Installing a custom package on Guix binary setup

Installing a custom package on Guix binary setup

[Vicente Vera]

Hello,

Currently i'm using a Guix binary installation on top of my GNU/Linux
distro. Setup went fine.

So far i've installed only substitutes (everything OK), but there are
some packages that I want to tweak a little.

How can I install a customized .scm package definition?

For example, I want to pass some configure flags to Emacs (such as
'#:configure-flags '("--without-dbus" ...)'). I copied
/gnu/store/dbf9i96ac2pbyaibg591bx90a8zhvngc-guix-latest/gnu/packages/emacs.scm
somewhere else, did some editing, but now I'm not sure what to do with
it.

Going through the mailing list i've found out that I might need to
build Guix from source to do such a thing, but want to know if it can
be done with a binary installation.

Re: Installing a custom package on Guix binary setup

[Thompson, David]

Hi Vicente,

On Mon, Aug 31, 2015 at 12:42 PM, Vicente Vera <vicentemvp@gmail.com> wrote:
> Hello,
>
> Currently i'm using a Guix binary installation on top of my GNU/Linux
> distro. Setup went fine.
>
> So far i've installed only substitutes (everything OK), but there are
> some packages that I want to tweak a little.
>
> How can I install a customized .scm package definition?
>
> For example, I want to pass some configure flags to Emacs (such as
> '#:configure-flags '("--without-dbus" ...)'). I copied
> /gnu/store/dbf9i96ac2pbyaibg591bx90a8zhvngc-guix-latest/gnu/packages/emacs.scm
> somewhere else, did some editing, but now I'm not sure what to do with
> it.
>
> Going through the mailing list i've found out that I might need to
> build Guix from source to do such a thing, but want to know if it can
> be done with a binary installation.

You'll want to create your own directory of Guile modules that contain
Guix package objects and configure the GUIX_PACKAGE_PATH environment
variable so Guix will find them.  See
<https://gnu.org/software/guix/manual/html_node/Package-Modules.html#Package-Modules>
for more details.

- Dave

Re: Installing a custom package on Guix binary setup

[Ludovic Courtès]

Vicente Vera <vicentemvp@gmail.com> skribis:

> How can I install a customized .scm package definition?
>
> For example, I want to pass some configure flags to Emacs (such as
> '#:configure-flags '("--without-dbus" ...)'). I copied
> /gnu/store/dbf9i96ac2pbyaibg591bx90a8zhvngc-guix-latest/gnu/packages/emacs.scm
> somewhere else, did some editing, but now I'm not sure what to do with
> it.

You’re on the right track. ;-)  Just drop that file somewhere and add
that somewhere to the ‘GUIX_PACKAGE_PATH’ environment variable:

  https://www.gnu.org/software/guix/manual/html_node/Package-Modules.html

HTH,
Ludo’.

Re: Installing a custom package on Guix binary setup

[Vicente Vera]

Wow, thanks! It worked fine. Instead of Emacs I built a modified R
package, without texlive and icedtea6. After defining the
GUIX_PACKAGE_PATH variable I moved there "my-R.scm", which included:

(define-module (my-r)
  #:use-module ...) ; same as in statistics.scm

(define-public my-r
  (package
   ...)) ; commenting out the unwanted inputs

Then ran 'guix package -i my-r'. Some substitutes were downloaded (I
guess that's not always safe/recommended?), R 3.2.2 got compiled and
that's it!

Now I can call R from the outside (i.e. Emacs and ESS). It complains
about some undefined locales but I'll check that later.


2015-08-31 17:15 GMT-03:00 Ludovic Courtès <ludo@gnu.org>:
> Vicente Vera <vicentemvp@gmail.com> skribis:
>
>> How can I install a customized .scm package definition?
>>
>> For example, I want to pass some configure flags to Emacs (such as
>> '#:configure-flags '("--without-dbus" ...)'). I copied
>> /gnu/store/dbf9i96ac2pbyaibg591bx90a8zhvngc-guix-latest/gnu/packages/emacs.scm
>> somewhere else, did some editing, but now I'm not sure what to do with
>> it.
>
> You’re on the right track. ;-)  Just drop that file somewhere and add
> that somewhere to the ‘GUIX_PACKAGE_PATH’ environment variable:
>
>   https://www.gnu.org/software/guix/manual/html_node/Package-Modules.html
>
> HTH,
> Ludo’.

Re: Installing a custom package on Guix binary setup

[Ricardo Wurmus]

> Wow, thanks! It worked fine. Instead of Emacs I built a modified R
> package, without texlive and icedtea6. After defining the
> GUIX_PACKAGE_PATH variable I moved there "my-R.scm", which included:
>
> (define-module (my-r)
>   #:use-module ...) ; same as in statistics.scm
>
> (define-public my-r
>   (package
>    ...)) ; commenting out the unwanted inputs

An alternative is to inherit from the “r” package in “statistics.scm”.

