[PATCH] import: Update Bioconductor release to 3.5.
>From de9f486828827b1d024cad4918eed3ed96202cc0 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 26 Apr 2017 10:30:52 +0200
Subject: [PATCH] import: Update Bioconductor release to 3.5.
* guix/import/cran.scm: Change Bioconductor release to 3.5.
---
guix/import/cran.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 4d36882..be34a75 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -122,11 +122,11 @@ package definition."
(define %cran-url "http://cran.r-project.org/web/packages/";)
(define %bioconductor-url "http://bioconductor.org/packages/";)
-;; The latest Bioconductor release is 3.4. Bioconductor packages should be
+;; The latest Bioconductor release is 3.5. Bioconductor packages should be
;; updated together.
(define %bioconductor-svn-url
(string-append "https://readonly:readonly@";
- "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/"
+ "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/"
"madman/Rpacks/"))
--
2.7.4
>From cf66fb44a3a8c706b69adbc49fc76d8aaeb47975 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 26 Apr 2017 10:59:47 +0200
Subject: [PATCH] gnu: Add r-bookdown.
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
---
gnu/packages/bioinformatics.scm | 22 ++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46e238f..3853a78 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6092,6 +6092,28 @@ categorize packages in a Bioconductor package repository according to keywords,
also known as views, in a controlled vocabulary.")
(license license:artistic2.0)))
+(define-public r-bookdown
+ (package
+ (name "r-bookdown")
+ (version "0.3")
+ (source (origin
+(method url-fetch)
+(uri (cran-uri "bookdown" version))
+(sha256
+ (base32
+ "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://github.com/rstudio/bookdown";)
+ (synopsis "Authoring books and technical documents with R markdown")
+ (description "This package provides output formats and utilities for
+authoring books and technical documents with R Markdown.")
+ (license license:gpl3)))
+
(define-public r-biocstyle
(package
(name "r-biocstyle")
--
2.7.4
>From f661fce758f3f051f4f951c4c7384c69268169d9 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 26 Apr 2017 11:02:28 +0200
Subject: [PATCH] gnu: Add r-delayedarray.
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46e238f..67e8d0c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6656,6 +6656,36 @@ binary variant call (BCF) and compressed indexed tab-delimited (tabix)
files.")
(license license:expat)))
+(define-public r-delayedarray
+ (package
+(name "r-delayedarray")
+(version "0.2.0")
+(source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DelayedArray" version))
+ (sha256
+ (base32
+"0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r"
+(properties
+ `((upstream-name . "DelayedArray")))
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)))
+(home-page "http://bioconductor.org/packages/DelayedArray";)
+(synopsis "Delayed operations on array-like objects")
+(description
+ "Wrapping an array-like object (typically an on-disk object) in a
+DelayedArray object allows one to perform common array operations on it
+without loading the object in memory. In order to reduce memory usage
+and optimize performance, operations on the object are either delayed
+or executed using a block processing mechanism. Note that this also
+works on in-memory array-like objects like DataFrame objects (typically
+with Rle columns), Matrix objects, and ordinary arrays and data frames.")
+(license license:artistic2.0)))
+
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
--
2.7.4
>From d4313b287e05efcf54f87160d6e34ea60bfbadf6 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 26 Apr 2017 11:01:23 +0200
Subject: [PATCH] gnu: Add r-genomeinfodbdata.
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
---
gnu/packages/bioinform
store reference detection (was Re: JARs and reference scanning)
From: Chris Marusich Subject: Re: JARs and reference scanning Date: Tue, 25 Apr 2017 22:34:02 -0700 I have to admit that I do not know at all how the reference scanning and dependency-tracking in the store works. As I understand it, the mechanism used by the Guix daemon (and the Nix daemon) for scanning references doesn't work when the output of a derivation is scrambled in some way (e.g. compressed). Therefore, if we use JAR files, they should not be compressed. The code scanning for reference is in nix/libstore/references.cc . It looks for base32 hashes encoded as character strings in the binaries. Could/should this be generalized somehow? Apart from compression, store filenames encoded with 16-bit character encodings also cause problems (can happen with Qt or WxWidgets). And the are probably more cases where it fails. Does it make sense to expand the reference detecting code (perhaps this would lead to too many different special cases?), or maybe provide a mechanism to force references when the daemon cannot detect them. I suppose you can always add a text file with a list of store items to the output, but maybe there's a more elegant way? Thomas
Re: [PATCH] gnu: Add Xfce Notification Daemon.
