* [bug#47972] [PATCH 2/6] gnu: Add snappy-with-clang6.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
@ 2021-04-23 14:31 ` Ricardo Wurmus
2021-04-23 14:31 ` [bug#47972] [PATCH 3/6] gnu: Add nanodbc-for-irods Ricardo Wurmus
` (5 subsequent siblings)
6 siblings, 0 replies; 10+ messages in thread
From: Ricardo Wurmus @ 2021-04-23 14:31 UTC (permalink / raw)
To: 47972; +Cc: Ricardo Wurmus
* gnu/packages/compression.scm (snappy-with-clang6): New variable.
---
gnu/packages/compression.scm | 37 +++++++++++++++++++++++++++++++++++-
1 file changed, 36 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 37a7d230fe..2b1dfcfab1 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2014, 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
@@ -76,6 +76,7 @@
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages gtk)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages man)
#:use-module (gnu packages maths)
#:use-module (gnu packages perl)
@@ -1132,6 +1133,40 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
100% bigger.")
(license license:asl2.0)))
+;; We need this for irods.
+(define-public snappy-with-clang6
+ (package
+ (inherit snappy)
+ (name "snappy-with-clang")
+ (arguments
+ `(#:configure-flags
+ '("-DBUILD_SHARED_LIBS=ON"
+ "-DCMAKE_CXX_COMPILER=clang++"
+ "-DCMAKE_CXX_FLAGS=-stdlib=libc++"
+ "-DCMAKE_EXE_LINKER_FLAGS=-lc++abi")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+ "/include/c++/v1")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (native-inputs
+ `(("clang" ,clang-toolchain-6)
+ ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
+ ("libcxxabi" ,libcxxabi-6)))))
+
(define-public p7zip
(package
(name "p7zip")
--
2.31.1
^ permalink raw reply related [flat|nested] 10+ messages in thread* [bug#47972] [PATCH 3/6] gnu: Add nanodbc-for-irods.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
2021-04-23 14:31 ` [bug#47972] [PATCH 2/6] gnu: Add snappy-with-clang6 Ricardo Wurmus
@ 2021-04-23 14:31 ` Ricardo Wurmus
2021-04-23 14:31 ` [bug#47972] [PATCH 4/6] gnu: Add fmt-for-irods Ricardo Wurmus
` (4 subsequent siblings)
6 siblings, 0 replies; 10+ messages in thread
From: Ricardo Wurmus @ 2021-04-23 14:31 UTC (permalink / raw)
To: 47972; +Cc: Ricardo Wurmus
* gnu/packages/databases.scm (nanodbc-for-irods): New variable.
---
gnu/packages/databases.scm | 37 +++++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index b956833557..d159c47af8 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -98,6 +98,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp)
#:use-module (gnu packages lisp-xyz)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages logging)
#:use-module (gnu packages man)
#:use-module (gnu packages maths)
@@ -2103,6 +2104,42 @@ a simpler and less verbose API for working with ODBC. Common tasks should be
easy, requiring concise and simple code.")
(license license:expat)))
+(define-public nanodbc-for-irods
+ (package
+ (inherit nanodbc)
+ (arguments
+ `(#:tests? #false
+ #:configure-flags
+ '("-DBUILD_SHARED_LIBS=ON"
+ ;; The tests require ODBC backends to be installed.
+ "-DNANODBC_DISABLE_TESTS=ON"
+ "-DCMAKE_CXX_COMPILER=clang++"
+ "-DCMAKE_CXX_FLAGS=-stdlib=libc++"
+ "-DCMAKE_EXE_LINKER_FLAGS=-lc++abi")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons (string-append (assoc-ref inputs "libcxx")
+ "/include/c++/v1")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (inputs
+ `(("unixodbc" ,unixodbc)
+ ("libcxx" ,libcxx+libcxxabi-6)
+ ("libcxxabi" ,libcxxabi-6)
+ ("clang" ,clang-6)))))
+
(define-public unqlite
(package
(name "unqlite")
--
2.31.1
^ permalink raw reply related [flat|nested] 10+ messages in thread* [bug#47972] [PATCH 4/6] gnu: Add fmt-for-irods.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
2021-04-23 14:31 ` [bug#47972] [PATCH 2/6] gnu: Add snappy-with-clang6 Ricardo Wurmus
2021-04-23 14:31 ` [bug#47972] [PATCH 3/6] gnu: Add nanodbc-for-irods Ricardo Wurmus
@ 2021-04-23 14:31 ` Ricardo Wurmus
2021-04-23 14:32 ` [bug#47972] [PATCH 5/6] gnu: Add irods Ricardo Wurmus
` (3 subsequent siblings)
6 siblings, 0 replies; 10+ messages in thread
From: Ricardo Wurmus @ 2021-04-23 14:31 UTC (permalink / raw)
To: 47972; +Cc: Ricardo Wurmus
* gnu/packages/pretty-print.scm (fmt-for-irods): New variable.