    (define-module (my own packages)
      #:use-module (guix packages)
      #:use-module (gnu packages statistics)
      #:use-module (srfi srfi-1))
      
    (define-public my-r
      (package (inherit r)
        (name "my-r")
        ;; modify only the inputs here
        (native-inputs (alist-delete "texlive" (package-native-inputs r)))       
        (inputs (alist-delete "icedtea6" (package-inputs r)))))

> Then ran 'guix package -i my-r'. Some substitutes were downloaded (I
> guess that's not always safe/recommended?), R 3.2.2 got compiled and
> that's it!

Substitutes are downloaded from hydra only if hydra has been authorized
as a source for binary substitutes.  You can revoke permission for hydra
or temporarily disable the use of substitutes with the flag
‘--no-substitutes’.

~~ Ricardo

R dependencies

[Ludovic Courtès]

Ricardo Wurmus <rekado@elephly.net> skribis:

> An alternative is to inherit from the “r” package in “statistics.scm”.
>
>     (define-module (my own packages)
>       #:use-module (guix packages)
>       #:use-module (gnu packages statistics)
>       #:use-module (srfi srfi-1))
>       
>     (define-public my-r
>       (package (inherit r)
>         (name "my-r")
>         ;; modify only the inputs here
>         (native-inputs (alist-delete "texlive" (package-native-inputs r)))       
>         (inputs (alist-delete "icedtea6" (package-inputs r)))))

Speaking of which: should we get rid of icedtea6:jdk in the default R
package (closure size: 1 GiB), and maybe of TeX Live (4 GiB)?  Or should
we provide, say, ‘r-light’ with the definition above?

I’m afraid having these two dependencies by default makes it
prohibitively expensive.

Ludo’.

'-light' vs. '-minimal' packages

[Alex Kost]

Ludovic Courtès (2015-09-02 16:09 +0300) wrote:

> Ricardo Wurmus <rekado@elephly.net> skribis:
>
>> An alternative is to inherit from the “r” package in “statistics.scm”.
>>
>>     (define-module (my own packages)
>>       #:use-module (guix packages)
>>       #:use-module (gnu packages statistics)
>>       #:use-module (srfi srfi-1))
>>
>>     (define-public my-r
>>       (package (inherit r)
>>         (name "my-r")
>>         ;; modify only the inputs here
>>         (native-inputs (alist-delete "texlive" (package-native-inputs r)))
>>         (inputs (alist-delete "icedtea6" (package-inputs r)))))
>
> Speaking of which: should we get rid of icedtea6:jdk in the default R
> package (closure size: 1 GiB), and maybe of TeX Live (4 GiB)?  Or should
> we provide, say, ‘r-light’ with the definition above?

We have ‘bash-light’ and ‘wpa-supplicant-light’; ‘bioperl-minimal’ and
‘cups-minimal’.  I think we should stick to a single name for such
light/minimal packages.  (I prefer "…-minimal")

-- 
Alex

Re: '-light' vs. '-minimal' packages

[Mathieu Lirzin]

Alex Kost <alezost@gmail.com> writes:

> Ludovic Courtès (2015-09-02 16:09 +0300) wrote:
>
>> Ricardo Wurmus <rekado@elephly.net> skribis:
>>
>>> An alternative is to inherit from the “r” package in “statistics.scm”.
>>>
>>>     (define-module (my own packages)
>>>       #:use-module (guix packages)
>>>       #:use-module (gnu packages statistics)
>>>       #:use-module (srfi srfi-1))
>>>
>>>     (define-public my-r
>>>       (package (inherit r)
>>>         (name "my-r")
>>>         ;; modify only the inputs here
>>>         (native-inputs (alist-delete "texlive" (package-native-inputs r)))
>>>         (inputs (alist-delete "icedtea6" (package-inputs r)))))
>>
>> Speaking of which: should we get rid of icedtea6:jdk in the default R
>> package (closure size: 1 GiB), and maybe of TeX Live (4 GiB)?  Or should
>> we provide, say, ‘r-light’ with the definition above?
>
> We have ‘bash-light’ and ‘wpa-supplicant-light’; ‘bioperl-minimal’ and
> ‘cups-minimal’.  I think we should stick to a single name for such
> light/minimal packages.  (I prefer "…-minimal")
                            ^^^
+1

--
Mathieu Lirzin

Re: '-light' vs. '-minimal' packages

[Ludovic Courtès]

Alex Kost <alezost@gmail.com> skribis:

> Ludovic Courtès (2015-09-02 16:09 +0300) wrote:
>
>> Ricardo Wurmus <rekado@elephly.net> skribis:
>>
>>> An alternative is to inherit from the “r” package in “statistics.scm”.
>>>
>>>     (define-module (my own packages)
>>>       #:use-module (guix packages)
>>>       #:use-module (gnu packages statistics)
>>>       #:use-module (srfi srfi-1))
>>>
>>>     (define-public my-r
>>>       (package (inherit r)
>>>         (name "my-r")
>>>         ;; modify only the inputs here
>>>         (native-inputs (alist-delete "texlive" (package-native-inputs r)))
>>>         (inputs (alist-delete "icedtea6" (package-inputs r)))))
>>
>> Speaking of which: should we get rid of icedtea6:jdk in the default R
>> package (closure size: 1 GiB), and maybe of TeX Live (4 GiB)?  Or should
>> we provide, say, ‘r-light’ with the definition above?
>
> We have ‘bash-light’ and ‘wpa-supplicant-light’; ‘bioperl-minimal’ and
> ‘cups-minimal’.  I think we should stick to a single name for such
> light/minimal packages.  (I prefer "…-minimal")

Right, I realized I hadn’t made up my mind.  “Minimal” is probably
preferable, indeed.  Let’s rename and bash-light in core-updates, and
wpa-supplicant-light in master.

Ludo’.

Re: R dependencies

[Vicente Vera]

Hello,

Going back to the R dependencies topic, I ran across an issue when
trying to draw a plot (with ggplot2). But first some context:

- I'm not using GuixSD but a binary installation over Manjaro OpenRC;
several base packages missing on Guix
- I only have other two Guix packages installed: xpdf & abbaye
- I installed ggplot2 through install.packages("ggplot2") in R (Guix package)

R complained about some fonts missing, but I think it could be related
to a missing X11 dependency (complete Xorg maybe?). What could it be?

2015-09-02 10:09 GMT-03:00 Ludovic Courtès <ludo@gnu.org>:
> Ricardo Wurmus <rekado@elephly.net> skribis:
>
>> An alternative is to inherit from the “r” package in “statistics.scm”.
>>
>>     (define-module (my own packages)
>>       #:use-module (guix packages)
>>       #:use-module (gnu packages statistics)
>>       #:use-module (srfi srfi-1))
>>
>>     (define-public my-r
>>       (package (inherit r)
>>         (name "my-r")
>>         ;; modify only the inputs here
>>         (native-inputs (alist-delete "texlive" (package-native-inputs r)))
>>         (inputs (alist-delete "icedtea6" (package-inputs r)))))
>
> Speaking of which: should we get rid of icedtea6:jdk in the default R
> package (closure size: 1 GiB), and maybe of TeX Live (4 GiB)?  Or should
> we provide, say, ‘r-light’ with the definition above?
>
> I’m afraid having these two dependencies by default makes it
> prohibitively expensive.
>
> Ludo’.

Re: R dependencies

[Ricardo Wurmus]

Hi Vicente,

> Going back to the R dependencies topic, I ran across an issue when
> trying to draw a plot (with ggplot2). But first some context:
>
> - I'm not using GuixSD but a binary installation over Manjaro OpenRC;
> several base packages missing on Guix
> - I only have other two Guix packages installed: xpdf & abbaye

All Guix packages capture the complete graph of dependencies, so you’ll
always end up with the dependent packages in ‘/gnu/store’ even if only
those packages appear in your profile that have been explicitly
installed.

> - I installed ggplot2 through install.packages("ggplot2") in R (Guix package)

Note that ggplot2 has been packaged for Guix:

    guix package -i r-ggplot2

> R complained about some fonts missing, but I think it could be related
> to a missing X11 dependency (complete Xorg maybe?). What could it be?

What is the exact error message you get?  Is any plot drawn at all?
What is the code you use to draw the plot?

~~ Ricardo

Re: '-light' vs. '-minimal' packages

[Alex Kost]

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Ludovic Courtès (2015-09-02 23:18 +0300) wrote:

> Alex Kost <alezost@gmail.com> skribis:
[...]
>> We have ‘bash-light’ and ‘wpa-supplicant-light’; ‘bioperl-minimal’ and
>> ‘cups-minimal’.  I think we should stick to a single name for such
>> light/minimal packages.  (I prefer "…-minimal")
>
> Right, I realized I hadn’t made up my mind.  “Minimal” is probably
> preferable, indeed.  Let’s rename and bash-light in core-updates, and
> wpa-supplicant-light in master.

OK, the patches for both are attached.


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From e040b70e23f04fca1c91123751ce8b6e28719bb8 Mon Sep 17 00:00:00 2001
From: Alex Kost <alezost@gmail.com>
Date: Thu, 3 Sep 2015 11:12:28 +0300
Subject: [PATCH] gnu: bash-light: Rename to bash-minimal.

