Re: Numpy failures

[Federico Beffa]

Andreas Enge  writes:

> python-numpy-bootstrap currently fails its tests on hydra, which entails a
> bunch of other failures. On my own x86_64 machines, the build succeeds,
> however.

We believe the reason being the fact that hydra doesn't handle the flag
'#:substitutable?' properly. As a result we have the following
situation:

1. hydra builds a version of ATLAS optimized for its CPU locally.

2. 'python-numpy-bootstrap' and co., on some architectures, probably get
an incompatible version of ATLAS and therefore fail to pass some tests.

You can check in the build log of 'python-numpy-bootstrap' that ATLAS,
despite the flas, is substituted (no local build on the slave).

At some point we should fix the support for '#:substitutable?' on hydra
(or the upcoming 'guix publish').

Regards,
Fede

Re: [PATCH] gnu: Add smartmontools.

[Taylan Ulrich Bayırlı/Kammer]

Mark H Weaver  writes:

> Debian claims that the license is gpl2, not gpl2+.
>
> Please be more careful checking licenses.  Debian tends to be very
> thorough about this, so a good method is to find the package on Debian,
> e.g. , select the appropriate
> package (preferably the same version or close to it) and then choose the
> "Copyright File" link in the right column.

OK, thanks for the tip.  However, both the README and individual source
files use the "or (at your option) any later version" phrasing.  I
wonder why Debian marked it gpl2?

Taylan

cannot use snippets with zip source

[Ricardo Wurmus]

Hi Guix,

I'm packaging HISAT whose sources are available as a zip archive.  This
means that I have to replace the unpack phase to use "unzip" to unpack
the source archive.  Unfortunately, it seems that I cannot use snippets
for "static" patches to the sources when a zip archive is used (rather
than a tarball).

When I use snippets, guix determines the decompression type to be "xz"
and then fails:


~~~
The following derivations will be built:
   /gnu/store/jra0psbhjkcf66rdmj5bshivf32nyf73-hisat-0.1.4.drv
   
/gnu/store/1hpkf8yl4hcifzalnwh2hj6qwi8jid3w-hisat-0.1.4-beta-source.tar.xz.drv
   /gnu/store/pri51516agpcm9k6asgbdmspxnim3l7q-hisat-0.1.4.drv
@ build-started 
/gnu/store/1hpkf8yl4hcifzalnwh2hj6qwi8jid3w-hisat-0.1.4-beta-source.tar.xz.drv 
- x86_64-linux 
/var/log/guix/drvs/1h//pkf8yl4hcifzalnwh2hj6qwi8jid3w-hisat-0.1.4-beta-source.tar.xz.drv.bz2
/gnu/store/c4km8376y174q7gxqahf4hc1i1xaqkqh-tar-1.28/bin/tar: This does not 
look like a tar archive
/gnu/store/c4km8376y174q7gxqahf4hc1i1xaqkqh-tar-1.28/bin/tar: Skipping to next 
header
/gnu/store/c4km8376y174q7gxqahf4hc1i1xaqkqh-tar-1.28/bin/tar: Exiting with 
failure status due to previous errors
builder for 
`/gnu/store/1hpkf8yl4hcifzalnwh2hj6qwi8jid3w-hisat-0.1.4-beta-source.tar.xz.drv'
 failed with exit code 1
@ build-failed 
/gnu/store/1hpkf8yl4hcifzalnwh2hj6qwi8jid3w-hisat-0.1.4-beta-source.tar.xz.drv 
- 1 builder for 
`/gnu/store/1hpkf8yl4hcifzalnwh2hj6qwi8jid3w-hisat-0.1.4-beta-source.tar.xz.drv'
 failed with exit code 1
cannot build derivation 
`/gnu/store/pri51516agpcm9k6asgbdmspxnim3l7q-hisat-0.1.4.drv': 1 dependencies 
couldn't be built
cannot build derivation 
`/gnu/store/jra0psbhjkcf66rdmj5bshivf32nyf73-hisat-0.1.4.drv': 1 dependencies 
couldn't be built
killing process 2524
guix build: error: build failed: build of 
`/gnu/store/jra0psbhjkcf66rdmj5bshivf32nyf73-hisat-0.1.4.drv' failed
~~~


That's probably due to the definiton of `decompression-type' in
`patch-and-repack' in the file guix/packages.scm:


~~
(define decompression-type
(cond ((string-suffix? "gz" source-file-name)  "gzip")
  ((string-suffix? "bz2" source-file-name) "bzip2")
  ((string-suffix? "lz" source-file-name)  "lzip")
  (else "xz")))
~~

Is there a way to use snippets with zip archives?  Could
`patch-and-repack' be modified to use the package's "unpack" phase
instead of implementing its own unpack mechanism?