---
gnu/packages/pretty-print.scm | 55 ++++++++++++++++++++++++++++++++++-
1 file changed, 54 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm
index 4662a1e717..7e7da53599 100644
--- a/gnu/packages/pretty-print.scm
+++ b/gnu/packages/pretty-print.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -41,6 +41,7 @@
#:use-module (gnu packages gperf)
#:use-module (gnu packages groff)
#:use-module (gnu packages gv)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages lua)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -189,6 +190,58 @@ to @code{IOStreams}.")
;; The library is bsd-2, but documentation and tests include other licenses.
(license (list bsd-2 bsd-3 psfl))))
+(define-public fmt-for-irods
+ (package
+ (name "fmt-for-irods")
+ (version "6.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/fmtlib/fmt/releases/download/"
+ version "/fmt-" version ".zip"))
+ (sha256
+ (base32 "1s1hxaby5byb07rgmrk4a0q11fxhz7b42khch7sp2qx974y0yrb3"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:tests? #f ; TODO: posix-mock-test segfaults
+ #:configure-flags
+ '("-DBUILD_SHARED_LIBS=ON"
+ "-DCMAKE_CXX_COMPILER=clang++"
+ "-DCMAKE_CXX_FLAGS=-stdlib=libc++"
+ "-DCMAKE_EXE_LINKER_FLAGS=-lc++abi")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons (string-append (assoc-ref inputs "libcxx")
+ "/include/c++/v1")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (inputs
+ `(("libcxx" ,libcxx+libcxxabi-6)
+ ("libcxxabi" ,libcxxabi-6)
+ ("clang" ,clang-6)))
+ (home-page "https://fmt.dev")
+ (synopsis "Small and fast C++ formatting library")
+ (description
+ "@code{fmt} (formerly @code{cppformat}) is a formatting library for C++.
+It can be used as a safe alternative to @code{printf} or as a fast alternative
+to @code{IOStreams}.")
+ ;; The library is bsd-2, but documentation and tests include other licenses.
+ (license (list bsd-2 bsd-3 psfl))))
+
(define-public source-highlight
(package
(name "source-highlight")
--
2.31.1
^ permalink raw reply related [flat|nested] 10+ messages in thread* [bug#47972] [PATCH 5/6] gnu: Add irods.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
` (2 preceding siblings ...)
2021-04-23 14:31 ` [bug#47972] [PATCH 4/6] gnu: Add fmt-for-irods Ricardo Wurmus
@ 2021-04-23 14:32 ` Ricardo Wurmus
2021-04-23 14:32 ` [bug#47972] [PATCH 6/6] gnu: Add irods-client-icommands Ricardo Wurmus
` (2 subsequent siblings)
6 siblings, 0 replies; 10+ messages in thread
From: Ricardo Wurmus @ 2021-04-23 14:32 UTC (permalink / raw)
To: 47972; +Cc: Ricardo Wurmus
* gnu/packages/irods.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
gnu/local.mk | 1 +
gnu/packages/irods.scm | 200 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 201 insertions(+)
create mode 100644 gnu/packages/irods.scm
diff --git a/gnu/local.mk b/gnu/local.mk
index 50b11a8ca2..f18fed6fbc 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -296,6 +296,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/installers.scm \
%D%/packages/ipfs.scm \
%D%/packages/irc.scm \
+ %D%/packages/irods.scm \
%D%/packages/iso-codes.scm \
%D%/packages/jami.scm \
%D%/packages/java.scm \
diff --git a/gnu/packages/irods.scm b/gnu/packages/irods.scm
new file mode 100644
index 0000000000..75a58d97cb
--- /dev/null
+++ b/gnu/packages/irods.scm
@@ -0,0 +1,200 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages irods)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix packages)
+ #:use-module (guix download)
+ #:use-module (guix build-system cmake)
+ #:use-module (guix utils)
+ #:use-module (gnu packages)
+ #:use-module (gnu packages backup)
+ #:use-module (gnu packages boost)
+ #:use-module (gnu packages check)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages cpp)
+ #:use-module (gnu packages databases)
+ #:use-module (gnu packages gcc)
+ #:use-module (gnu packages kerberos)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages llvm)
+ #:use-module (gnu packages logging)
+ #:use-module (gnu packages networking)
+ #:use-module (gnu packages pretty-print)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages serialization)
+ #:use-module (gnu packages tls)
+ #:use-module (srfi srfi-1))
+
+(define-public irods
+ (package
+ (name "irods")
+ (version "4.2.8")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/irods/irods/releases/download/"
+ version "/irods-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0ny54c3r0j692rvbr4iibg7xgd2i7g9x8yyrw04j889bywix14rc"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list
