* [PATCH] gnu: r: Use uname from Guix
@ 2016-10-26 15:11 Roel Janssen
2016-10-27 13:58 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Roel Janssen @ 2016-10-26 15:11 UTC (permalink / raw)
To: guix-devel
Dear Guix,
When running R, it executes a wrapper script that relies on
@code{uname} to be available in PATH:
> R_HOME_DIR=/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R
> if test "${R_HOME_DIR}" = "/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R"; then
> case "linux-gnu" in
> linux*)
> run_arch=`uname -m`
> case "$run_arch" in
> x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
> libnn=lib64
Running R in a pure, ad-hoc environment will therefore signal a warning
that it cannot execute "uname".
With the following patch, it no longer makes this assumption. Instead
it uses an absolute path to a uname binary from the Guix store.
From e364cb25204edea4d8bfb9cfc52764f811c58e72 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Wed, 26 Oct 2016 17:09:19 +0200
Subject: [PATCH] gnu: r: Use uname from Guix
* gnu/packages/statistics.scm (r): Use uname from Guix.
---
gnu/packages/statistics.scm | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 1b8d074..5e4cd8c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -118,6 +118,12 @@ be output in text, PostScript, PDF or HTML.")
"/lib/R/lib"))
#:phases
(modify-phases %standard-phases
+ (add-before 'configure 'patch-uname
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
+ "/bin/uname")))
+ (substitute* "src/scripts/R.sh.in"
+ (("uname") uname-bin)))))
(add-before
'configure 'set-default-pager
;; Set default pager to "cat", because otherwise it is "false",
@@ -169,6 +175,7 @@ be output in text, PostScript, PDF or HTML.")
`(;; We need not only cairo here, but pango to ensure that tests for the
;; "cairo" bitmapType plotting backend succeed.
("pango" ,pango)
+ ("coreutils" ,coreutils)
("curl" ,curl)
("tzdata" ,tzdata)
("gfortran" ,gfortran)
--
2.10.0
Kind regards,
Roel Janssen
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: r: Use uname from Guix
2016-10-26 15:11 [PATCH] gnu: r: Use uname from Guix Roel Janssen
@ 2016-10-27 13:58 ` Ricardo Wurmus
2016-10-27 14:38 ` Roel Janssen
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2016-10-27 13:58 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
Roel Janssen <roel@gnu.org> writes:
> Dear Guix,
>
> When running R, it executes a wrapper script that relies on
> @code{uname} to be available in PATH:
>
>> R_HOME_DIR=/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R
>> if test "${R_HOME_DIR}" = "/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R"; then
>> case "linux-gnu" in
>> linux*)
>> run_arch=`uname -m`
>> case "$run_arch" in
>> x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
>> libnn=lib64
>
> Running R in a pure, ad-hoc environment will therefore signal a warning
> that it cannot execute "uname".
>
> With the following patch, it no longer makes this assumption. Instead
> it uses an absolute path to a uname binary from the Guix store.
>
>From e364cb25204edea4d8bfb9cfc52764f811c58e72 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Wed, 26 Oct 2016 17:09:19 +0200
> Subject: [PATCH] gnu: r: Use uname from Guix
>
> * gnu/packages/statistics.scm (r): Use uname from Guix.
> ---
> gnu/packages/statistics.scm | 7 +++++++
> 1 file changed, 7 insertions(+)
>
> diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
> index 1b8d074..5e4cd8c 100644
> --- a/gnu/packages/statistics.scm
> +++ b/gnu/packages/statistics.scm
> @@ -118,6 +118,12 @@ be output in text, PostScript, PDF or HTML.")
> "/lib/R/lib"))
> #:phases
> (modify-phases %standard-phases
> + (add-before 'configure 'patch-uname
> + (lambda* (#:key inputs #:allow-other-keys)
> + (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
> + "/bin/uname")))
> + (substitute* "src/scripts/R.sh.in"
> + (("uname") uname-bin)))))
Please add #t to the end, because “substitute*” doesn’t have a return value.