~~ Ricardo

[PATCH]: gnu: Add HISAT.

[Ricardo Wurmus]

Attached is a patch to add HISAT, another popular read aligner.

I would have really liked to use snippets here for a few static changes
to the sources, but it seems that snippets cannot be used with zip
archives (see my earlier message to the mailing list).

~~ Ricardo

>From 305768bfef9bf4bc8d57828e27b8439dedd574bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Mon, 9 Feb 2015 12:13:26 +0100
Subject: [PATCH] gnu: Add HISAT.

* gnu/packages/bioinformatics.scm (hisat): New variable.
---
 gnu/packages/bioinformatics.scm | 77 -
 1 file changed, 76 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c0d1438..425558d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -29,8 +29,9 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages python))
+  #:use-module (gnu packages python)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages zip))
 
 (define-public bedtools
   (package
@@ -181,6 +182,80 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
 Illumina, Roche 454, and the SOLiD platform.")
 (license license:gpl3)))
 
+(define-public hisat
+  (package
+(name "hisat")
+(version "0.1.4")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"http://ccb.jhu.edu/software/hisat/downloads/hisat-";
+version "-beta-source.zip"))
+  (sha256
+   (base32
+"1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"
+(build-system gnu-build-system)
+(arguments
+ '(#:tests? #f ;no check target
+   #:make-flags '("allall")
+   #:phases
+   (alist-replace
+'unpack
+(lambda* (#:key source #:allow-other-keys)
+  (and (zero? (system* "unzip" source))
+   (chdir "hisat-0.1.4-beta")))
+(alist-cons-after
+ 'unpack 'patch-sources
+ (lambda _
+   ;; XXX Cannot use snippet because zip files are not supported
+   (substitute* "Makefile"
+ (("^CC = .*$") "CC = gcc")
+ (("^CPP = .*$") "CPP = g++")
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
+   (substitute* '("hisat-build" "hisat-inspect")
+ (("/usr/bin/env") (which "env"
+ (alist-replace
+  'install
+  (lambda* (#:key outputs #:allow-other-keys)
+(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+  (mkdir-p bin)
+  (for-each (lambda (file)
+  (copy-file file (string-append bin file)))
+'("hisat"
+  "hisat-build"
+  "hisat-build-s"
+  "hisat-build-l"
+  "hisat-align-s"
+  "hisat-align-l"
+  "hisat-inspect"
+  "hisat-inspect-s"
+  "hisat-inspect-l"
+  "hisat-build-s-debug"
+  "hisat-build-l-debug"
+  "hisat-align-s-debug"
+  "hisat-align-l-debug"
+  "hisat-inspect-s-debug"
+  "hisat-inspect-l-debug"
+  (alist-delete 'configure %standard-phases))
+(native-inputs
+ `(("unzip" ,unzip)))
+(inputs
+ `(("perl" ,perl)
+   ("python" ,python)
+   ("zlib" ,zlib)))
+(home-page "http://ccb.jhu.edu/software/hisat/index.shtml";)
+(synopsis "Hierarchical indexing for spliced alignment of transcripts")
+(description
+ "HISAT is a fast and sensitive spliced alignment program for mapping
+RNA-seq reads.  In addition to one global FM index that represents a whole
+genome, HISAT uses a large set of small FM indexes that collectively cover the
+whole genome.  These small indexes (called local indexes) combined with
+several alignment strategies enable effective alignment of RNA-seq reads, in
+particular, reads spanning multiple exons.")
+(license license:gpl3)))
+
 (define-public samtools
   (package
 (name "samtools")
-- 
2.1.0

Re: cannot use snippets with zip source

[Andreas Enge]

On Mon, Feb 09, 2015 at 11:54:02AM +0100, Ricardo Wurmus wrote:
> I'm packaging HISAT whose sources are available as a zip archive.  This
> means that I have to replace the unpack phase to use "unzip" to unpack
> the source archive.  Unfortunately, it seems that I cannot use snippets
> for "static" patches to the sources when a zip archive is used (rather
> than a tarball).

Actually, I recently wondered about the same thing concerning a single
file I wanted to download and patch. I suppose this makes the problem
even worse... Anyway, in my case it is more a distraction, as I can easily
run the snippet in the install phase.

Andreas

Re: [ART] Logo proposal

[Andreas Enge]

Hello!