+ "-DCMAKE_BUILD_TYPE=Release"
+ (string-append "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath="
+ (assoc-ref %outputs "out") "/lib")
+ (string-append "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath="
+ (assoc-ref %outputs "out") "/lib")
+ (string-append "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath="
+ (assoc-ref %outputs "out") "/lib")
+
+ ;; Configuration aborts if no generator format is set
+ "-DCPACK_GENERATOR=TGZ"
+
+ ;; Configuration attempts to guess the distribution with Python.
+ "-DIRODS_LINUX_DISTRIBUTION_NAME=guix"
+ "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1"
+
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG="
+ (assoc-ref %build-inputs "clang"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="
+ (assoc-ref %build-inputs "clang-runtime"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ="
+ (assoc-ref %build-inputs "cppzmq"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE="
+ (assoc-ref %build-inputs "libarchive"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_AVRO="
+ (assoc-ref %build-inputs "avro-cpp"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_BOOST="
+ (assoc-ref %build-inputs "boost"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_ZMQ="
+ (assoc-ref %build-inputs "zeromq"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_JSON="
+ (assoc-ref %build-inputs "json"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CATCH2="
+ (assoc-ref %build-inputs "catch2"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_NANODBC="
+ (assoc-ref %build-inputs "nanodbc"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_FMT="
+ (assoc-ref %build-inputs "fmt")))
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unset-Werror
+ (lambda _
+ ;; -Werror kills the build due to a comparison REQUIRE(errs.size() == err->len);
+ ;; in unit_tests/src/test_irods_lifetime_manager.cpp
+ (substitute* "CMakeLists.txt"
+ (("-Werror") ""))))
+ (add-after 'unpack 'remove-FHS-and-prefix-assumptions
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("CMakeLists.txt"
+ "cmake/server.cmake"
+ "cmake/development_library.cmake"
+ "cmake/runtime_library.cmake")
+ (("usr/") ""))
+ (substitute* "lib/core/src/irods_default_paths.cpp"
+ (("path.append\\(\"usr\"\\)") "path")
+ (("path.remove_filename\\(\\).remove_filename\\(\\).remove_filename\\(\\)")
+ "path.remove_filename().remove_filename()"))
+ (substitute* "scripts/irods/paths.py"
+ (("'usr', 'lib', 'irods'") "'lib', 'irods'"))
+ (substitute* "scripts/irods/pypyodbc.py"
+ (("\"/usr/lib/libodbc.so\"")
+ (string-append (assoc-ref inputs "unixodbc") "/lib/libodbc.so")))))
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+ "/include/c++/v1")
+ (string-append (assoc-ref inputs "catch2")
+ "/include/catch2")
+ (string-append (assoc-ref inputs "json")
+ "/include/nlohmann")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (inputs
+ `(("avro-cpp" ,(package
+ (inherit avro-cpp-1.9)
+ (arguments
+ `(#:configure-flags
+ '("-DCMAKE_CXX_COMPILER=clang++"
+ "-DCMAKE_CXX_FLAGS=-stdlib=libc++"
+ "-DCMAKE_EXE_LINKER_FLAGS=-lc++abi -lz")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "lang/c++")))
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+ "/include/c++/v1")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (inputs
+ `(("boost" ,boost-for-irods)
+ ("clang" ,clang-toolchain-6)
+ ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
+ ("libcxxabi" ,libcxxabi-6)
+ ("snappy" ,snappy-with-clang6)
+ ("zlib" ,zlib)))))
+ ("boost" ,boost-for-irods)
+ ("cppzmq" ,cppzmq)
+ ("fmt" ,fmt-for-irods)
+ ("json" ,json-modern-cxx)
+ ("libarchive" ,libarchive)
+ ("libcxxabi" ,libcxxabi-6) ; we need this for linking with -lc++abi
+ ("linux-pam" ,linux-pam)
+ ("mit-krb5" ,mit-krb5)
+ ("nanodbc" ,nanodbc-for-irods)
+ ("openssl" ,openssl)
+ ("python" ,python-wrapper)
+ ("unixodbc" ,unixodbc)
+ ("zeromq" ,zeromq)))
+ (native-inputs
+ `(("catch2" ,catch-framework2)
+ ("clang" ,clang-toolchain-6)
+ ("clang-runtime" ,clang-runtime-6)
+ ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)))
+ (home-page "https://irods.org")
+ (synopsis "Data management software")
+ (description "The Integrated Rule-Oriented Data System (iRODS) is data
+management software. iRODS virtualizes data storage resources, so users can
+take control of their data, regardless of where and on what device the data is
+stored.")