Hi Efraim,
On Mon, 24 Apr 2017 22:22:43 +0300
Efraim Flashner wrote:
> The collection of inputs makes me wonder if it should be glib-or-gtk
> build-system and not "just" gnu-build-system. I don't have a good way to
> test if its necessary, but I'd look around.
Here's an updated patch using glib-or-gtk-build-system. I've removed
superfluous inputs, some where even superfluous with the gnu-build-system as
well, (I initially based the inputs on the build instructions provided with
the package). It's quite tidy now :)
Best,
Petter
From 75dfd4702327021481339ce9928ce5be17db45be Mon Sep 17 00:00:00 2001
From: Petter
Date: Fri, 21 Apr 2017 15:33:22 +0200
Subject: [PATCH] gnu: Add Xfce Notification Daemon.
* gnu/packages/xfce.scm (xfce4-notifyd): New variable.
---
gnu/packages/xfce.scm | 32
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm
index fce47d93c..6ec9f241b 100644
--- a/gnu/packages/xfce.scm
+++ b/gnu/packages/xfce.scm
@@ -5,6 +5,7 @@
;;; Copyright © 2016 Florian Paul Schmidt
;;; Copyright © 2016 Kei Kebreau
;;; Copyright © 2017 Ricardo Wurmus
+;;; Copyright © 2017 Petter
;;;
;;; This file is part of GNU Guix.
;;;
@@ -26,6 +27,7 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
+ #:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system gnu)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
@@ -850,3 +852,33 @@ calendar applications. It also includes a panel clock
plugin and an
international clock application capable of simultaneously showing clocks from
several different time zones.")
(license gpl2+)))
+
+(define-public xfce4-notifyd
+ (package
+(name "xfce4-notifyd")
+(version "0.3.6")
+(source (origin
+ (method url-fetch)
+ (uri (string-append "http://archive.xfce.org/src/apps/";
+ name "/" (version-major+minor version) "/"
+ name "-" version ".tar.bz2"))
+ (sha256
+ (base32
+"1ybcfqfynr33g5hp2lgq17s8qyx7rq6fd2iwrpwcvm6kml6prjpl"
+(build-system glib-or-gtk-build-system)
+(native-inputs
+ `(("intltool" ,intltool)
+ ("pkg-config" ,pkg-config)))
+(inputs
+ `(("libxfce4ui" ,libxfce4ui)
+ ("libnotify" ,libnotify)))
+(home-page "https://goodies.xfce.org/projects/applications/xfce4-notifyd";)
+(synopsis "Show notification bubbles on Xfce")
+(description
+ "The Xfce Notify Daemon (xfce4-notifyd for short) is a smallish program
+that implements the “server-side” portion of the Freedesktop desktop
+notifications specification. Applications that wish to pop up a notification
+bubble in a standard way can implicitly make use of xfce4-notifyd to do so by
+sending standard messages over D-Bus using the org.freedesktop.Notifications
+interface.")
+(license gpl2)))
--
2.12.2
pgpIg7INXESP1.pgp
Description: OpenPGP digital signature
Re: [PATCH] gnu: Add Xfce Notification Daemon.
I forgot to wrap "org.freedesktop.Notifications" in the description in
@code{..}, as suggested by Marius. Here it is with this as well.