I like all logos I have seen so far, but as Taylan I think we should not
brand GSD too much and stay as close as we can to the GNU brand.

And send more packages - I have the impression our rate slowed down since
we reached the 1000 packages milestone ;-)

Andreas

[PATCH]: gnu: Add STAR.

[Ricardo Wurmus]

Hi Guix,

here's another aligner for RNA-seq data.  The description is rather
dense but that's what I came up with after deleting as much as I could
from the description here:

http://bioinformatics.oxfordjournals.org/content/29/1/15

~~ Ricardo

>From efd3b0fd1b5ed0b7ca0168e3356c950482b694d6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Mon, 9 Feb 2015 15:38:30 +0100
Subject: [PATCH] gnu: Add STAR.

* gnu/packages/bioinformatics.scm (star): New variable.
---
 gnu/packages/bioinformatics.scm | 48 +
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 425558d..c8fff5f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -31,6 +31,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages vim)
   #:use-module (gnu packages zip))
 
 (define-public bedtools
@@ -360,3 +361,50 @@ algorithms and data structures for string representation and their
 manipulation, online and indexed string search, efficient I/O of
 bioinformatics file formats, sequence alignment, and more.")
 (license license:bsd-3)))
+
+(define-public star
+  (package
+(name "star")
+(version "2.4.0j")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://github.com/alexdobin/STAR/archive/STAR_";
+version ".tar.gz"))
+  (sha256
+   (base32
+"1y3bciych1aw6s7k8sy1saj23dcan9wk4d4f96an499slkxwz712"))
+  (modules '((guix build utils)))
+  (snippet
+   '(substitute* "source/Makefile"
+  (("/bin/rm") "rm")
+(build-system gnu-build-system)
+(arguments
+ '(#:tests? #f ;no check target
+   #:make-flags '("STAR")
+   #:phases
+   (alist-cons-after
+'unpack 'enter-source-dir (lambda _ (chdir "source"))
+(alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+   (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (copy-file "STAR" (string-append bin "STAR"
+ (alist-delete
+  'configure %standard-phases)
+(native-inputs
+ `(("vim" ,vim))) ; for xxd
+(inputs
+ `(("zlib" ,zlib)))
+(home-page "https://github.com/alexdobin/STAR";)
+(synopsis "Universal RNA-seq aligner")
+(description
+ "The Spliced Transcripts Alignment to a Reference (STAR) software is
+based on a previously undescribed RNA-seq alignment algorithm that uses
+sequential maximum mappable seed search in uncompressed suffix arrays followed
+by seed clustering and stitching procedure.  In addition to unbiased de novo
+detection of canonical junctions, STAR can discover non-canonical splices and
+chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
+sequences.")
+(license license:gpl3)))
-- 
2.1.0

Re: [PATCH]: Add Ant.

[Ricardo Wurmus]

Ludovic Courtès writes:
>> According to the docs[1],
>>
>> "ANT_HOME is used by the launcher script for finding the
>>  libraries. JAVA_HOME is used by the launcher for finding the
>>  JDK/JRE to use."
>>
>> So, it would indeed make sense to modify the "launcher script"
>> (whichever this is, probably "ant") to set ANT_HOME before continuing.
>> I'm not a Java person, though, so I don't know if this is considered
>> bad.
>
> I think this would be fine.

I just ran "ant" after setting JAVA_HOME but without setting ANT_HOME,
and it appeared to work just fine.  I don't really have anything to test
this with at the moment, but it seems to me that maybe ANT_HOME isn't
required after all.

>> I even wonder if we should make icedtea6 a build-time input only to
>> compile the libraries, so that one would not need to have icedtea6
>> installed at all.  Or should there be multiple variants of Java packages
>> akin to what we do with Python modules?  I must admit that I find this
>> rather confusing.  How closely do we have to tie Java applications /
>> libraries to a particular version of the JDK?  Are there any insights
>> you could share about how it's done in Nix?
>
> This commit from Nixpkgs gives some insight:
>
> commit 54d172141435d61813666ccb6dbfe8a58a9ce896
> Author: Eelco Dolstra 
> Date:   Fri Jan 3 13:29:06 2014 +0100
>
> ant: Update to 1.9.3
> 
> Also, Ant no longer has a build-time dependency on a particular JDK.
> It finds the JDK via $JAVA_HOME or $PATH (by looking up javac).  This
> way, we don't need to have separate packages like apacheAntOpenJDK and
> apacheAntOracleJDK.  It also seems reasonable: after all, installing
> GNU Make doesn't give you a C compiler either.  It does mean that
> instead of
> 
>   buildInputs = [ ant ];
> 
> you now need to write something like
> 
>   buildInputs = [ ant jdk ];
>
> However, the Nixpkgs does not actually build Ant; it just reuses
> pre-built binaries, which may not be what we want.