* gnu/packages/bash.scm (bash-light): Rename to ...
  (bash-minimal): ...this.
  (static-bash): Use it.
* gnu/packages/make-bootstrap.scm (%bash-static): Use it.
---
 gnu/packages/bash.scm           | 6 +++---
 gnu/packages/make-bootstrap.scm | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm
index fcfa337..180c64e 100644
--- a/gnu/packages/bash.scm
+++ b/gnu/packages/bash.scm
@@ -214,10 +214,10 @@ without modification.")
      (license gpl3+)
      (home-page "http://www.gnu.org/software/bash/"))))
 
-(define-public bash-light
+(define-public bash-minimal
   ;; A stripped-down Bash for non-interactive use.
   (package (inherit bash)
-    (name "bash-light")
+    (name "bash-minimal")
     (inputs '())                                ; no readline, no curses
     (arguments
      (let ((args `(#:modules ((guix build gnu-build-system)
@@ -242,7 +242,7 @@ without modification.")
 (define-public static-bash
   ;; Statically-linked Bash that contains nothing but the 'bash' binary and
   ;; 'sh' symlink, without any reference.
-  (let ((bash (static-package bash-light)))
+  (let ((bash (static-package bash-minimal)))
     (package
       (inherit bash)
       (name "bash-static")
diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index 904aaed..8923faf 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/gnu/packages/make-bootstrap.scm
@@ -115,7 +115,7 @@ for `sh' in $PATH, and without nscd, and with static NSS modules."
                                 #:native-inputs native-inputs))
 
 (define %bash-static
-  (static-package bash-light))
+  (static-package bash-minimal))
 
 (define %static-inputs
   ;; Packages that are to be used as %BOOTSTRAP-INPUTS.
-- 
2.5.1


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From 3deea5ea0cc104993ab665863105d7ad672f5ea0 Mon Sep 17 00:00:00 2001
From: Alex Kost <alezost@gmail.com>
Date: Thu, 3 Sep 2015 11:23:30 +0300
Subject: [PATCH] gnu: wpa-supplicant-light: Rename to wpa-supplicant-minimal.

* gnu/packages/admin.scm (wpa-supplicant-light): Rename to ...
  (wpa-supplicant-minimal): ...this.
  (wpa-supplicant): Use it.
* gnu/system/install.scm (installation-os): Use it.
---
 gnu/packages/admin.scm | 10 +++++-----
 gnu/system/install.scm |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 53cf65e..70b2bb2 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -703,9 +703,9 @@ commands and their arguments.")
     ;; See <http://www.sudo.ws/sudo/license.html>.
     (license license:x11)))
 
-(define-public wpa-supplicant-light
+(define-public wpa-supplicant-minimal
   (package
-    (name "wpa-supplicant-light")
+    (name "wpa-supplicant-minimal")
     (version "2.4")
     (source (origin
               (method url-fetch)
@@ -795,12 +795,12 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
     (license license:bsd-3)))
 
 (define-public wpa-supplicant
-  (package (inherit wpa-supplicant-light)
+  (package (inherit wpa-supplicant-minimal)
     (name "wpa-supplicant")
     (inputs `(("dbus" ,dbus)
-              ,@(package-inputs wpa-supplicant-light)))
+              ,@(package-inputs wpa-supplicant-minimal)))
     (arguments
-     (substitute-keyword-arguments (package-arguments wpa-supplicant-light)
+     (substitute-keyword-arguments (package-arguments wpa-supplicant-minimal)
        ((#:phases phases)
         `(alist-cons-after
           'configure 'configure-for-dbus
diff --git a/gnu/system/install.scm b/gnu/system/install.scm
index e7e5d4a..9314462 100644
--- a/gnu/system/install.scm
+++ b/gnu/system/install.scm
@@ -344,7 +344,7 @@ Use Alt-F2 for documentation.
                      parted ddrescue
                      grub                  ;mostly so xrefs to its manual work
                      cryptsetup
-                     wireless-tools iw wpa-supplicant-light iproute
+                     wireless-tools iw wpa-supplicant-minimal iproute
                      ;; XXX: We used to have GNU fdisk here, but as of version
                      ;; 2.0.0a, that pulls Guile 1.8, which takes unreasonable
                      ;; space; furthermore util-linux's fdisk is already
-- 
2.5.1

[PATCH] R dependencies

[Ricardo Wurmus]

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Ludovic Courtès <ludo@gnu.org> writes:

> Speaking of which: should we get rid of icedtea6:jdk in the default R
> package (closure size: 1GiB), and maybe of TeX Live (4GiB)?  Or should
> we provide, say, ‘r-light’ with the definition above?
>
> I’m afraid having these two dependencies by default makes it
> prohibitively expensive.

I investigated this a bit and found that the JDK is not really needed at
build time.  The first patch includes a comment explaining why we
dropped the JDK from the inputs.

The second patch adds build phases to install the info documentation.