+ (license license:bsd-3)))
--
2.31.1
^ permalink raw reply related [flat|nested] 10+ messages in thread* [bug#47972] [PATCH 6/6] gnu: Add irods-client-icommands.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
` (3 preceding siblings ...)
2021-04-23 14:32 ` [bug#47972] [PATCH 5/6] gnu: Add irods Ricardo Wurmus
@ 2021-04-23 14:32 ` Ricardo Wurmus
2021-04-24 11:02 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Maxime Devos
2021-06-10 8:28 ` [bug#47972] Add irods Ludovic Courtès
6 siblings, 0 replies; 10+ messages in thread
From: Ricardo Wurmus @ 2021-04-23 14:32 UTC (permalink / raw)
To: 47972; +Cc: Ricardo Wurmus
* gnu/packages/irods.scm (irods-client-icommands): New variable.
---
gnu/packages/irods.scm | 137 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 137 insertions(+)
diff --git a/gnu/packages/irods.scm b/gnu/packages/irods.scm
index 75a58d97cb..e757c1d80a 100644
--- a/gnu/packages/irods.scm
+++ b/gnu/packages/irods.scm
@@ -20,10 +20,12 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages backup)
+ #:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
@@ -34,6 +36,7 @@
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages logging)
+ #:use-module (gnu packages man)
#:use-module (gnu packages networking)
#:use-module (gnu packages pretty-print)
#:use-module (gnu packages python)
@@ -198,3 +201,137 @@ management software. iRODS virtualizes data storage resources, so users can
take control of their data, regardless of where and on what device the data is
stored.")
(license license:bsd-3)))
+
+(define-public irods-client-icommands
+ (package
+ (name "irods-client-icommands")
+ (version "4.2.8")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/irods/irods_client_icommands")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "069n647p5ypf44gim8z26mwayg5lzgk7r9qyyqd8f9n7h0p4jxpn"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:tests? #false ; not clear how to run tests
+ #:configure-flags
+ (list
+ "-DCMAKE_BUILD_TYPE=Release"
+
+ ;; Configuration attempts to guess the distribution with Python.