From 922cbeb402ece8dbd0d592489069d7ccda64d702 Mon Sep 17 00:00:00 2001
From: Petter
Date: Fri, 21 Apr 2017 15:33:22 +0200
Subject: [PATCH] gnu: Add Xfce Notification Daemon.
* gnu/packages/xfce.scm (xfce4-notifyd): New variable.
---
gnu/packages/xfce.scm | 32
1 file changed, 32 insertions(+)
diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm
index fce47d93c..c8786dd69 100644
--- a/gnu/packages/xfce.scm
+++ b/gnu/packages/xfce.scm
@@ -5,6 +5,7 @@
;;; Copyright © 2016 Florian Paul Schmidt
;;; Copyright © 2016 Kei Kebreau
;;; Copyright © 2017 Ricardo Wurmus
+;;; Copyright © 2017 Petter
;;;
;;; This file is part of GNU Guix.
;;;
@@ -26,6 +27,7 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
+ #:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system gnu)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
@@ -850,3 +852,33 @@ calendar applications. It also includes a panel clock
plugin and an
international clock application capable of simultaneously showing clocks from
several different time zones.")
(license gpl2+)))
+
+(define-public xfce4-notifyd
+ (package
+(name "xfce4-notifyd")
+(version "0.3.6")
+(source (origin
+ (method url-fetch)
+ (uri (string-append "http://archive.xfce.org/src/apps/";
+ name "/" (version-major+minor version) "/"
+ name "-" version ".tar.bz2"))
+ (sha256
+ (base32
+"1ybcfqfynr33g5hp2lgq17s8qyx7rq6fd2iwrpwcvm6kml6prjpl"
+(build-system glib-or-gtk-build-system)
+(native-inputs
+ `(("intltool" ,intltool)
+ ("pkg-config" ,pkg-config)))
+(inputs
+ `(("libxfce4ui" ,libxfce4ui)
+ ("libnotify" ,libnotify)))
+(home-page "https://goodies.xfce.org/projects/applications/xfce4-notifyd";)
+(synopsis "Show notification bubbles on Xfce")
+(description
+ "The Xfce Notify Daemon (xfce4-notifyd for short) is a smallish program
+that implements the “server-side” portion of the Freedesktop desktop
+notifications specification. Applications that wish to pop up a notification
+bubble in a standard way can implicitly make use of xfce4-notifyd to do so by
+sending standard messages over D-Bus using the
+@code{org.freedesktop.Notifications} interface.")
+(license gpl2)))
--
2.12.2
pgpGAwn96HKFK.pgp
Description: OpenPGP digital signature
Re: [PATCH] gnu: Add Xfce Notification Daemon.
Petter writes: > Hi Efraim, > > On Mon, 24 Apr 2017 22:22:43 +0300 > Efraim Flashner wrote: > >> The collection of inputs makes me wonder if it should be glib-or-gtk >> build-system and not "just" gnu-build-system. I don't have a good way to >> test if its necessary, but I'd look around. > > Here's an updated patch using glib-or-gtk-build-system. I've removed > superfluous inputs, some where even superfluous with the gnu-build-system as > well, (I initially based the inputs on the build instructions provided with > the package). It's quite tidy now :) Takk! Pushed as b63106089a1eb2ac76303886f926f74967879386. By the way, patches should now be sent to the new "guix-patc...@gnu.org" issue tracker. :-) signature.asc Description: PGP signature
Re: [PATCH] gnu: Add Xfce Notification Daemon.
