Merge branch 'master' into core-updates

6 files changed, 238 insertions, 0 deletions

diff --git a/gnu/packages/patches/collectd-5.11.0-noinstallvar.patch b/gnu/packages/patches/collectd-5.11.0-noinstallvar.patch
new file mode 100644
index 0000000000..39cd9c763e
--- /dev/null
+++ b/gnu/packages/patches/collectd-5.11.0-noinstallvar.patch
@@ -0,0 +1,21 @@
+Disable creation of /var and /etc
+
+--- a/Makefile.am	2020-03-08 16:57:09.511535600 +0100
++++ b/Makefile.am	2020-04-21 11:36:49.827182272 +0200
+@@ -2376,16 +2376,6 @@
+ endif
+ 
+ install-exec-hook:
+-	$(mkinstalldirs) $(DESTDIR)$(localstatedir)/run
+-	$(mkinstalldirs) $(DESTDIR)$(localstatedir)/lib/$(PACKAGE_NAME)
+-	$(mkinstalldirs) $(DESTDIR)$(localstatedir)/log
+-	$(mkinstalldirs) $(DESTDIR)$(sysconfdir)
+-	if test -e $(DESTDIR)$(sysconfdir)/collectd.conf; \
+-	then \
+-		$(INSTALL) -m 0640 $(builddir)/src/collectd.conf $(DESTDIR)$(sysconfdir)/collectd.conf.pkg-orig; \
+-	else \
+-		$(INSTALL) -m 0640 $(builddir)/src/collectd.conf $(DESTDIR)$(sysconfdir)/collectd.conf; \
+-	fi; \
+ 	$(mkinstalldirs) $(DESTDIR)$(cpkgdatadir)
+ 	$(INSTALL) -m 0644 $(srcdir)/src/types.db $(DESTDIR)$(cpkgdatadir)/types.db;
+ 	$(INSTALL) -m 0644 $(srcdir)/src/postgresql_default.conf \
diff --git a/gnu/packages/patches/grocsvs-dont-use-admiral.patch b/gnu/packages/patches/grocsvs-dont-use-admiral.patch
new file mode 100644
index 0000000000..cb976e19b0
--- /dev/null
+++ b/gnu/packages/patches/grocsvs-dont-use-admiral.patch
@@ -0,0 +1,69 @@
+python-admiral doesn't have a license
+https://github.com/nspies/admiral/issues/3
+
+diff --git a/setup.py b/setup.py
+index 692b6a0..568f381 100755
+--- a/setup.py
++++ b/setup.py
+@@ -20,7 +20,7 @@ setup(
+         'console_scripts' : ["grocsvs = grocsvs.main:main"]
+     },
+ 
+-    install_requires = ["admiral", "h5py", "networkx>=2.0", "pandas", "pybedtools", 
++    install_requires = ["h5py", "networkx>=2.0", "pandas", "pybedtools", 
+                         "pyfaidx", "pysam>=0.10.0", "scipy", "ipython-cluster-helper",
+                         "pygraphviz", "psutil"],
+ 
+diff --git a/src/grocsvs/jobmanagers.py b/src/grocsvs/jobmanagers.py
+index 6da0b58..112d7ff 100755
+--- a/src/grocsvs/jobmanagers.py
++++ b/src/grocsvs/jobmanagers.py
+@@ -41,34 +41,3 @@ class MultiprocessingCluster(Cluster):
+         pool = multiprocessing.Pool(processes=self.processes)
+         return pool.map_async(fn, args).get(999999)
+ 
+-
+-class AdmiralCluster(Cluster):
+-    def map(self, fn, args):
+-        from admiral import jobmanagers, remote
+-
+-        cluster_options = self.cluster_settings.cluster_options.copy()
+-        
+-        scheduler = cluster_options.pop("scheduler")
+-
+-        jobmanager_class = jobmanagers.get_jobmanager(scheduler)
+-        jobmanager = jobmanager_class(
+-            batch_dir=self.batch_dir, log_dir=self.batch_dir)
+-
+-
+-        if not "mem" in cluster_options:
+-            cluster_options["mem"] = "16g"
+-        if not "time" in cluster_options:
+-            cluster_options["time"] = "12h"
+-
+-        jobs = []
+-        #for i, arg in enumerate(args):
+-
+-        job_name = args[0].__class__.__name__
+-        args = [[arg] for arg in args]
+-        job = remote.run_remote(fn, jobmanager, job_name, args=args,
+-                                array=True, overwrite=True, **cluster_options)
+-
+-        result = jobmanagers.wait_for_jobs([job], wait=5, progress=True)
+-
+-        if not result:
+-            raise Exception("Some chunks failed to complete")
+diff --git a/src/grocsvs/pipeline.py b/src/grocsvs/pipeline.py
+index ab1bb2d..350976f 100755
+--- a/src/grocsvs/pipeline.py
++++ b/src/grocsvs/pipeline.py
+@@ -8,8 +8,7 @@ from grocsvs import utilities
+ def make_jobmanager(jobmanager_settings, processes, batch_dir):
+     jobmanager_classes = {"IPCluster":jobmanagers.IPCluster,
+                           "local":    jobmanagers.LocalCluster,
+-                          "multiprocessing": jobmanagers.MultiprocessingCluster,
+-                          "admiral": jobmanagers.AdmiralCluster}
++                          "multiprocessing": jobmanagers.MultiprocessingCluster}
+ 
+     cls = jobmanager_classes[jobmanager_settings.cluster_type]
+     return cls(processes, jobmanager_settings, batch_dir)
diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch
new file mode 100644
index 0000000000..cc7d7459a8
--- /dev/null
+++ b/gnu/packages/patches/gromacs-tinyxml2.patch
@@ -0,0 +1,67 @@
+Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs
+build.
