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-rw-r--r--gnu/packages/bioconductor.scm29
1 files changed, 29 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce64a3052f..78ad278893 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -72,6 +72,35 @@
database, assembled using data from REACTOME.")
(license license:cc-by4.0)))
+(define-public r-bluster
+ (package
+ (name "r-bluster")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bluster" version))
+ (sha256
+ (base32
+ "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
+ (properties `((upstream-name . "bluster")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/bluster")
+ (synopsis "Clustering algorithms for Bioconductor")
+ (description"This package wraps common clustering algorithms in an easily
+extended S4 framework. Backends are implemented for hierarchical, k-means
+and graph-based clustering. Several utilities are also provided to compare
+and evaluate clustering results.")
+ (license license:gpl3)))
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
nded-build-trace?'. (guix-build): Parameterize CURRENT-TERMINAL-COLUMNS. Use 'build-status-updater'. * guix/scripts/environment.scm (%default-options): Add 'print-extended-build-trace?'. (guix-environment): Wrap body in 'with-status-report'. * guix/scripts/pack.scm (%default-options): Add 'print-build-trace?' and 'print-extended-build-trace?'. (guix-pack): Wrap body in 'with-status-report'. * guix/scripts/package.scm (%default-options, guix-package): Likewise. * guix/scripts/system.scm (%default-options, guix-system): Likewise. * guix/scripts/pull.scm (%default-options, guix-pull): Likewise. * guix/scripts/substitute.scm (progress-report-port): Don't call STOP when TOTAL is zero. (process-substitution): Add #:print-build-trace? and honor it. (guix-substitute)[print-build-trace?]: New variable. Pass #:print-build-trace? to 'process-substitution'. * guix/status.scm: New file. * guix/store.scm (set-build-options): Add #:print-extended-build-trace?; pass it into PAIRS. (%protocol-version): Bump. (protocol-version, nix-server-version): New procedures. (current-store-protocol-version): New variable. (with-store, build-things): Parameterize it. * guix/ui.scm (build-output-port): Remove. (colorize-string): Export. * po/guix/POTFILES.in: Add guix/status.scm. * tests/status.scm: New file. * Makefile.am (SCM_TESTS): Add it. * nix/libstore/worker-protocol.hh (PROTOCOL_VERSION): Bump to 0x162. * nix/libstore/build.cc (DerivationGoal::registerOutputs) (SubstitutionGoal::finished): Print a "@ hash-mismatch" trace before throwing. Ludovic Courtès 2018-06-22build: Remove leftover reference to nix/libstore/schema.sql....This is a followup to 3931c76154d4f418d5ea9acc5e47bf911d371c24. Reported by Julien Lepiller. * nix/local.mk (EXTRA_DIST): Remove schema.sql. Ludovic Courtès 2018-06-14Remove 'guix-register' and its traces....* Makefile.am (SH_TESTS): Remove tests/guix-register.sh. * build-aux/pre-inst-env.in (GUIX_REGISTER): Remove. * gnu/build/install.scm (directives): Remove outdated comment. * gnu/build/vm.scm (root-partition-initializer): Update comment. * gnu/packages/package-management.scm (guix-register): Remove. * guix/config.scm.in (%sbindir, %guix-register-program): Remove. * guix/scripts/system.scm (install): Adjust docstring. * guix/self.scm (make-config.scm): Remove #:guix. Do not generate %sbindir and %guix-register-program. (specification->package): Remove "guix". * nix/guix-register/guix-register.cc: Remove. * nix/libstore/store-api.cc (decodeValidPathInfo): Remove. * nix/libstore/store-api.hh (decodeValidPathInfo): Remove declaration. * nix/local.mk (sbin_PROGRAMS, guix_register_SOURCES) (guix_register_CPPFLAGS, guix_register_LDFLAGS): Remove. * tests/guix-register.sh: Remove. Ludovic Courtès 2018-06-14database: 'with-database' can now initialize new databases....* nix/libstore/schema.sql: Rename to... * guix/store/schema.sql: ... this. * Makefile.am (nobase_dist_guilemodule_DATA): Add it. * nix/local.mk (%D%/libstore/schema.sql.hh): Adjust accordingly. * guix/store/database.scm (sql-schema): New variable. (sqlite-exec, initialize-database, call-with-database): New procedures. (with-database): Rewrite in terms of 'call-with-database'. * tests/store-database.scm ("new database"): New test. * guix/self.scm (compiled-guix)[*core-modules*]: Add 'schema.sql' to #:extra-files. Ludovic Courtès 2018-06-08build: Do not add all of $(BUILT_SOURCES) to $(CLEANFILES)....Reported by Gábor Boskovits <boskovits@gmail.com>. Fixes <https://bugs.gnu.org/31700>. * nix/local.mk (CLEANFILES): Add nothing but schema.sql.hh. Ludovic Courtès 2018-05-17daemon: Allow building for armhf-linux on aarch64-linux....