+ "-DIRODS_LINUX_DISTRIBUTION_NAME=guix"
+ "-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1"
+
+ (string-append "-DIRODS_DIR="
+ (assoc-ref %build-inputs "irods")
+ "/lib/irods/cmake")
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG="
+ (assoc-ref %build-inputs "clang"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="
+ (assoc-ref %build-inputs "clang-runtime"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ="
+ (assoc-ref %build-inputs "cppzmq"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE="
+ (assoc-ref %build-inputs "libarchive"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_AVRO="
+ (assoc-ref %build-inputs "avro-cpp"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_BOOST="
+ (assoc-ref %build-inputs "boost"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_ZMQ="
+ (assoc-ref %build-inputs "zeromq"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_JSON="
+ (assoc-ref %build-inputs "json"))
+ (string-append "-DIRODS_EXTERNALS_FULLPATH_FMT="
+ (assoc-ref %build-inputs "fmt")))
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unset-Werror ;
+ (lambda _ ;
+ ;; -Werror kills the build due to a deprecation warning
+ (substitute* "CMakeLists.txt" ;
+ (("-Werror") ""))))
+ (add-after 'unpack 'remove-/usr-prefix
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("usr/") ""))))
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+ "/include/c++/v1")
+ (string-append (assoc-ref inputs "json")
+ "/include/nlohmann")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (inputs
+ `(("avro-cpp" ,(package
+ (inherit avro-cpp-1.9)
+ (arguments
+ `(#:configure-flags
+ '("-DCMAKE_CXX_COMPILER=clang++"
+ "-DCMAKE_CXX_FLAGS=-stdlib=libc++"
+ "-DCMAKE_EXE_LINKER_FLAGS=-lc++abi -lz")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "lang/c++")))
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
+ "/include/c++/v1")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (inputs
+ `(("boost" ,boost-for-irods)
+ ("clang" ,clang-toolchain-6)
+ ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
+ ("libcxxabi" ,libcxxabi-6)
+ ("snappy" ,snappy-with-clang6)
+ ("zlib" ,zlib)))))
+ ("boost" ,boost-for-irods)
+ ("cppzmq" ,cppzmq)
+ ("fmt" ,fmt-for-irods)
+ ("irods" ,irods)
+ ("json" ,json-modern-cxx)
+ ("libarchive" ,libarchive)
+ ("libcxxabi" ,libcxxabi-6) ; we need this for linking with -lc++abi
+ ("mit-krb5" ,mit-krb5)
+ ("openssl" ,openssl)
+ ("zeromq" ,zeromq)))
+ (native-inputs
+ `(("clang" ,clang-toolchain-6)
+ ("clang-runtime" ,clang-runtime-6)
+ ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
+ ("help2man" ,help2man)
+ ("which" ,which)))
+ (home-page "https://irods.org")
+ (synopsis "Data management software")
+ (description "The Integrated Rule-Oriented Data System (iRODS) is data
+management software. iRODS virtualizes data storage resources, so users can
+take control of their data, regardless of where and on what device the data is
+stored.")
+ (license license:bsd-3)))
--
2.31.1
^ permalink raw reply related [flat|nested] 10+ messages in thread* [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
` (4 preceding siblings ...)
2021-04-23 14:32 ` [bug#47972] [PATCH 6/6] gnu: Add irods-client-icommands Ricardo Wurmus
@ 2021-04-24 11:02 ` Maxime Devos
2021-06-10 8:28 ` [bug#47972] Add irods Ludovic Courtès
6 siblings, 0 replies; 10+ messages in thread
From: Maxime Devos @ 2021-04-24 11:02 UTC (permalink / raw)
To: Ricardo Wurmus, 47972
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Ricardo Wurmus schreef op vr 23-04-2021 om 16:31 [+0200]:
> *+;; Sadly, this is needed for irods. It won't link with 1.69 or later.
> +(define-public boost-for-irods
> + [...]
> + (native-inputs
> + `(("clang" ,clang-6)
> + ("libcxx" ,libcxx+libcxxabi-6)
> + ("libcxxabi" ,libcxxabi-6)
"libcxx" and "libcxxabi" look lik they should be in "inputs", but perhaps something
special is going on here.
> + ("perl" ,perl)
> + ("tcsh" ,tcsh)))
> + (arguments
> + `(#:tests? #f
> + #:make-flags
> + (list "threading=multi" "link=shared"
> + "cxxflags=-stdlib=libc++"
> + "--without-python"
> +
> + ;; Set the RUNPATH to $libdir so that the libs find each other.
> + (string-append "linkflags=-stdlib=libc++ -Wl,-rpath="
> + (assoc-ref %outputs "out") "/lib"))
> + #:phases
> + (modify-phases %standard-phases
> + (delete 'bootstrap)
> + (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
> + (lambda* (#:key inputs #:allow-other-keys)
> + (let ((gcc (assoc-ref inputs "gcc")))
For cross-compilation, this should be (assoc-ref (or native-inputs inputs) "gcc").
> + (setenv "CPLUS_INCLUDE_PATH"
Maybe you need to set "CROSS_CPLUS_INCLUDE_PATH" here instead, not sure though.
> + (string-join
> + (cons (string-append (assoc-ref inputs "libcxx")
> + "/include/c++/v1")
> + ;; Hide GCC's C++ headers so that they do not interfere with
> + ;; the Clang headers.