On Wed, 26 Apr 2017 16:39:19 +0200 Marius Bakke wrote: > > Takk! Pushed as b63106089a1eb2ac76303886f926f74967879386. > > By the way, patches should now be sent to the new "guix-patc...@gnu.org" > issue tracker. :-) Supert! :) Yes, I realized this a couple of days ago. I'll write an e-mail discussing the state of this in the online manual. Best, Petter pgpekWAYB0lrT.pgp Description: OpenPGP digital signature
Doc: reference to guix-devel for submitting patches
Hi Guix, I quite recently realized I sent a couple of patches to guix-devel, whereas they should now go to guix-patches. I use the online manual and the current state is that there's a couple of references to guix-devel for submitting patches. https://www.gnu.org/software/guix/manual/html_node/Submitting-Patches.html#Submitting-Patches >We welcome contributions in the form of patches as produced by git format-patch > sent to the mailing list Where "mailing list" is mailto:guix-devel@gnu.org. This is updated in the repository however, so I assume the online manual will reflect this shortly. But here, https://www.gnu.org/software/guix/manual/html_node/Contributing.html#Contributing it says > Please get in touch with us on guix-devel@gnu.org and #guix on the Freenode > IRC network. We welcome ideas, bug reports, patches, and anything that may be > helpful to the project. And here, https://www.gnu.org/software/guix/manual/html_node/Packaging-Guidelines.html#Packaging-Guidelines the user is referred to the Contributing node. > Once your package builds correctly, please send us a patch (see Contributing). I think at least one of the latter two nodes could use an update to better inform the soon-to-be-contributor that patches should go to guix-patches. Not sure what the better fix is though. What do you think? Best, Petter
Re: [PATCH] gnu: Add cool-retro-term.
On Tue, 25 Apr 2017 22:36:27 -0500
Eric Bavier wrote:
> Could you ping the developer about porting some of these fixes to their
> fork? I think we'd want to create a local patch for at least the first
> commit. The others could wait for a new release.
Sure, I'll do that!
> > +(inputs
> > + `(("qt" ,qt)))
>
> Does this package need all of qt, or could we use the component
> packages instead?
I don't know. I'll do some experiments and see.
> > +(synopsis "Terminal emulator mimicking old cathode ray tube (CRT)
> > +screens")
>
> I'd like to shorten this to "Terminal emulator"
Ok.
> > +(description
> > + "Cool-retro-term (crt) is a terminal emulator which mimics the
> > look and +feel of the old cathode ray tube (CRT) screens. It has been
> > designed to be +eye-candy, customizable, and reasonably lightweight.")
> > +(home-page "https://github.com/Swordfish90/cool-retro-term";)
> > +(license (list license:gpl2 license:gpl3)
>
> The license seems unclear: 1) there is both a gpl-2.txt and gpl-3.txt
> in $topsrcdir, but no mention of which actually applies in any of the
> source files, 2) $topsrcdir/packaging/debian/copyright claims GPL-3,
> while 4) $topsrcdir/packaging/rpm/cool-retro-term.spec and
> $topsrcdir/packaging/appdata/cool-retro-term.appdata.xml both claim
> GPL-3.0+, and 5) the qmltermwidget component appears to be under
> gpl2+. IANAL but this suggests license:gpl2+ to me. Does that seem
> right?
I can't answer this, hopefully someone else will chime in.
> It would not hurt to also list the SIL license, for
> $topsrcdir/app/qml/fonts/modern-hermit, and the X11 license for
> fonts/modern-pro-font-win-tweaked and fonts/modern-proggy-tiny.
>
> The fonts/modern-envy-code-r font probably needs to be stripped; it's
> license is non-free; from 'Read Me.txt':
>
> "Free to use but redistribution prohibited."
>
> and the fonts/1977-apple2, fonts/1977-commodore-pet, probably also needs
> to be stripped as non-free; from 'FreeLicense.txt':
>
> "1. The User may not sell copies of the Software for a fee."
>
> The fonts/1979-atari-400-800 font seems to be non-free license, which is
> not mentioned in the 'ReadMe.rtf' but only on the WayBack Machine at
> https://web-beta.archive.org/web/20080907111008/http://www2.bitstream.net/~marksim/atarimac/fonts.html
> :
>
> "These fonts are freeware and may not be offered for sale seperately
> or as part of a collection."
>
> The fonts/1982-commodore64 font is licensed under non-free terms; see
> fonts/1982-commodore64/license.txt
>
> The only mention of a license for fonts/1985-ibm-pc-vga is at
> http://www.dafont.com/font-comment.php?file=perfect_dos_vga_437 where
> the author says "The license is this: this font is free to use in
> whatever you want.", but that probably "doesn't count".
