* [PATCH] New procedure for CRAN URIs.
@ 2015-09-17 15:13 Ricardo Wurmus
2015-09-18 9:40 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2015-09-17 15:13 UTC (permalink / raw)
To: guix-devel
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Hi Guix,
after it was reported that the plain CRAN URI only points to the latest
version of a package and previous versions are archived at a different
URI, I took Dave’s advice and wrote a ‘cran-uri’ procedure that produces
a list of URI strings for a given R package name and a version.
Only one of the two URIs will be correct as the archives don’t contain
the latest version. The first patch adds the procedure, the second
makes the importer generate a package expression containing the
procedure call, and the last updates all existing R packages to use this
procedure.
I’d like to amend and push Vicente’s useful patches for r-dplyr once
this patch set has been accepted.
Thanks for your patience!
~~ Ricardo
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From 702458583776bd28c865ffdf06977262b3901ee5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Sep 2015 17:00:18 +0200
Subject: [PATCH 1/3] build: Add cran-uri procedure.
* guix/build-system/r.scm (cran-uri): New procedure.
---
guix/build-system/r.scm | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
index 4daec5e..da06cb1 100644
--- a/guix/build-system/r.scm
+++ b/guix/build-system/r.scm
@@ -28,7 +28,8 @@
#:use-module (srfi srfi-26)
#:export (%r-build-system-modules
r-build
- r-build-system))
+ r-build-system
+ cran-uri))
;; Commentary:
;;
@@ -36,6 +37,15 @@
;;
;; Code:
+(define (cran-uri name version)
+ "Return a list of URI strings for the R package archive on CRAN for the
+release corresponding to NAME and VERSION. As only the most recent version is
+available via the first URI, the second URI points to the archived version."
+ (list (string-append "mirror://cran/src/contrib/"
+ name "_" version ".tar.gz")
+ (string-append "mirror://cran/src/contrib/Archive/"
+ name "/" name "_" version ".tar.gz")))
+
(define %r-build-system-modules
;; Build-side modules imported by default.
`((guix build r-build-system)
--
2.1.0
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From 05dc8656928709bfc2ea021a4d0d03b02bb79840 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Sep 2015 17:02:42 +0200
Subject: [PATCH 2/3] import: cran-sxml->sexp: Use cran-uri in package
expression.
* guix/import/cran.scm (cran-sxml->sexp): Use the cran-uri procedure in
the generated package expression.
---
guix/import/cran.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 8ed5e54..585cb9f 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -165,7 +165,7 @@ representation of the package page."
(version ,version)
(source (origin
(method url-fetch)
- (uri (string-append ,@(factorize-uri source-url version)))
+ (uri (cran-uri ,name version))
(sha256
(base32
,(bytevector->nix-base32-string (file-sha256 tarball))))))
--
2.1.0
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From 27abdabf051fc19781c05f7fa2bdb6bc3cf7728f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Sep 2015 17:04:35 +0200
Subject: [PATCH 3/3] gnu: Use cran-uri in source expressions.
* gnu/packages/statistics.scm (r-colorspace, r-dichromat, r-digest,
r-gtable, r-labeling, r-magrittr, r-munsell, r-rcpp, r-plyr, r-proto,
r-rcolorbrewer, r-stringi, r-stringr, r-reshape2, r-scales, r-ggplot2,
r-assertthat, r-lazyeval, r-dbi): Use cran-uri in source expressions.
---
gnu/packages/statistics.scm | 58 +++++++++++++++------------------------------
1 file changed, 19 insertions(+), 39 deletions(-)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6ccb97f..54c9abc 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -141,8 +141,7 @@ available, greatly increasing its breadth and scope.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/colorspace_"
- version ".tar.gz"))
+ (uri (cran-uri "colorspace" version))
(sha256
(base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
(build-system r-build-system)
@@ -162,8 +161,7 @@ colors are provided.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/dichromat_"
- version ".tar.gz"))
+ (uri (cran-uri "dichromat" version))
(sha256
(base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
(build-system r-build-system)
@@ -181,8 +179,7 @@ effects of different types of color-blindness.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/digest_"
- version ".tar.gz"))
+ (uri (cran-uri "digest" version))
(sha256
(base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih"))))
(build-system r-build-system)
@@ -207,8 +204,7 @@ OpenSSL should be used.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/gtable_"
- version ".tar.gz"))
+ (uri (cran-uri "gtable" version))
(sha256
(base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
(build-system r-build-system)
@@ -226,8 +222,7 @@ OpenSSL should be used.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/labeling_"
- version ".tar.gz"))
+ (uri (cran-uri "labeling" version))
(sha256
(base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
(build-system r-build-system)
@@ -244,8 +239,7 @@ algorithms.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/magrittr_"
- version ".tar.gz"))
+ (uri (cran-uri "magrittr" version))
(sha256
(base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
(build-system r-build-system)
@@ -266,8 +260,7 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/munsell_"
- version ".tar.gz"))
+ (uri (cran-uri "munsell" version))
(sha256
(base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
(build-system r-build-system)
@@ -287,8 +280,7 @@ Munsell colour system.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/Rcpp_"
- version ".tar.gz"))
+ (uri (cran-uri "Rcpp" version))
(sha256