+
+This patch fixes three issues:
+
+- cmake now errors out if using multiple target_link_libraries with mixed styles
+  of signatures.
+
+- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the
+  new API: document.ErrorStr() & tinyxml2::XML_SUCCESS.
+
+Those fixes will be submitted for inclusion to upstream, but may not be suitable
+there as long as they still keep the old version bundled.
+
+First hunk has already been requested for merging. Third is in discussion. Second
+will only be sent if third is OK'ed.
+
+diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt
+--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200
++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt   2020-05-01 22:52:16.356000000 +0200
+@@ -73,7 +73,7 @@
+ 
+ if(HAVE_TINYXML2)
+     include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR})
+-    target_link_libraries(testutils ${TinyXML2_LIBRARIES})
++    target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES})
+ else()
+     include_directories(BEFORE SYSTEM "../external/tinyxml2")
+ endif()
+diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp
+--- gromacs-2020.2/src/testutils/refdata_xml.cpp        2020-04-30 18:33:44.000000000 +0200
++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp  2020-05-01 23:17:09.556000000 +0200
+@@ -206,21 +206,12 @@
+     document.LoadFile(path.c_str());
+     if (document.Error())
+     {
+-        const char* errorStr1 = document.GetErrorStr1();
+-        const char* errorStr2 = document.GetErrorStr2();
++        const char* errorStr = document.ErrorStr();
+         std::string errorString("Error was ");
+-        if (errorStr1)
+-        {
+-            errorString += errorStr1;
+-        }
+-        if (errorStr2)
+-        {
+-            errorString += errorStr2;
+-        }
+-        if (!errorStr1 && !errorStr2)
+-        {
++        if (errorStr)
++            errorString += errorStr;
++        else
+             errorString += "not specified.";
+-        }
+         GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n."
+                                 + errorString + "\n"));
+     }
+@@ -371,7 +362,7 @@
+     XMLElementPtr rootElement = createRootElement(&document);
+     createChildElements(rootElement, rootEntry);
+ 
+-    if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR)
++    if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS)
+     {
+         GMX_THROW(TestException("Reference data saving failed in " + path));
+     }
diff --git a/gnu/packages/patches/musl-cross-locale.patch b/gnu/packages/patches/musl-cross-locale.patch
new file mode 100644
index 0000000000..7634eda381
--- /dev/null
+++ b/gnu/packages/patches/musl-cross-locale.patch
@@ -0,0 +1,20 @@
+Disable locales other than C and POSIX because of a compilation error.
+By Danny Milosavljevic <dannym@scratchpost.org>
+This patch is distributed under BSD-3 license.