Would it be okay if we moved icedtea6 from inputs to native-inputs?  Ant
cannot run without Java, but which Java version should be used depends
on JAVA_HOME.  To compile the Ant libraries we only need *some* JDK at
build time, so I think making this a native input is appropriate.

Attached is an updated patch.

What do you think?

~~ Ricardo

>From 977facdd8e70f4d8c0016e39ca87f53060464099 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus 
Date: Fri, 30 Jan 2015 16:57:13 +0100
Subject: [PATCH] gnu: Add Ant.

* gnu/packages/java.scm (ant-minimal): New variable.
---
 gnu/packages/java.scm | 49 +
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 4a86f63..80ef21a 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -48,6 +48,55 @@
   #:use-module (gnu packages zip)
   #:use-module (gnu packages texinfo))
 
+(define-public ant-minimal
+  (package
+(name "ant-minimal")
+(version "1.9.4")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://www.apache.org/dist/ant/source/apache-ant-";
+version "-src.tar.gz"))
+  (sha256
+   (base32
+"09kf5s1ir0rdrclsy174bsvbdcbajza9fja490w4mmvcpkw3zpak"
+(build-system gnu-build-system)
+(arguments
+ `(#:tests? #f ; Tests require hamcrest-core, which needs Ant to build.
+   #:phases
+   (alist-cons-after
+'unpack 'remove-scripts
+;; Remove bat / cmd scripts for DOS as well as the antRun and runant
+;; wrappers.
+(lambda _
+  (for-each delete-file
+(find-files "src/script"
+"(.*\\.(bat|cmd)|runant.*|antRun.*)")))
+(alist-replace
+ 'build
+ (lambda _
+   (setenv "JAVA_HOME"
+   (assoc-ref %build-inputs "icedtea6"))
+   ;; disable tests to avoid dependecy on hamcrest-core
+   (substitute* "build.xml"
+ (("depends=\"jars,test-jar\"") "depends=\"jars\""))
+   (system* "bash" "bootstrap.sh"
+(string-append "-Ddist.dir="
+   (assoc-ref %outputs "out"
+ (alist-delete
+  'configure
+  (alist-delete 'install %standard-phases))
+(native-inputs
+ `(("icedtea6" ,icedtea6)))
+(home-page "http://ant.apache.org";)
+(synopsis "Build tool for Java")
+(description
+ "Ant is a platform-independent build tool for Java.  It is similar to
+make but is implemented using the Java language, requires the Java platform,
+and is best suited to building Java projects.  Ant uses XML to describe the
+build process and its dependencies, whereas Make uses Makefile format.")
+(license license:asl2.0)))
+
 (define-public icedtea6
   (package
 (name "icedtea6")
-- 
2.1.0

[PATCH] gnu: ffmpeg: Add 'lame' input.

[Federico Beffa]

I would like to propose to add 'lame' as an input to ffmpeg. This
activates mp3 encoding support.

Regards,
Fede
From d4f12db8c07961543e3bb55a1d342680b925cc63 Mon Sep 17 00:00:00 2001
From: Federico Beffa 
Date: Mon, 9 Feb 2015 16:05:39 +0100
Subject: [PATCH] gnu: ffmpeg: Add 'lame' input.

* gnu/packages/video.scm (ffmpeg): Add 'lame' input and corresponding
  configure flag.
---
 gnu/packages/video.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 5008749..31e5d70 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -73,6 +73,7 @@
  `(("fontconfig" ,fontconfig)
("freetype" ,freetype)
("opus" ,opus)
+   ("lame" ,lame)
("libtheora" ,libtheora)
("libvorbis" ,libvorbis)
("libvpx" ,libvpx)
@@ -167,6 +168,7 @@
   "--enable-fontconfig"
   ;; "--enable-gnutls" ; causes test failures
   "--enable-libfreetype"
+  "--enable-libmp3lame"
   "--enable-libopus"
   "--enable-libspeex"
   "--enable-libtheora"
-- 
1.8.4

Re: [PATCH] gnu: ffmpeg: Add 'lame' input.

[Andreas Enge]

On Mon, Feb 09, 2015 at 04:14:35PM +0100, Federico Beffa wrote:
> I would like to propose to add 'lame' as an input to ffmpeg. This
> activates mp3 encoding support.