Removing texlive is possible as well, but it results in the loss of the
following files:

./lib/R/library/grid
  /doc
    displaylist.R
    displaylist.Rnw
    frame.R
    frame.Rnw
    grid.R
    grid.Rnw
    grobs.R
    grobs.Rnw
    index.html
    interactive.R
    interactive.Rnw
    locndimn.R
    locndimn.Rnw
    moveline.R
    moveline.Rnw
    nonfinite.R
    nonfinite.Rnw
    plotexample.R
    plotexample.Rnw
    rotated.R
    rotated.Rnw
    saveload.R
    saveload.Rnw
    sharing.R
    sharing.Rnw
    viewports.R
    viewports.Rnw
  /Meta
    vignette.rds

./lib/R/library/parallel
  /doc
    index.html
    parallel.R
    parallel.Rnw
  /Meta
    vignette.rds

./lib/R/library/utils
  /doc
    index.html
    Sweave.R
    Sweave.Rnw
  /Meta
    vignette.rds

Note that these Rnw files are all literate programming sources
containing the sources that are untangled to .R files and the PDF
documentation.  Interestingly, the source tarball already contains the
PDF files (e.g. the one installed to
“lib/R/library/grid/doc/viewports.pdf”), so we don’t need texlive to
generate them.

Attached are the three patches.

~~ Ricardo


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From 11e8a484733b492ff5ecd6119b9bdef238be6e67 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 3 Sep 2015 11:41:07 +0200
Subject: [PATCH 1/3] gnu: r: Drop IcedTea from inputs.

* gnu/packages/statistics.scm (r)[inputs]: Remove "icedtea6".
---
 gnu/packages/statistics.scm | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b84c48d..b1cc5cf 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -84,6 +84,16 @@
          "--with-system-pcre"
          "--with-system-tre"
          "--with-system-xz")))
+    ;; R has some support for Java.  When the JDK is available at configure
+    ;; time environment variables pointing to the JDK will be recorded under
+    ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
+    ;; CMD javareconf".  "R CMD javareconf" appears to only be used to update
+    ;; the recorded environment variables in $R_HOME/etc.  Refer to
+    ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
+    ;; for additional information.
+
+    ;; As the JDK is a rather large input with only very limited effects on R,
+    ;; we decided to drop it.
     (native-inputs
      `(("bzip2" ,bzip2)
        ("perl" ,perl)
@@ -97,7 +107,6 @@
        ("cairo" ,cairo)
        ("gfortran" ,gfortran)
        ("icu4c" ,icu4c)
-       ("icedtea6" ,icedtea6 "jdk")
        ("lapack" ,lapack)
        ("libjpeg" ,libjpeg)
        ("libpng" ,libpng)
-- 
2.1.0


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From 17f4d01ce2b7bb4b41e565ac43463425e79b6c30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 3 Sep 2015 11:41:36 +0200
Subject: [PATCH 2/3] gnu: r: Install info documentation.

* gnu/packages/statistics.scm (r)[arguments]: Add phases "make-info" and
  "install-info" to build and install info documentation.
---
 gnu/packages/statistics.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b1cc5cf..ec705c2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -68,7 +68,11 @@
          (add-before
           'check 'set-timezone
           ;; Some tests require the timezone to be set.
-          (lambda _ (setenv "TZ" "UTC") #t)))
+          (lambda _ (setenv "TZ" "UTC") #t))
+         (add-after 'build 'make-info
+          (lambda _ (zero? (system* "make" "info"))))
+         (add-after 'build 'install-info
+          (lambda _ (zero? (system* "make" "install-info")))))
        #:configure-flags
        '("--with-blas=openblas"
          "--with-lapack"
-- 
2.1.0


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From d4982f4574579fe60e005807aace966279824f01 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 3 Sep 2015 12:09:47 +0200
Subject: [PATCH 3/3] gnu: r: Drop texlive from native-inputs.

* gnu/packages/statistics.scm (r)[native-inputs]: Remove "texlive".
---
 gnu/packages/statistics.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index ec705c2..7cb61c9 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -102,7 +102,6 @@
      `(("bzip2" ,bzip2)
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
-       ("texlive" ,texlive) ; needed to make vignettes
        ("texinfo" ,texinfo) ; for building HTML manuals
        ("which" ,which) ; for tests/Examples/base-Ex.R
        ("xz" ,xz)))
-- 
2.1.0

Re: R dependencies

[Vicente Vera]

Hi,

Sure. The error message is this:

X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 5 at size
15 could not be loaded

No plot is being drawn; only a blank window appears.

The code:

ggplot(data = fig1, aes(x = Var1, y = Freq, fill =
brewer.pal(length(levels(the_data$VARIABLE1)), "Set3"))) +
    geom_bar(stat = "identity") +
    scale_fill_identity() +
    labs(x = "x", y = "y") +
    geom_text(aes(label = perc), vjust = 2, size = 4, colour =
"black", fontface = "bold") +
    scale_x_discrete(labels = c("a", "b", "c")) +
    theme(panel.background = element_blank(),
          line = element_blank(),
          axis.text.y = element_blank())

On my base system, R 3.2.1 + ggplot2 draws the plot with no problem.