>
> I could not find license info for a few of the other fonts.
>
> OTOH I recall a discussion on IRC recently about fonts embedded in
> packages being treated as non-functional data, and thus OK from a FSDG
> perspective. But I would want verification on that.
Let's see if someone can shine some light on this.
> Sorry for the dump. I'd like to work these things out; it looks like a
> fun terminal to use.
No problem, there's the right way and there's the not-right way!
Let's do it right! :)
Best,
Petter
pgpcNkcNzaue4.pgp
Description: OpenPGP digital signature
Re: store reference detection (was Re: JARs and reference scanning)
On April 26, 2017 4:53:33 AM PDT, Thomas Danckaert wrote: [...] >The code scanning for reference is in nix/libstore/references.cc . >It looks for base32 hashes encoded as character strings in the >binaries. > >Could/should this be generalized somehow? Apart from compression, >store filenames encoded with 16-bit character encodings also cause >problems (can happen with Qt or WxWidgets). And the are probably >more cases where it fails. > >Does it make sense to expand the reference detecting code (perhaps >this would lead to too many different special cases?), or maybe >provide a mechanism to force references when the daemon cannot detect >them. I suppose you can always add a text file with a list of store >items to the output, but maybe there's a more elegant way? > >Thomas The text file idea with the dependencies that Hartmut proposed seems an elegant solution; it would make the reference searching process cheaper and available for any kind of format.
Re: Doc: reference to guix-devel for submitting patches
Hi Petter! I think all of the different mailing lists used by Guix and their intended use should be mentioned and or corrected in the manual (sending patches , reporting bugs, discussing ideas or requesting help, etc.)
Staging merged!
On Tue, Apr 25, 2017 at 02:33:13PM -0400, Leo Famulari wrote: > I just merged master into staging and started a new evaluation. Barring > any new complications, I plan to merge staging into master later today. I merged the staging branch into the master branch as 2018eea07bb00663d2f0cec9d9085d51afa4513b and started a new evaluation. Most of the substitutes should already be available. Some notable changes are updates to mesa, xorg-server, gtk+, and tzdata. Thanks to Marius for working on the branch! signature.asc Description: PGP signature
Re: Helping with Guix on Hurd: my notes
Thank you Jan for sharing these precious notes! I've saved your message; I had started looking into Hurd last year, but then turned my attention to Guix and have been (slowly) making myself at home here. I intend to restart investigating Hurd as things stabilize on the Guix side :). They are destined to work together anyway ;) Maxim signature.asc Description: PGP signature
Re: Staging merged!
Leo Famulari writes: > On Tue, Apr 25, 2017 at 02:33:13PM -0400, Leo Famulari wrote: >> I just merged master into staging and started a new evaluation. Barring >> any new complications, I plan to merge staging into master later today. > > I merged the staging branch into the master branch as > 2018eea07bb00663d2f0cec9d9085d51afa4513b and started a new evaluation. > Most of the substitutes should already be available. > > Some notable changes are updates to mesa, xorg-server, gtk+, and tzdata. > > Thanks to Marius for working on the branch! Yay, thanks a lot for taking care of this! -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net
Re: [PATCH] import: Update Bioconductor release to 3.5.
Roel Janssen writes:
> From de9f486828827b1d024cad4918eed3ed96202cc0 Mon Sep 17 00:00:00 2001
> From: Roel Janssen
> Date: Wed, 26 Apr 2017 10:30:52 +0200
> Subject: [PATCH] import: Update Bioconductor release to 3.5.
>
> * guix/import/cran.scm: Change Bioconductor release to 3.5.
