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-rw-r--r--gnu/packages/bioconductor.scm24
1 files changed, 24 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bae472c8ac..d3e16cd859 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11637,6 +11637,30 @@ segments fit (the relative error) to integer copy numbers for each percentage
of @dfn{tumor cells} (cells with divergent segments).")
(license license:gpl2)))
+(define-public r-acgh
+ (package
+ (name "r-acgh")
+ (version "1.72.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "aCGH" version))
+ (sha256
+ (base32
+ "1r1q6iq3g7svfn5m4jxlxp413djb40mvf6lh595y86sgwav5k6l4"))))
+ (properties `((upstream-name . "aCGH")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
+ (home-page "https://bioconductor.org/packages/aCGH")
+ (synopsis
+ "Classes and functions for array comparative genomic hybridization data")
+ (description
+ "This package provides functions for reading
+@dfn{array comparative genomic hybridization} (aCGH) data from image analysis
+output files and clone information files, creation of @code{aCGH} objects for
+storing these data. Basic methods are accessing/replacing, subsetting,
+printing and plotting @code{aCGH} objects.")
+ (license license:gpl2)))
+
;; This is a CRAN package, but it depends on Bioconductor packages, so we put
;; it here.
(define-public r-activedriverwgs
vail'>...* gnu/installer.scm (installer-program): Improve readability by using define at top-level. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Josselin Poiret 2022-02-02installer: Add crash dump upload support....Suggested-by: Josselin Poiret <dev@jpoiret.xyz> * gnu/installer/dump.scm: New file. * gnu/installer/newt/dump.scm: New file. * gnu/local.mk (INSTALLER_MODULES): Add them. * gnu/installer/record.scm (<installer>)[dump-page]: New field. * gnu/installer/steps.scm (%current-result): New variable. (run-installer-steps): Update it. * gnu/installer.scm (installer-program): Add tar and gip to the installer path. Add guile-webutils and gnutls to the Guile extensions. Generate and send the crash dump report. * gnu/installer/newt.scm (exit-error): Add a report argument. Display the report id. (dump-page): New procedure. (newt-installer): Update it. Mathieu Othacehe 2022-01-14installer: Check if ci.guix.gnu.org can be reached....* gnu/installer.scm (installer-program): Add gnutls extension. * gnu/installer/newt/network.scm (wait-service-online): Check if the CI server can be reached. Mathieu Othacehe 2021-09-23installer: Support XFS....* gnu/installer/newt/partition.scm (run-fs-type-page): Add ‘xfs’ to the list box. * gnu/installer/parted.scm (user-fs-type-name, user-fs-type->mount-type) (partition-filesystem-user-type): Add ‘xfs’ mapping. (create-xfs-file-system): New procedure. (format-user-partitions): Use it. * gnu/installer.scm (set-installer-path): Add xfsprogs. Tobias Geerinckx-Rice 2021-01-12installer: Fix crash in parameters menu....Fixes: <https://issues.guix.gnu.org/45378>. * gnu/installer/newt/keymap.scm (run-layout-page): Return false when "Continue" button is pressed. (run-keymap-page): Do not try to compute variants if layout is false. Also do not try to format the result if layout is false. * gnu/installer.scm (compute-keymap-step): Do not apply keymap if "run-keymap-page" returns false. Mathieu Othacehe 2020-12-11install: Discover local substitute servers....* gnu/installer/substitutes.scm: New file. * gnu/installer/newt/substitutes.scm: New file. * gnu/local.mk (INSTALLER_MODULES): Add them. * po/guix/POTFILES.in: Add gnu/installer/newt/substitutes.scm. * gnu/installer/proxy.scm (with-silent-shepherd): Move to ... * gnu/installer/utils.scm: ... here. * gnu/installer/record.scm (<installer>)[substitutes-page]: New field. * gnu/installer/newt.scm (substitutes-page): New procedure, (newt-installer): register it. * gnu/installer.scm (installer-steps): Add "substitutes-page" step. * gnu/system/install.scm (%installation-services): Add avahi-service-type and enable substitute server discover in guix-service-type. [<name-service-switch>]: Set it to %mdns-host-lookup-nss. Mathieu Othacehe 2020-10-18installer: Call setlocale after init gettext....