It might be related to a missing font or font alias in the Guix store
(not familiar enough with it to catch the issue).

Now, I didn't installed ggplot2 through Guix, so that could be a problem.

2015-09-03 3:29 GMT-03:00 Ricardo Wurmus <rekado@elephly.net>:
> Hi Vicente,
>
>> Going back to the R dependencies topic, I ran across an issue when
>> trying to draw a plot (with ggplot2). But first some context:
>>
>> - I'm not using GuixSD but a binary installation over Manjaro OpenRC;
>> several base packages missing on Guix
>> - I only have other two Guix packages installed: xpdf & abbaye
>
> All Guix packages capture the complete graph of dependencies, so you’ll
> always end up with the dependent packages in ‘/gnu/store’ even if only
> those packages appear in your profile that have been explicitly
> installed.
>
>> - I installed ggplot2 through install.packages("ggplot2") in R (Guix package)
>
> Note that ggplot2 has been packaged for Guix:
>
>     guix package -i r-ggplot2
>
>> R complained about some fonts missing, but I think it could be related
>> to a missing X11 dependency (complete Xorg maybe?). What could it be?
>
> What is the exact error message you get?  Is any plot drawn at all?
> What is the code you use to draw the plot?
>
> ~~ Ricardo
>

Re: '-light' vs. '-minimal' packages

[Ludovic Courtès]

Alex Kost <alezost@gmail.com> skribis:

> From e040b70e23f04fca1c91123751ce8b6e28719bb8 Mon Sep 17 00:00:00 2001
> From: Alex Kost <alezost@gmail.com>
> Date: Thu, 3 Sep 2015 11:12:28 +0300
> Subject: [PATCH] gnu: bash-light: Rename to bash-minimal.
>
> * gnu/packages/bash.scm (bash-light): Rename to ...
>   (bash-minimal): ...this.
>   (static-bash): Use it.
> * gnu/packages/make-bootstrap.scm (%bash-static): Use it.

This should go to ‘core-updates’, where there’s an additional reference
to update in commencement.scm.  OK with this change.

> From 3deea5ea0cc104993ab665863105d7ad672f5ea0 Mon Sep 17 00:00:00 2001
> From: Alex Kost <alezost@gmail.com>
> Date: Thu, 3 Sep 2015 11:23:30 +0300
> Subject: [PATCH] gnu: wpa-supplicant-light: Rename to wpa-supplicant-minimal.
>
> * gnu/packages/admin.scm (wpa-supplicant-light): Rename to ...
>   (wpa-supplicant-minimal): ...this.
>   (wpa-supplicant): Use it.
> * gnu/system/install.scm (installation-os): Use it.

OK for ‘master’.

Thanks,
Ludo’.

Re: [PATCH] R dependencies

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 11e8a484733b492ff5ecd6119b9bdef238be6e67 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 3 Sep 2015 11:41:07 +0200
> Subject: [PATCH 1/3] gnu: r: Drop IcedTea from inputs.
>
> * gnu/packages/statistics.scm (r)[inputs]: Remove "icedtea6".

[...]

> From 17f4d01ce2b7bb4b41e565ac43463425e79b6c30 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 3 Sep 2015 11:41:36 +0200
> Subject: [PATCH 2/3] gnu: r: Install info documentation.
>
> * gnu/packages/statistics.scm (r)[arguments]: Add phases "make-info" and
>   "install-info" to build and install info documentation.

[...]

> From d4982f4574579fe60e005807aace966279824f01 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 3 Sep 2015 12:09:47 +0200
> Subject: [PATCH 3/3] gnu: r: Drop texlive from native-inputs.
>
> * gnu/packages/statistics.scm (r)[native-inputs]: Remove "texlive".

OK for all three.  Thanks for taking the time to investigate!

Ludo’.

Re: '-light' vs. '-minimal' packages

[Alex Kost]

[-- Attachment #1: Type: text/plain, Size: 1066 bytes --]

Ludovic Courtès (2015-09-04 00:11 +0300) wrote:

> Alex Kost <alezost@gmail.com> skribis:
>
>> From e040b70e23f04fca1c91123751ce8b6e28719bb8 Mon Sep 17 00:00:00 2001
>> From: Alex Kost <alezost@gmail.com>
>> Date: Thu, 3 Sep 2015 11:12:28 +0300
>> Subject: [PATCH] gnu: bash-light: Rename to bash-minimal.
>>
>> * gnu/packages/bash.scm (bash-light): Rename to ...
>>   (bash-minimal): ...this.
>>   (static-bash): Use it.
>> * gnu/packages/make-bootstrap.scm (%bash-static): Use it.
>
> This should go to ‘core-updates’, where there’s an additional reference
> to update in commencement.scm.  OK with this change.