Sounds good!

Andreas

Re: [ART] Logo proposal

[Amirouche Boubekki]

> I like all logos I have seen so far, but as Taylan I think we should not
> brand GSD too much and stay as close as we can to the GNU brand

Luis GSD logo is really close to GNU branding. Looks more modern. Maybe it
should use the same colors?

On Mon Feb 09 2015 at 1:38:01 PM Andreas Enge  wrote:

> Hello!
>
> I like all logos I have seen so far, but as Taylan I think we should not
> brand GSD too much and stay as close as we can to the GNU brand.
>
> And send more packages - I have the impression our rate slowed down since
> we reached the 1000 packages milestone ;-)
>
> Andreas
>
>
>

Re: [PATCH 3/4] gnu: bootstrap: Add the location of where ld.so is located on Hurd systems.

[Manolis Ragkousis]

Pushed.

Thanks,
Manolis

Re: [PATCH 4/4] gnu: gcc: Also substitute the dynamic linker name for GNU, (ie. Hurd) systems.

[Marek Benc]

On 02/08/2015 12:22 AM, Ludovic Courtès wrote:



Would this slightly more concise approach work:



diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index 6143f5b..5cb7f8b 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -202,10 +202,11 @@ where the OS part is overloaded to denote a specific 
ABI---into GCC

  ;; Fix the dynamic linker's file name.
  (substitute* (find-files "gcc/config"
- "^linux(64|-elf|-eabi)?\\.h$")
-  (("#define GLIBC_DYNAMIC_LINKER([^ ]*).*$" _ suffix)
-   (format #f "#define GLIBC_DYNAMIC_LINKER~a \"~a\"~%"
-   suffix
+ "^(gnu|linux)(64|-elf|-eabi)?\\.h$")
+  (("#define (GLIBC|GNU_USER)_DYNAMIC_LINKER([^ ]*).*$" _
+kind suffix)
+   (format #f "#define ~a_DYNAMIC_LINKER~a \"~a\"~%"
+   kind suffix
 (string-append libc ,(glibc-dynamic-linker)

  ;; Tell where to find libstdc++, libc, and `?crt*.o', except





Most probably yes, but the previous part of the code (which joins the 
lines defining a dynamic linker) will also need to be modified to take 
GNU_USER_DYNAMIC_LINKER into account, as the code also substitutes some 
entries in the linux.h files, which are usually multiline (most of the 
time, a CHOOSE_DYNAMIC_LINKER macro)...


Sorry, I'm way too weak of a schemer to do that, even though it's 
probably incredibly simple...





Thanks,
Ludo’.



--
Marek.

Re: A secure multimedia workstation

[Dirk Scheuring]

Ludo wrote:

> Ideally, it would boil down to preparing a custom 'operating-system'
declaration-with all the services and packages of interest ready to
use-that users would inherit from to further customize things.

Yes, that would be the idea. You here and and your relatives (1) are way
further up the curve, of course, so I'm greatly encouraged by getting
what seems to be a "sounds reasonable" reply from you. This thing has
just migrated from the "crazy fantasy" to the "important side project"
stage for me.

> At this point the Guix System Distribution is still very much for
hackers rather than newcomers, but I would love to see projects like
this one grow.

I reckon that it will take me some years to learn how to build what I
can now only describe, but I also know why I want to spend the time: I
plan to use computers for decades more; I figured out that most of my
problems with them might be solvable by freedom, statelessness, and
homoiconicity; and Guix offers exactly these features. This makes it
seem worth the investment.

> Thanks for your interest.

Thanks for your work. Thanks to all of you here. I believe that Guix
matters, so carry on, please.

Dirk

(1)
https://www.domenkozar.com/2014/03/11/why-puppet-chef-ansible-arent-good-enough-and-we-can-do-better/

Re: A secure multimedia workstation

[David Thompson]

Dirk Scheuring  writes:

> https://www.domenkozar.com/2014/03/11/why-puppet-chef-ansible-arent-good-enough-and-we-can-do-better/

I really like this article.  It does a good job of classifying the
various configuration management tools in mainstream use (imperative,
stateful declarative) and showing how the stateless declarative
configuration offered by Nix and Guix is both simpler and technically
superior.