> guix/import/cran.scm | 4 ++--
> 1 file changed, 2 insertions(+), 2 deletions(-)
Excellent! I planned to do this next week, but I’m glad you beat me to
it :)
>
> +(define-public r-bookdown
> + (package
> + (name "r-bookdown")
> + (version "0.3")
> + (source (origin
> +(method url-fetch)
> +(uri (cran-uri "bookdown" version))
> +(sha256
> + (base32
> + "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"
> + (build-system r-build-system)
> + (propagated-inputs
> + `(("r-htmltools" ,r-htmltools)
> + ("r-knitr" ,r-knitr)
> + ("r-rmarkdown" ,r-rmarkdown)
> + ("r-yaml" ,r-yaml)))
> + (home-page "https://github.com/rstudio/bookdown";)
> + (synopsis "Authoring books and technical documents with R markdown")
> + (description "This package provides output formats and utilities for
> +authoring books and technical documents with R Markdown.")
> + (license license:gpl3)))
> +
LGTM. Sadly, it does indeed seem to be GPLv3 only.
> From f661fce758f3f051f4f951c4c7384c69268169d9 Mon Sep 17 00:00:00 2001
> From: Roel Janssen
> Date: Wed, 26 Apr 2017 11:02:28 +0200
> Subject: [PATCH] gnu: Add r-delayedarray.
>
> * gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
[…]
> +(define-public r-delayedarray
> + (package
> +(name "r-delayedarray")
> +(version "0.2.0")
> +(source (origin
> + (method url-fetch)
> + (uri (bioconductor-uri "DelayedArray" version))
> + (sha256
> + (base32
> +"0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r"
> +(properties
> + `((upstream-name . "DelayedArray")))
> +(build-system r-build-system)
> +(propagated-inputs
> + `(("r-biocgenerics" ,r-biocgenerics)
> + ("r-s4vectors" ,r-s4vectors)
> + ("r-iranges" ,r-iranges)
> + ("r-matrixstats" ,r-matrixstats)))
> +(home-page "http://bioconductor.org/packages/DelayedArray";)
> +(synopsis "Delayed operations on array-like objects")
> +(description
> + "Wrapping an array-like object (typically an on-disk object) in a
> +DelayedArray object allows one to perform common array operations on
> it
@code{DelayedArray}
> +without loading the object in memory. In order to reduce memory usage
> +and optimize performance, operations on the object are either delayed
> +or executed using a block processing mechanism. Note that this also
> +works on in-memory array-like objects like DataFrame objects
> (typically
@code{DataFrame}
> +with Rle columns), Matrix objects, and ordinary arrays and data frames.")
> +(license license:artistic2.0)))
> +
Okay with these changes.
> From d4313b287e05efcf54f87160d6e34ea60bfbadf6 Mon Sep 17 00:00:00 2001
> From: Roel Janssen
> Date: Wed, 26 Apr 2017 11:01:23 +0200
> Subject: [PATCH] gnu: Add r-genomeinfodbdata.
>
> * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
> ---
[…]
> +(define-public r-genomeinfodbdata
> + (package
> +(name "r-genomeinfodbdata")
> +(version "0.99.0")
> +(source (origin
> + (method url-fetch)
> + (uri (bioconductor-uri "GenomeInfoDbData" version))
> + (sha256
> + (base32
> +"120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25"
> +(properties
> + `((upstream-name . "GenomeInfoDbData")))
> +(build-system r-build-system)
> +(home-page "http://bioconductor.org/packages/GenomeInfoDbData";)
> +(synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
> +(description
> + "This package contains data for mapping between NCBI taxonomy ID and
> +species. It is used by functions in the GenomeInfoDb package.")
> +(license license:artistic2.0)))
> +
LGTM!
I’d be happy if you could take care of the mass update. I should note
that sometimes new inputs are required. To find them I usually run the
update in a separate branch where I’ve applied changes to import anew
and compare with the existing package expression when updating. It’s on
my list to clean this all up and submit my changes for review. It’s
ugly but it works pretty well. If you’re interested I could send you a
patch.
--
Ricardo
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
https://elephly.net