I made this patch specifically for ‘core-updates’ and I don't see any
reference to ‘bash-light’ in (gnu packages commencement) there.  AFAICS
‘bash-light’ is used in ‘static-bash-for-glibc’ only in master.  Or do I
miss anything?

I have also noticed that there is another ‘…-light’ package in
‘core-updates’ — ‘coreutils-light’, so I'm attaching the patch to rename
this one as well.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-coreutils-light-Rename-to-coreutils-minimal.patch --]
[-- Type: text/x-patch, Size: 1716 bytes --]

From 91c7da081fc532892ce6e351a7a719d162d6196a Mon Sep 17 00:00:00 2001
From: Alex Kost <alezost@gmail.com>
Date: Fri, 4 Sep 2015 15:50:11 +0300
Subject: [PATCH] gnu: coreutils-light: Rename to coreutils-minimal.

* gnu/packages/base.scm (coreutils-light): Rename to ...
  (coreutils-minimal): ...this.
* gnu/packages/commencement.scm (%boot5-inputs): Use it.
---
 gnu/packages/base.scm         | 4 ++--
 gnu/packages/commencement.scm | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index f4efce2..76fd111 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -293,11 +293,11 @@ functionality beyond that which is outlined in the POSIX standard.")
    (license gpl3+)
    (home-page "http://www.gnu.org/software/coreutils/")))
 
-(define-public coreutils-light
+(define-public coreutils-minimal
   ;; Coreutils without its optional dependencies.
   (package
     (inherit coreutils)
-    (name "coreutils-light")
+    (name "coreutils-minimal")
     (outputs '("out"))
     (inputs '())))
 
diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index caadc94..006aee5 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -734,7 +734,7 @@ exec \"~a\" \"$@\"\n"
 
       ;; Grep's test suite uses 'timeout' from Coreutils to execute command,
       ;; and yet these commands need to see the valid 'LOCPATH'.
-      ("coreutils" ,(new-libc-package coreutils-light))
+      ("coreutils" ,(new-libc-package coreutils-minimal))
 
       ;; We just wrap the remaining binaries (tar, gzip, xz, etc.)  so that
       ;; they ignore 'LOCPATH' (if they did not, they would be hit by an
-- 
2.4.3

Re: [PATCH] R dependencies

[Ludovic Courtès]

Now the closure of R is down from 5 GiB to 518 MiB, which is cool.  :-)

It seems we might be able to go further, because somewhere there are
presumably unwanted dependencies being retained, such as Texinfo & Perl,
ld-wrapper & Binutils, Gawk and other build-time tools:

--8<---------------cut here---------------start------------->8---
$ guix size r
substitute: updating list of substitutes from 'http://hydra.gnu.org'... 100.0%
store item                                                       total    self
/gnu/store/yqng7qmf0jrq8lkbivqpifx83rqmym61-r-3.2.2                518.0    55.5  10.7%
/gnu/store/2x8w06phz69hq7yr457xy0n46vws0wpl-texinfo-6.0            154.5     8.0   1.5%
/gnu/store/mziw9w93gxb1qd0ikxj6zx2w238995lg-ld-wrapper-0           152.3     0.0   0.0%
/gnu/store/gjs5zk5366a4bdwyy6vv1x8cfx7b092m-perl-5.16.1            140.2    49.2   9.5%
/gnu/store/chc76a6vpwl2cb7pq1qwl6b1ws6xagqv-cairo-1.14.2           135.8     6.1   1.2%
/gnu/store/jcdqm0221hcq39bbbxa6z2kmkfhy27r0-icu4c-55.1             125.9    34.9   6.7%
/gnu/store/5ibx7chxjqr5mnmg0glsx41l85rmwp81-openblas-0.2.14        120.2    60.0  11.6%
/gnu/store/ig1ibsz49ng15p0x6vlild3qfnlhwwx8-libxt-1.1.4            110.7     2.7   0.5%
/gnu/store/0ah2z399hmqm5mk9arw6rlywz836j8zy-guile-2.0.11           107.9    16.1   3.1%
/gnu/store/1ncynbg14adkn9a277b8zc1qjq6kswfy-glib-2.44.0            101.6    13.1   2.5%
/gnu/store/xnyf5pzlwrq35qv47g3w70jagsgm1djz-libsm-1.2.2             92.3     0.3   0.1%
/gnu/store/2afa3pvl8amwb4ql8xk6q8gfvwk143l5-util-linux-2.25.2       91.5    10.8   2.1%
/gnu/store/xz3mf13izfr44135w0760vzxga5v0950-bash-4.3.39             87.9     6.3   1.2%
[...]
--8<---------------cut here---------------end--------------->8---

It Would Be Nice™ to identify where these references come from and
whether they can be discarded.

Thanks,
Ludo’.