-- 
David Thompson
Web Developer - Free Software Foundation - http://fsf.org
GPG Key: 0FF1D807
Support the FSF: https://fsf.org/donate

Re: A secure multimedia workstation

[Andreas Enge]

On Mon, Feb 09, 2015 at 06:33:02PM +0100, Dirk Scheuring wrote:
> I reckon that it will take me some years to learn how to build what I
> can now only describe

Years, I do not know. Hopefully less! Definitely you could start helping 
the Guix project (and your own project) by packaging software that you are
interested in and that we do not provide yet. Some guile/scheme knowledge
is helpful, but not strictly required, see
   https://www.gnu.org/software/guix/guix-ghm-andreas-20130823.pdf
Some experience in installing software by hand is needed, though.
The irc channel is usually a good place to ask for advice.

Andreas

[PATCH] gnu: Add openntpd.

[Taylan Ulrich Bayırlı/Kammer]

>From d9e0a4d07ee7e82582589b1e1cd3be218dd6b08f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Taylan=20Ulrich=20Bay=C4=B1rl=C4=B1/Kammer?=
 
Date: Mon, 9 Feb 2015 21:39:41 +0100
Subject: [PATCH] gnu: Add openntpd.

* gnu/packages/ntp.scm (openntpd): New variable.
---
 gnu/packages/ntp.scm | 21 +
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/ntp.scm b/gnu/packages/ntp.scm
index 24ce2f5..c81484c 100644
--- a/gnu/packages/ntp.scm
+++ b/gnu/packages/ntp.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 John Darrington 
 ;;; Copyright © 2014, 2015 Mark H Weaver 
+;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -61,3 +62,23 @@ computers over a network.")
  "http://www.eecis.udel.edu/~mills/ntp/html/copyright.html";
  "A non-copyleft free licence from the University of Delaware"))
(home-page "http://www.ntp.org";)))
+
+(define-public openntpd
+  (package
+(name "openntpd")
+(version "5.7p3")
+(source (origin
+  (method url-fetch)
+  ;; XXX Use mirror://openbsd
+  (uri (string-append
+"http://ftp.openbsd.org/pub/OpenBSD/OpenNTPD/openntpd-";
+version ".tar.gz"))
+  (sha256
+   (base32
+"0filjmb3b8rc39bvhm8q2azzj10ljfgq41qih71pxv919j57qhag"
+(build-system gnu-build-system)
+(home-page "http://www.openntpd.org/";)
+(synopsis "NTP client and server by the OpenBSD Project")
+(description "OpenNTPD is the OpenBSD Project's implementation of a client
+and server for the Network Time Protocol.")
+(license l:isc)))
-- 
2.2.1

Re: [ART] Logo proposal

[Ludovic Courtès]

Luis Felipe López Acevedo  skribis:

> I made some logos for Guix and GuixSD:
>
> * http://sirgazil.bitbucket.org/static/temp/img/guix/Guix.png
> * http://sirgazil.bitbucket.org/static/temp/img/guix/GuixSD.png
>
> I understand if you prefer using the current Guix logo and no logo for
> GuixSD, though. I just wanted to share anyways.

I’m very impressed by both, I like them!

It raises the two questions you mention.  I sympathize both with what
you wrote before and your current hesitation wrt. branding.

I need to think more (and read more what others think) but yeah, why not
a GuixSD logo.

Thank you!

Ludo’.

[PATCH] gnu: Add ltrace.

[Taylan Ulrich Bayırlı/Kammer]

>From 2f8c97c384afc5b3ae1b17382024f7c3458a576f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Taylan=20Ulrich=20Bay=C4=B1rl=C4=B1/Kammer?=
 
Date: Mon, 9 Feb 2015 23:35:03 +0100
Subject: [PATCH] gnu: Add ltrace.

* gnu/packages/linux.scm (ltrace): New variable.
---
 gnu/packages/linux.scm | 24 
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 09e2a4c..bb06208 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2012 Nikita Karetnikov 
 ;;; Copyright © 2014, 2015 Mark H Weaver 
 ;;; Copyright © 2015 Federico Beffa 
+;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -670,6 +671,29 @@ images more compressible.")
 trace of all the system calls made by a another process/program.")
 (license bsd-3)))
 
+(define-public ltrace
+  (package
+(name "ltrace")
+(version "0.7.3")
+(source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.ltrace.org/ltrace_"; version
+ ".orig.tar.bz2"))
+ (sha256
+  (base32
+   "00wmbdghqbz6x95m1mcdd3wd46l6hgcr4wggdp049dbifh3qqvqf"
+(build-system gnu-build-system)
+(inputs `(("libelf" ,libelf)))
+(arguments
+ '(#:configure-flags '("--disable-werror")))
+(home-page "http://www.ltrace.org/";)
+(synopsis "Library call tracer for Linux")
+(description
+ "ltrace intercepts and records dynamic library calls which are called by
+an executed process and the signals received by that process.  It can also
+intercept and print the system calls executed by the program.")
+(license gpl2+)))
+
 (define-public alsa-lib
   (package
 (name "alsa-lib")
-- 
2.2.1

Re: [PATCH] gnu: Add ltrace.