(base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38"))))
(build-system r-build-system)
@@ -312,8 +304,7 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/plyr_"
- version ".tar.gz"))
+ (uri (cran-uri "plyr" version))
(sha256
(base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
(build-system r-build-system)
@@ -335,7 +326,7 @@ panels or collapse high-dimensional arrays to simpler summary statistics.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/proto_" version ".tar.gz"))
+ (uri (cran-uri "proto" version))
(sha256
(base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
(build-system r-build-system)
@@ -353,8 +344,7 @@ prototype-based, rather than class-based object oriented ideas.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/RColorBrewer_"
- version ".tar.gz"))
+ (uri (cran-uri "RColorBrewer" version))
(sha256
(base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
(build-system r-build-system)
@@ -373,10 +363,7 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org")
(source
(origin
(method url-fetch)
- (uri (string-append
- "mirror://cran/src/contrib/stringi_"
- version
- ".tar.gz"))
+ (uri (cran-uri "stringi" version))
(sha256
(base32
"183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
@@ -402,8 +389,7 @@ transliteration, concatenation, date-time formatting and parsing, etc.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/stringr_"
- version ".tar.gz"))
+ (uri (cran-uri "stringr" version))
(sha256
(base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
(build-system r-build-system)
@@ -427,8 +413,7 @@ the input of another.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/reshape2_"
- version ".tar.gz"))
+ (uri (cran-uri "reshape2" version))
(sha256
(base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
(build-system r-build-system)
@@ -450,8 +435,7 @@ using just two functions: melt and dcast (or acast).")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/scales_"
- version ".tar.gz"))
+ (uri (cran-uri "scales" version))
(sha256
(base32 "12xrmn1vh64dl46bq7n7pa427aicb2ifjrby9in3m32nyvir0kac"))))
(build-system r-build-system)
@@ -477,8 +461,7 @@ legends.")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/ggplot2_"
- version ".tar.gz"))
+ (uri (cran-uri "ggplot2" version))
(sha256
(base32 "0794kjqi3lrxb33lr1mykd58959hlgkhdn259vj8fxrh65mqw920"))))
(build-system r-build-system)
@@ -506,8 +489,7 @@ aesthetic attributes.")
(version "0.1")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/assertthat_"
- version ".tar.gz"))
+ (uri (cran-uri "assertthat" version))
(sha256
(base32
"0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
@@ -527,8 +509,7 @@ wrong.")
(version "0.1.10")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/lazyeval_"
- version ".tar.gz"))
+ (uri (cran-uri "lazyeval" version))
(sha256
(base32
"02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
@@ -546,8 +527,7 @@ evaluation (NSE) in R.")
(version "0.3.1")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/DBI_"
- version ".tar.gz"))
+ (uri (cran-uri "DBI" version))
(sha256
(base32
"0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw"))))
--
2.1.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] New procedure for CRAN URIs.
2015-09-17 15:13 [PATCH] New procedure for CRAN URIs Ricardo Wurmus
@ 2015-09-18 9:40 ` Ludovic Courtès
2015-09-18 9:50 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Ludovic Courtès @ 2015-09-18 9:40 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 702458583776bd28c865ffdf06977262b3901ee5 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 17 Sep 2015 17:00:18 +0200
> Subject: [PATCH 1/3] build: Add cran-uri procedure.
>
> * guix/build-system/r.scm (cran-uri): New procedure.
Sounds like a good idea.
You might as well come up with ‘cran-origin’:
(define (cran-origin package version)
(origin
(method url-fetch)
…))
WDYT?
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] New procedure for CRAN URIs.
2015-09-18 9:40 ` Ludovic Courtès
@ 2015-09-18 9:50 ` Ricardo Wurmus
2015-09-18 19:26 ` Ludovic Courtès
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2015-09-18 9:50 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
Ludovic Courtès <ludo@gnu.org> writes:
>> * guix/build-system/r.scm (cran-uri): New procedure.
>
> Sounds like a good idea.
>
> You might as well come up with ‘cran-origin’:
>
> (define (cran-origin package version)
> (origin
> (method url-fetch)
> …))
>
> WDYT?
I wouldn’t know how to deal with the hash then. Isn’t it better to have
a static hash in the package definition rather than compute it when
‘(cran-origin ...)’ is evaled? Or should it be called like this instead:
(cran-origin "name" version
"verylonghash1234")
~~ Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] New procedure for CRAN URIs.
2015-09-18 9:50 ` Ricardo Wurmus
@ 2015-09-18 19:26 ` Ludovic Courtès
0 siblings, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2015-09-18 19:26 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> Ludovic Courtès <ludo@gnu.org> writes:
>
>>> * guix/build-system/r.scm (cran-uri): New procedure.
>>
>> Sounds like a good idea.
>>
>> You might as well come up with ‘cran-origin’:
>>
>> (define (cran-origin package version)
>> (origin
>> (method url-fetch)
>> …))
>>
>> WDYT?
>
> I wouldn’t know how to deal with the hash then.
Arf, yes, forget my comment; the solution you propose looks best.
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2015-09-18 19:26 UTC | newest]
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2015-09-17 15:13 [PATCH] New procedure for CRAN URIs Ricardo Wurmus
2015-09-18 9:40 ` Ludovic Courtès
2015-09-18 9:50 ` Ricardo Wurmus
2015-09-18 19:26 ` Ludovic Courtès
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