+See https://github.com/osresearch/heads/pull/610
+diff -ruN b/source/patches/gcc-5.3.0-locale.diff guix-build-musl-cross-0.1-3.a8a6649.drv-12/source/patches/gcc-5.3.0-locale.diff
+--- a/patches/gcc-5.3.0-locale.diff	1970-01-01 01:00:00.000000000 +0100
++++ b/patches/gcc-5.3.0-locale.diff	2020-05-02 14:20:47.213564509 +0200
+@@ -0,0 +1,12 @@
++--- gcc-5.3.0/libstdc++-v3/config/locale/gnu/ctype_members.cc.orig	2020-05-02 14:16:31.376147000 +0200
+++++ gcc-5.3.0/libstdc++-v3/config/locale/gnu/ctype_members.cc	2020-05-02 14:16:56.716279576 +0200
++@@ -47,7 +47,8 @@
++ 	this->_S_create_c_locale(this->_M_c_locale_ctype, __s); 
++ 	this->_M_toupper = this->_M_c_locale_ctype->__ctype_toupper;
++ 	this->_M_tolower = this->_M_c_locale_ctype->__ctype_tolower;
++-	this->_M_table = this->_M_c_locale_ctype->__ctype_b;
+++	//this->_M_table = this->_M_c_locale_ctype->__ctype_b;
+++	throw 3;
++       }
++   }
++ 
diff --git a/gnu/packages/patches/rust-nettle-disable-vendor.patch b/gnu/packages/patches/rust-nettle-disable-vendor.patch
new file mode 100644
index 0000000000..5b52821cdb
--- /dev/null
+++ b/gnu/packages/patches/rust-nettle-disable-vendor.patch
@@ -0,0 +1,13 @@
+Subject: nettle: clear out "vendored" feature cruft from build.rs
+From: Daniel Kahn Gillmor's avatarDaniel Kahn Gillmor <dkg@fifthhorseman.net>
+
+https://salsa.debian.org/rust-team/debcargo-conf/-/commit/b608e6beaa1d38c14fc16ad53780d94954a91900
+https://sources.debian.org/src/rust-nettle/7.0.0-1/debian/patches/disable-vendor.diff/
+--- a/Cargo.toml	1969-12-31 19:00:00.000000000 -0500
++++ b/Cargo.toml	2019-10-23 19:12:01.076181971 -0400
+@@ -35,4 +35,4 @@
+ version = "1"
+ 
+ [features]
+-vendored = ["nettle-sys/vendored"]
++vendored = []
diff --git a/gnu/packages/patches/rust-nettle-sys-disable-vendor.patch b/gnu/packages/patches/rust-nettle-sys-disable-vendor.patch
new file mode 100644
index 0000000000..ae5ef5ebe0
--- /dev/null
+++ b/gnu/packages/patches/rust-nettle-sys-disable-vendor.patch
@@ -0,0 +1,48 @@
+Subject: nettle-sys: clear out "vendored" feature cruft from build.rs
+From: Daniel Kahn Gillmor's avatarDaniel Kahn Gillmor <dkg@fifthhorseman.net>
+
+https://salsa.debian.org/rust-team/debcargo-conf/-/commit/0c71150ad26bb66a8396dcdab055181af232ddc5
+https://sources.debian.org/src/rust-nettle-sys/2.0.4-3/debian/patches/disable-vendor.diff/
+--- a/Cargo.toml	2019-10-23 13:08:07.000000000 -0400
++++ b/Cargo.toml	2019-10-23 14:08:46.644064014 -0400
+@@ -29,12 +29,9 @@
+ version = "0.51.1"
+ default-features = false
+ 
+-[build-dependencies.nettle-src]
+-version = "3.5.1-0"
+-optional = true
+-
+ [build-dependencies.pkg-config]
+ version = "0.3"
+ 
+ [features]
+ vendored = ["nettle-src"]
++nettle-src = []
+diff --git a/build.rs b/build.rs
+index 44f7af3..ede4b2f 100644
+--- a/build.rs
++++ b/build.rs
+@@ -1,7 +1,5 @@
+ extern crate bindgen;
+ extern crate pkg_config;
+-#[cfg(feature = "vendored")]
+-extern crate nettle_src;
+ 
+ use std::env;
+ use std::fs;
+@@ -36,14 +34,6 @@ fn main() {
+     println!("cargo:rerun-if-env-changed=NETTLE_STATIC");
+     println!("cargo:rerun-if-env-changed={}", NETTLE_PREGENERATED_BINDINGS);
+ 
+-    #[cfg(feature = "vendored")]
+-    {
+-        let artifacts = nettle_src::Build::new().build();
+-        println!("cargo:vendored=1");
+-        env::set_var("PKG_CONFIG_PATH",
+-                     artifacts.lib_dir().join("pkgconfig"));
+-    }
+-
+     let nettle = pkg_config::probe_library("nettle hogweed").unwrap();
+ 
+     let mode = match env::var_os("NETTLE_STATIC") {