[David Thompson]

"Taylan Ulrich Bayırlı/Kammer"  writes:

> From 2f8c97c384afc5b3ae1b17382024f7c3458a576f Mon Sep 17 00:00:00 2001
> From: =?UTF-8?q?Taylan=20Ulrich=20Bay=C4=B1rl=C4=B1/Kammer?=
>  
> Date: Mon, 9 Feb 2015 23:35:03 +0100
> Subject: [PATCH] gnu: Add ltrace.
>
> * gnu/packages/linux.scm (ltrace): New variable.
> ---
>  gnu/packages/linux.scm | 24 
>  1 file changed, 24 insertions(+)
>
> diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
> index 09e2a4c..bb06208 100644
> --- a/gnu/packages/linux.scm
> +++ b/gnu/packages/linux.scm
> @@ -4,6 +4,7 @@
>  ;;; Copyright © 2012 Nikita Karetnikov 
>  ;;; Copyright © 2014, 2015 Mark H Weaver 
>  ;;; Copyright © 2015 Federico Beffa 
> +;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer 
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -670,6 +671,29 @@ images more compressible.")
>  trace of all the system calls made by a another process/program.")
>  (license bsd-3)))
>  
> +(define-public ltrace
> +  (package
> +(name "ltrace")
> +(version "0.7.3")
> +(source (origin
> + (method url-fetch)
> + (uri (string-append "http://www.ltrace.org/ltrace_"; version
> + ".orig.tar.bz2"))
> + (sha256
> +  (base32
> +   "00wmbdghqbz6x95m1mcdd3wd46l6hgcr4wggdp049dbifh3qqvqf"
> +(build-system gnu-build-system)
> +(inputs `(("libelf" ,libelf)))
> +(arguments
> + '(#:configure-flags '("--disable-werror")))

Could you add a comment explaining why this flag is necessary?

> +(home-page "http://www.ltrace.org/";)
> +(synopsis "Library call tracer for Linux")
> +(description
> + "ltrace intercepts and records dynamic library calls which are called by
> +an executed process and the signals received by that process.  It can also
> +intercept and print the system calls executed by the program.")
> +(license gpl2+)))
> +
>  (define-public alsa-lib
>(package
>  (name "alsa-lib")
> -- 
> 2.2.1
>
>

Looks good otherwise!

-- 
David Thompson
Web Developer - Free Software Foundation - http://fsf.org
GPG Key: 0FF1D807
Support the FSF: https://fsf.org/donate

Re: Package List on Web Site

[Ludovic Courtès]

David Thompson  skribis:

> Ludovic Courtès  writes:
>
>> John Darrington  skribis:
>>
>>> In particular, I have noticed that http://gnu.org/s/guix/package-list.html 
>>> is now
>>> over 1.5 MB in size and is startign to take an unacceptably long time to 
>>> load (at
>>> least for me).
>>
>> I think it’s rendering that takes time, not transfer per se (unless you
>> have a very slow connection.)
>>
>> I would like it to use David’s guix-web JS code to add the search box
>> and multiple-page split.  I suspect this would address the rendering
>> time and usability issues.  But of course, that would need help from
>> someone knowledgeable...  :-)
>
> We could make a specialized application that did this, since guix-web
> will soon enough be concerned with authentication and other things that
> aren't needed here.  To do things the way guix-web does, it would
> require a Guile server component for the JSON API.

I was thinking of something simpler: statically generate
package-list.html (as we currently do, with list-packages.scm), but
instead of spitting out the HTML table directly, produce the JSON data
that guix-web’s browser-side code expects.

>> It would be ideal if this were done in a “progressive enhancement”
>> fashion, such that it can still be viewed in emacs-w3m.
>
> Yes, agreed.  This would be the hardest part, because guix-web is
> designed as a "single-page application", using JavaScript for all
> rendering.  I would be inclined to write this package list browser in
> the same fashion, because it results in much more elegant code than the
> jQuery soup we would otherwise be in.
>
> What should the non-JS fallback viewer look like?  Should we just
> display the full list as we do now?

I think so.

Ludo’.

Re: cannot use snippets with zip source

[Ludovic Courtès]

Ricardo Wurmus  skribis:

> Is there a way to use snippets with zip archives?