* gnu/installer.scm (installer-program)[init-gettext]: Change locale from C, installed at the program start. Miguel Ángel Arruga Vivas 2020-09-23installer: Fix docstring typo....* gnu/installer.scm (build-compiled-file): Fix a typo in the docstring. Tobias Geerinckx-Rice 2020-08-25Remove "guile-zlib" extension when unused....This is a follow-up of 755f365b02b42a5d1e8ef3000dadef069553a478. As (zlib) is autoloaded in (gnu build linux-modules), "guile-zlib" is needed as an extension only when it is effectively used. * gnu/installer.scm (installer-program): Remove "guile-zlib" from the extensions. * gnu/machine/ssh.scm (machine-check-initrd-modules): Ditto. * gnu/services.scm (activation-script): Ditto. * gnu/services/base.scm (default-serial-port): Ditto, (agetty-shepherd-service): ditto, (udev-service-type): ditto. * gnu/system/image.scm (gcrypt-sqlite3&co): Ditto. * gnu/system/shadow.scm (account-shepherd-service): Ditto. Mathieu Othacehe 2020-08-25linux-libre: Support module compression....This commit adds support for GZIP compression for linux-libre kernel modules. The initrd modules are kept uncompressed as the initrd is already compressed as a whole. The linux-libre kernel also supports XZ compression, but as Guix does not have any available bindings for now, and the compression time is far more significant, GZIP seems to be a better option. * gnu/build/linux-modules.scm (modinfo-section-contents): Use 'call-with-gzip-input-port' to read from a module file using '.gz' extension, (strip-extension): new procedure, (dot-ko): adapt to support compression, (ensure-dot-ko): ditto, (file-name->module-name): ditto, (find-module-file): ditto, (load-linux-module*): ditto, (module-name->file-name/guess): ditto, (module-name-lookup): ditto, (write-module-name-database): ditto, (write-module-alias-database): ditto, (write-module-device-database): ditto. * gnu/installer.scm (installer-program): Add "guile-zlib" to the extensions. * gnu/machine/ssh.scm (machine-check-initrd-modules): Ditto. * gnu/services.scm (activation-script): Ditto. * gnu/services/base.scm (default-serial-port): Ditto, (agetty-shepherd-service): ditto, (udev-service-type): ditto. * gnu/system/image.scm (gcrypt-sqlite3&co): Ditto. * gnu/system/linux-initrd.scm (flat-linux-module-directory): Add "guile-zlib" to the extensions and make sure that the initrd only contains uncompressed module files. * gnu/system/shadow.scm (account-shepherd-service): Add "guile-zlib" to the extensions. * guix/profiles.scm (linux-module-database): Ditto. Mathieu Othacehe 2020-08-06installer: Remove logical devices....If a device contains an active logical volume, BLKRRPART will report that the device is busy. This will cause this device to be filtered by "non-install-devices" procedure, which is not desired. Make sure to deactivate all logical volumes before device probing. Fixes <https://issues.guix.gnu.org/42683>. * gnu/installer.scm (installer-program): Add lvm2-static to the inputs. * gnu/installer/parted.scm (remove-logical-devices): New procedure, (init-parted): call it. Mathieu Othacehe 2020-07-26installer: Add NTFS support....This adds support for creating and editing NTFS partitions. It is however not possible yet to create root NTFS partitions, as overlaying on top of a fuse partition does not seem supported. * gnu/installer.scm (installer-program): Add "ntfs-3g" to the inputs. * gnu/installer/parted.scm (user-fs-type-name, user-fs-type->mount-type, partition-filesystem-user-type, create-ntfs-file-system, format-user-partitions): Add NTFS support. * gnu/installer/newt/partition.scm (run-fs-type-page): Add NTFS support. Mathieu Othacehe 2020-06-26installer: Use latest Guile....Since the installer is loading Guix modules built with Guile 3.0.4, the installer script must be run by the same Guile version to avoid a bytecode incompatibility. This is a follow-up of a2991de0f44a5f4db71ddad67e914fe3344a4505. * gnu/installer.scm (installer-program): Use guile3.0-latest for the installation script. Mathieu Othacehe