* nix/libstore/build.cc (canBuildLocally): Allow building armhf-linux builds on aarch64-linux. (DerivationGoal::runChild) Throw error if attempting to build for armhf-linux on an unsupported platform. * doc/guix.texi (Invoking guix build): Document how to build natively for armhf-linux on aarch64-linux. Add note that on some aarch64 machines this is unsupported. Efraim Flashner 2018-04-19guix-daemon: Disable garbage collection for remote connections....* nix/nix-daemon/nix-daemon.cc (isRemoteConnection): New variable. (performOp): For wopCollectGarbage, throw an error when isRemoteConnection is set. (acceptConnection): Set isRemoteConnection when connection is not AF_UNIX. * tests/guix-daemon.sh: Add a test for the new behavior. Roel Janssen 2018-03-30daemon: Remove unused schema upgrade code....* nix/libstore/local-store.cc (LocalStore): Remove upgrade code. (LocalStore::queryValidPathsOld, LocalStore::queryPathInfoOld) (LocalStore::upgradeStore6, makeMutable) (LocalStore::upgardeStore7): Remove. * nix/libstore/local-store.hh: Adjust accordingly. Ludovic Courtès 2018-03-30daemon: Remove dead code....* nix/libstore/globals.cc (Settings::loadConfFile, Settings::unpack): Remove. * nix/libstore/globals.hh: Adjust accordingly. * nix/libstore/misc.cc (queryMissing): Remove. * nix/libstore/misc.hh: Adjust accordingly. * nix/libstore/store-api.cc (followLinksToStore) (followLinksToStorePath, computeStorePathForHash): Remove. * nix/libstore/store-api.hh: Adjust accordingly. Ludovic Courtès 2018-01-11daemon: Always try to execute the builder regardless of the platform....* nix/libstore/build.cc (runChild): Move platform check after 'execve' call. Check specifically for ENOEXEC. Ludovic Courtès 2018-01-07daemon: Make libbz2 an optional dependency....* config-daemon.ac: Don't bail out when libbz2 is missing. Define 'HAVE_LIBBZ2' Automake conditional. * nix/libstore/build.cc: Wrap relevant bits in '#if HAVE_BZLIB_H'. * nix/libstore/globals.cc (Settings::Settings): 'logCompression' defaults to COMPRESSION_GZIP when HAVE_BZLIB_H is false. * nix/libstore/globals.hh (CompressionType): Make 'COMPRESSION_BZIP2' conditional on HAVE_BZLIB_H. * nix/local.mk (guix_register_LDADD, guix_daemon_LDADD): Add -lbz2 only when HAVE_LIBBZ2. * nix/nix-daemon/guix-daemon.cc (parse_opt): Ignore "bzip2" when not HAVE_BZLIB_H. Ludovic Courtès 2018-01-07daemon: Add gzip log compression....* nix/nix-daemon/guix-daemon.cc (GUIX_OPT_LOG_COMPRESSION): New macro. (options): Mark "disable-log-compression" as hidden and add "log-compression". (parse_opt): Handle GUIX_OPT_LOG_COMPRESSION. * nix/libstore/build.cc (DerivationGoal): Add 'gzLogFile'. (openLogFile): Initialize it when 'logCompression' is COMPRESSION_GZIP. (closeLogFile, handleChildOutput): Honor 'gzLogFile'. * nix/libstore/globals.hh (Settings)[compressLog]: Remove. [logCompression]: New field. (CompressionType): New enum. * nix/libstore/globals.cc (Settings::Settings): Initialize it. (update): Remove '_get' call for 'compressLog'. * nix/local.mk (guix_daemon_LDADD, guix_register_LDADD): Add -lz. * guix/store.scm (log-file): Handle '.gz' log files. * tests/guix-daemon.sh: Add test with '--log-compression=gzip'. * doc/guix.texi (Invoking guix-daemon): Adjust accordingly. * config-daemon.ac: Check for libz and zlib.h. Ludovic Courtès 2017-12-31list-runtime-root: Fix off-by-one in 'strip-drop' call....Fixes <https://bugs.gnu.org/29862>. Reported by Danny Milosavljevic <dannym@scratchpost.org>. * nix/scripts/list-runtime-roots.in (canonicalize-store-item): Define 'store' with a trailing "/". Have the 'string-prefix?' call match the 'string-drop' call. Ludovic Courtès 2017-11-26list-runtime-roots: Ignore ESRCH while reading from /proc....Fixes <https://bugs.gnu.org/29368>. Reported by Martin Castillo <castilma@uni-bremen.de>. * nix/scripts/list-runtime-roots.in (referenced-files): Ignore ESRCH. Ludovic Courtès 2017-11-12list-runtime-roots: Ignore PIDs we cannot access....This allows running as non-root. Fixes a regression introduced in b8f59cdc20e9d83ce63523ef917e95fcee07f134. * nix/scripts/list-runtime-roots.in (referenced-files): Handle EACCES in addition to ENOENT. Ludovic Courtès 2017-11-12list-runtime-roots: Canonicalize store items....Looking at 'addAdditionalRoots' in libstore/gc.cc, it looks like it should always have been this way. In practice it probably doesn't make much of a difference. * nix/scripts/list-runtime-roots.in (canonicalize-store-item): New procedure. <top level>: Use it. Ludovic Courtès 2017-11-12list-runtime-roots: Do not use 'lsof'....This makes things a bit faster (0.8s instead of 1.4s on my laptop). * nix/scripts/list-runtime-roots.in (lsof-roots): Remove. (proc-fd-roots): Return the empty list when 'scandir' returns #f. (referenced-files): New procedure. Use it at the top level. Ludovic Courtès