Currently no, as you noted.  That could be fixed though (please file it
to bug-g...@gnu.org so we don’t lose track of it.)

> Could `patch-and-repack' be modified to use the package's "unpack"
> phase instead of implementing its own unpack mechanism?

Not really, but we can fix ‘patch-and-repack’ anyway.

Thanks,
Ludo’.

Re: bug#19805: Numpy failures

[Ludovic Courtès]

Federico Beffa  skribis:

> Andreas Enge  writes:
>
>> python-numpy-bootstrap currently fails its tests on hydra, which entails a
>> bunch of other failures. On my own x86_64 machines, the build succeeds,
>> however.
>
> We believe the reason being the fact that hydra doesn't handle the flag
> '#:substitutable?' properly. As a result we have the following
> situation:
>
> 1. hydra builds a version of ATLAS optimized for its CPU locally.
>
> 2. 'python-numpy-bootstrap' and co., on some architectures, probably get
> an incompatible version of ATLAS and therefore fail to pass some tests.
>
> You can check in the build log of 'python-numpy-bootstrap' that ATLAS,
> despite the flas, is substituted (no local build on the slave).

Oh.  Actually, slaves do not use substitutes at all, but they receive
missing store items from hydra.gnu.org when builds are offloaded.  So I
suppose they receive something built on hydra.gnu.org, which may be
incompatible.

> At some point we should fix the support for '#:substitutable?' on hydra

That probably means that #:substitutable? should be propagated–i.e.,
that anything depending on ATLAS should not be substituted.

Thanks for investigating!

Ludo’.

Re: [PATCH]: gnu: Add HISAT.

[Ludovic Courtès]

Ricardo Wurmus  skribis:

> From 305768bfef9bf4bc8d57828e27b8439dedd574bd Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus 
> Date: Mon, 9 Feb 2015 12:13:26 +0100
> Subject: [PATCH] gnu: Add HISAT.
>
> * gnu/packages/bioinformatics.scm (hisat): New variable.

Overall looks good to me.  A couple of comments:

> + (alist-replace
> +  'install
> +  (lambda* (#:key outputs #:allow-other-keys)
> +(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
> +  (mkdir-p bin)
> +  (for-each (lambda (file)
> +  (copy-file file (string-append bin file)))
> +'("hisat"
> +  "hisat-build"
> +  "hisat-build-s"
> +  "hisat-build-l"
> +  "hisat-align-s"
> +  "hisat-align-l"
> +  "hisat-inspect"
> +  "hisat-inspect-s"
> +  "hisat-inspect-l"
> +  "hisat-build-s-debug"
> +  "hisat-build-l-debug"
> +  "hisat-align-s-debug"
> +  "hisat-align-l-debug"
> +  "hisat-inspect-s-debug"
> +  "hisat-inspect-l-debug"

If it’s possible to avoid the whole list using ‘find-files’ or
‘scandir’, that would be nicer IMO.  If it’s not, that’s fine.

> +(license license:gpl3)))

GPLv3-only?

Thanks!

Ludo’.

Re: [PATCH]: gnu: Add STAR.

[Ludovic Courtès]

Ricardo Wurmus  skribis:

> From efd3b0fd1b5ed0b7ca0168e3356c950482b694d6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus 
> Date: Mon, 9 Feb 2015 15:38:30 +0100
> Subject: [PATCH] gnu: Add STAR.
>
> * gnu/packages/bioinformatics.scm (star): New variable.

LGTM!

> +(license license:gpl3)))

GPLv3-only?

Thanks,
Ludo'.

Re: [PATCH] gnu: Add smartmontools.

[Mark H Weaver]

taylanbayi...@gmail.com (Taylan Ulrich "Bayırlı/Kammer") writes:

> Mark H Weaver  writes:
>
>> Debian claims that the license is gpl2, not gpl2+.
>>
>> Please be more careful checking licenses.  Debian tends to be very
>> thorough about this, so a good method is to find the package on Debian,
>> e.g. , select the appropriate
>> package (preferably the same version or close to it) and then choose the
>> "Copyright File" link in the right column.
>
> OK, thanks for the tip.  However, both the README and individual source
> files use the "or (at your option) any later version" phrasing.  I
> wonder why Debian marked it gpl2?

Indeed, you are right, and Debian is wrong.  Nevermind :)

One more unrelated suggestion, while I'm at it: in the synopsis and
description, I think it would be better to write "S.M.A.R.T." rather
than "SMART".  What do you think?

Anyway, okay to push.

Thanks!
  Mark