> + (delete (string-append gcc "/include/c++")
> + (string-split (getenv "CPLUS_INCLUDE_PATH")
> + #\:)))
> + ":"))
> + (format #true
> + "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
> + (getenv "CPLUS_INCLUDE_PATH")))))
> + (replace 'configure
> + (lambda* (#:key inputs outputs #:allow-other-keys)
> + (let ((icu (assoc-ref inputs "icu4c"))
> + (zlib (assoc-ref inputs "zlib"))
> + (out (assoc-ref outputs "out")))
> + (substitute* '("libs/config/configure"
> + "libs/spirit/classic/phoenix/test/runtest.sh"
> + "tools/build/src/engine/execunix.c"
> + "tools/build/src/engine/Jambase"
> + "tools/build/src/engine/jambase.c")
> + (("/bin/sh") (which "sh")))
When cross-compiling, "which" looks in the 'native-inputs', and not 'inputs'.
For tools/**/*.c, you should use (string-append (assoc-ref inputs "bash") "/bin/sh")
or something like that. If/when <https://issues.guix.gnu.org/47869> is merged,
you can write the simpler (which "sh" inputs) instead, but that's not (yet) the case.
> +
> + (setenv "SHELL" (which "sh"))
> + (setenv "CONFIG_SHELL" (which "sh"))
> +
> + (invoke "./bootstrap.sh"
> + (string-append "--prefix=" out)
> + ;; Auto-detection looks for ICU only in traditional
> + ;; install locations.
> + (string-append "--with-icu=" icu)
> + "--with-toolset=clang"))))
> + (replace 'build
> + (lambda* (#:key inputs make-flags #:allow-other-keys)
> + (let ((zlib (assoc-ref inputs "zlib")))
The ((zlib (assoc-ref ...))) binding seems unused here.
Greetings,
Maxime.
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^ permalink raw reply [flat|nested] 10+ messages in thread* [bug#47972] Add irods.
2021-04-23 14:31 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Ricardo Wurmus
` (5 preceding siblings ...)
2021-04-24 11:02 ` [bug#47972] [PATCH 1/6] gnu: Add boost-for-irods Maxime Devos
@ 2021-06-10 8:28 ` Ludovic Courtès
2021-06-14 14:48 ` bug#47972: " Ricardo Wurmus
6 siblings, 1 reply; 10+ messages in thread
From: Ludovic Courtès @ 2021-06-10 8:28 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: 47972
Hi Ricardo,
Ricardo Wurmus <rekado@elephly.net> skribis:
> * gnu/packages/boost.scm (boost-for-irods): New variable.
[...]
> +;; Sadly, this is needed for irods. It won't link with 1.69 or later.
> +(define-public boost-for-irods
> + (package
> + (name "boost-for-irods")
> + (version "1.68.0")
For this and the other “for-irods” packages, how about:
1. Inheriting from the original package (‘boost’ in this case), to at
least avoid duplicating the synopsis, description, and license?
2. Adding the ‘hidden?’ property, because they are not meant to be
installed on their own?
Apart from that, it LGTM.
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 10+ messages in thread* bug#47972: Add irods.
2021-06-10 8:28 ` [bug#47972] Add irods Ludovic Courtès
@ 2021-06-14 14:48 ` Ricardo Wurmus
0 siblings, 0 replies; 10+ messages in thread
From: Ricardo Wurmus @ 2021-06-14 14:48 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: 47972-done
Ludovic Courtès <ludovic.courtes@inria.fr> writes:
> Hi Ricardo,
>
> Ricardo Wurmus <rekado@elephly.net> skribis:
>
>> * gnu/packages/boost.scm (boost-for-irods): New variable.
>
> [...]
>
>> +;; Sadly, this is needed for irods. It won't link with 1.69
>> or later.
>> +(define-public boost-for-irods
>> + (package
>> + (name "boost-for-irods")
>> + (version "1.68.0")
>
> For this and the other “for-irods” packages, how about:
>
> 1. Inheriting from the original package (‘boost’ in this
> case), to at
> least avoid duplicating the synopsis, description, and
> license?
>
> 2. Adding the ‘hidden?’ property, because they are not meant
> to be
> installed on their own?
Done.
I also addressed what I could of Maxime’s comments. Thank you.
I split out the package variant of avro-cpp that is used by both
irods packages and pushed the patch series to the “master” branch.
--
Ricardo
^ permalink raw reply [flat|nested] 10+ messages in thread