> (add-before
> 'configure 'set-default-pager
> ;; Set default pager to "cat", because otherwise it is "false",
> @@ -169,6 +175,7 @@ be output in text, PostScript, PDF or HTML.")
> `(;; We need not only cairo here, but pango to ensure that tests for the
> ;; "cairo" bitmapType plotting backend succeed.
> ("pango" ,pango)
> + ("coreutils" ,coreutils)
> ("curl" ,curl)
> ("tzdata" ,tzdata)
> ("gfortran" ,gfortran)
This looks good to me. Thanks!
~~ Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: r: Use uname from Guix
2016-10-27 13:58 ` Ricardo Wurmus
@ 2016-10-27 14:38 ` Roel Janssen
0 siblings, 0 replies; 3+ messages in thread
From: Roel Janssen @ 2016-10-27 14:38 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus writes:
> Roel Janssen <roel@gnu.org> writes:
>
>> Dear Guix,
>>
>> When running R, it executes a wrapper script that relies on
>> @code{uname} to be available in PATH:
>>
>>> R_HOME_DIR=/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R
>>> if test "${R_HOME_DIR}" = "/gnu/store/dz83xhn43qc2dpdrja8mhx78l7qffqvq-r-3.3.0/lib/R"; then
>>> case "linux-gnu" in
>>> linux*)
>>> run_arch=`uname -m`
>>> case "$run_arch" in
>>> x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
>>> libnn=lib64
>>
>> Running R in a pure, ad-hoc environment will therefore signal a warning
>> that it cannot execute "uname".
>>
>> With the following patch, it no longer makes this assumption. Instead
>> it uses an absolute path to a uname binary from the Guix store.
>>
>>From e364cb25204edea4d8bfb9cfc52764f811c58e72 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Wed, 26 Oct 2016 17:09:19 +0200
>> Subject: [PATCH] gnu: r: Use uname from Guix
>>
>> * gnu/packages/statistics.scm (r): Use uname from Guix.
>> ---
>> gnu/packages/statistics.scm | 7 +++++++
>> 1 file changed, 7 insertions(+)
>>
>> diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
>> index 1b8d074..5e4cd8c 100644
>> --- a/gnu/packages/statistics.scm
>> +++ b/gnu/packages/statistics.scm
>> @@ -118,6 +118,12 @@ be output in text, PostScript, PDF or HTML.")
>> "/lib/R/lib"))
>> #:phases
>> (modify-phases %standard-phases
>> + (add-before 'configure 'patch-uname
>> + (lambda* (#:key inputs #:allow-other-keys)
>> + (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
>> + "/bin/uname")))
>> + (substitute* "src/scripts/R.sh.in"
>> + (("uname") uname-bin)))))
>
> Please add #t to the end, because “substitute*” doesn’t have a return value.
Right. I will try to remember this better in the future too.
>> (add-before
>> 'configure 'set-default-pager
>> ;; Set default pager to "cat", because otherwise it is "false",
>> @@ -169,6 +175,7 @@ be output in text, PostScript, PDF or HTML.")
>> `(;; We need not only cairo here, but pango to ensure that tests for the
>> ;; "cairo" bitmapType plotting backend succeed.
>> ("pango" ,pango)
>> + ("coreutils" ,coreutils)
>> ("curl" ,curl)
>> ("tzdata" ,tzdata)
>> ("gfortran" ,gfortran)
>
> This looks good to me. Thanks!
Thanks! I applied the changes above and pushed it in b5ce25cc0.
Kind regards,
Roel Janssen
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2016-10-27 14:37 UTC | newest]
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2016-10-26 15:11 [PATCH] gnu: r: Use uname from Guix Roel Janssen
2016-10-27 13:58 ` Ricardo Wurmus
2016-10-27 14:38 ` Roel Janssen
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