLineFromFile("/proc/sys/kernel/osrelease"); + } + + /** |