Re: '-light' vs. '-minimal' packages

[Ludovic Courtès]

Alex Kost <alezost@gmail.com> skribis:

> Ludovic Courtès (2015-09-04 00:11 +0300) wrote:
>
>> Alex Kost <alezost@gmail.com> skribis:
>>
>>> From e040b70e23f04fca1c91123751ce8b6e28719bb8 Mon Sep 17 00:00:00 2001
>>> From: Alex Kost <alezost@gmail.com>
>>> Date: Thu, 3 Sep 2015 11:12:28 +0300
>>> Subject: [PATCH] gnu: bash-light: Rename to bash-minimal.
>>>
>>> * gnu/packages/bash.scm (bash-light): Rename to ...
>>>   (bash-minimal): ...this.
>>>   (static-bash): Use it.
>>> * gnu/packages/make-bootstrap.scm (%bash-static): Use it.
>>
>> This should go to ‘core-updates’, where there’s an additional reference
>> to update in commencement.scm.  OK with this change.
>
> I made this patch specifically for ‘core-updates’ and I don't see any
> reference to ‘bash-light’ in (gnu packages commencement) there.  AFAICS
> ‘bash-light’ is used in ‘static-bash-for-glibc’ only in master.  Or do I
> miss anything?
>
> I have also noticed that there is another ‘…-light’ package in
> ‘core-updates’ — ‘coreutils-light’, so I'm attaching the patch to rename
> this one as well.

Right, it’s ‘coreutils-light’ that I had in mind.

> From 91c7da081fc532892ce6e351a7a719d162d6196a Mon Sep 17 00:00:00 2001
> From: Alex Kost <alezost@gmail.com>
> Date: Fri, 4 Sep 2015 15:50:11 +0300
> Subject: [PATCH] gnu: coreutils-light: Rename to coreutils-minimal.
>
> * gnu/packages/base.scm (coreutils-light): Rename to ...
>   (coreutils-minimal): ...this.
> * gnu/packages/commencement.scm (%boot5-inputs): Use it.

Please push, thanks!

Ludo’.

Re: R dependencies

[Vicente Vera]

Hello again,

Finally solved this:

Error in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 2 at size
11 could not be loaded

The problem arose because R wasn't using cairo for font rendering.
Some simple configurations in ~/.Rprofile solved it:

setHook(packageEvent("grDevices", "onLoad"),
        function(...) grDevices::X11.options(type = "cairo",
                                             antialias = "subpixel"))

The code changes the X11 device (used for plotting) type from "XLib"
to "cairo", once it gets called.

(just for the record, i'm not using GuixSD)

2015-09-03 11:55 GMT-03:00 Vicente Vera <vicentemvp@gmail.com>:
> Hi,
>
> Sure. The error message is this:
>
> X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 5 at size
> 15 could not be loaded
>
> No plot is being drawn; only a blank window appears.
>
> The code:
>
> ggplot(data = fig1, aes(x = Var1, y = Freq, fill =
> brewer.pal(length(levels(the_data$VARIABLE1)), "Set3"))) +
>     geom_bar(stat = "identity") +
>     scale_fill_identity() +
>     labs(x = "x", y = "y") +
>     geom_text(aes(label = perc), vjust = 2, size = 4, colour =
> "black", fontface = "bold") +
>     scale_x_discrete(labels = c("a", "b", "c")) +
>     theme(panel.background = element_blank(),
>           line = element_blank(),
>           axis.text.y = element_blank())
>
> On my base system, R 3.2.1 + ggplot2 draws the plot with no problem.
>
> It might be related to a missing font or font alias in the Guix store
> (not familiar enough with it to catch the issue).
>
> Now, I didn't installed ggplot2 through Guix, so that could be a problem.
>
> 2015-09-03 3:29 GMT-03:00 Ricardo Wurmus <rekado@elephly.net>:
>> Hi Vicente,
>>
>>> Going back to the R dependencies topic, I ran across an issue when
>>> trying to draw a plot (with ggplot2). But first some context:
>>>
>>> - I'm not using GuixSD but a binary installation over Manjaro OpenRC;
>>> several base packages missing on Guix
>>> - I only have other two Guix packages installed: xpdf & abbaye
>>
>> All Guix packages capture the complete graph of dependencies, so you’ll
>> always end up with the dependent packages in ‘/gnu/store’ even if only
>> those packages appear in your profile that have been explicitly
>> installed.
>>
>>> - I installed ggplot2 through install.packages("ggplot2") in R (Guix package)
>>
>> Note that ggplot2 has been packaged for Guix:
>>
>>     guix package -i r-ggplot2
>>
>>> R complained about some fonts missing, but I think it could be related
>>> to a missing X11 dependency (complete Xorg maybe?). What could it be?
>>
>> What is the exact error message you get?  Is any plot drawn at all?
>> What is the code you use to draw the plot?
>>
>> ~~ Ricardo
>>