From 6998ecba74a59203aad927733d2ac5738235e115 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:24:09 +0100
Subject: gnu: r-bsgenome-celegans-ucsc-ce10: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10)[source]: Use
bioconductor-uri.
[arguments]: Permit substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 89547be66d..5e727eae5d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -76,21 +76,14 @@ (define-public r-bsgenome-celegans-ucsc-ce10
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Celegans.UCSC.ce10_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
+ version 'annotation))
(sha256
(base32
"1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
(properties
`((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From 149f351f3871d1ad751ee4ebd2b389bbdcba4727 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:25:10 +0100
Subject: gnu: r-bsgenome-dmelanogaster-ucsc-dm6: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm6)[source]:
Use bioconductor-uri.
[arguments]: Permit substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5e727eae5d..e332e0c0f2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -101,21 +101,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm6
(version "1.4.1")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm6_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
+ version 'annotation))
(sha256
(base32
"1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
(properties
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From 87073b7ecba65ac541d244dc1f5270ae74736b25 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:26:22 +0100
Subject: gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e332e0c0f2..786c083a21 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -126,21 +126,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm3_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
+ version 'annotation))
(sha256
(base32
"19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
(properties
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From bf05ece1a2fe7042b8720953b2f298fe2a63dec8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:27:15 +0100
Subject: gnu: r-bsgenome-dmelanogaster-ucsc-dm3-masked: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked)[source]:
Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 786c083a21..9e7078cae2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -151,12 +151,8 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
(version "1.3.99")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
+ version 'annotation))
(sha256
(base32
"1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
--
cgit v1.2.3
From 88e7c7db59c28186bdce46ad65e9a5f4f81f27b0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:28:04 +0100
Subject: gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9e7078cae2..dd6b038442 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -182,21 +182,14 @@ (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
(version "0.99.1")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.1000genomes.hs37d5_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
+ version 'annotation))
(sha256
(base32
"1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From a47646bd05b0bf9af461149a731842a68a650b44 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:28:34 +0100
Subject: gnu: r-bsgenome-hsapiens-ucsc-hg19-masked: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked)[source]:
Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index dd6b038442..096f0f9677 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -206,12 +206,8 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
(version "1.3.99")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.UCSC.hg19.masked_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
+ version 'annotation))
(sha256
(base32
"0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
--
cgit v1.2.3
From 21f6dae73dabcabd1f313afa76d7750127a67000 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:28:54 +0100
Subject: gnu: r-bsgenome-mmusculus-ucsc-mm9: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 096f0f9677..19f1b1f440 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -237,21 +237,14 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm9_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
+ version 'annotation))
(sha256
(base32
"1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
(properties
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From 51dc4a2d7084e7c6f6968257f5a5f4c0f650dedc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:29:26 +0100
Subject: gnu: r-bsgenome-mmusculus-ucsc-mm9-masked: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked)[source]:
Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 19f1b1f440..99856b17ba 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -261,12 +261,8 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
(version "1.3.99")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "http://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm9.masked_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
+ version 'annotation))
(sha256
(base32
"00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
--
cgit v1.2.3
From f83404bc5b2703ff7b4c9987e1eed48646454a1e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:29:56 +0100
Subject: gnu: r-bsgenome-mmusculus-ucsc-mm10: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 99856b17ba..ef5df8e5a9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -292,21 +292,14 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Mmusculus.UCSC.mm10_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
+ version 'annotation))
(sha256
(base32
"12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
(properties
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From 1c05e637a440b1b65d5d5bc27790db9df91b71b2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:30:35 +0100
Subject: gnu: r-org-ce-eg-db: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-org-ce-eg-db)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ef5df8e5a9..39333c2944 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -317,11 +317,7 @@ (define-public r-org-ce-eg-db
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Ce.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
(sha256
(base32
"1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
--
cgit v1.2.3
From b0dfc79b0de0dceb01276b7a3ad7494be6c0b7f0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:30:58 +0100
Subject: gnu: r-org-dm-eg-db: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-org-dm-eg-db)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 39333c2944..4c87649699 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -339,11 +339,7 @@ (define-public r-org-dm-eg-db
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Dm.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
(sha256
(base32
"1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
--
cgit v1.2.3
From 7bb65a2227b924602fe079e8e03fd95db89ccdaa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:31:19 +0100
Subject: gnu: r-org-dr-eg-db: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-org-dr-eg-db)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4c87649699..6b48a2f671 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -361,11 +361,7 @@ (define-public r-org-dr-eg-db
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Dr.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
(sha256
(base32
"1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
--
cgit v1.2.3
From f53becc6d89979b6a51f47bb095f4c52732f2b54 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:31:46 +0100
Subject: gnu: r-org-hs-eg-db: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-org-hs-eg-db)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6b48a2f671..11276e93bd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -383,11 +383,7 @@ (define-public r-org-hs-eg-db
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Hs.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
(sha256
(base32
"1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
--
cgit v1.2.3
From 411be88bf32caf00c8f31600e3280ae95a85c4e7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:32:03 +0100
Subject: gnu: r-org-mm-eg-db: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-org-mm-eg-db)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 11276e93bd..fdb7ff0be8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -405,11 +405,7 @@ (define-public r-org-mm-eg-db
(version "3.7.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Mm.eg.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
(sha256
(base32
"1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
--
cgit v1.2.3
From e7a8cf2e6ebdf045b90adf08c182680efe8746c1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:32:22 +0100
Subject: gnu: r-bsgenome-hsapiens-ucsc-hg19: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fdb7ff0be8..4132973418 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -427,21 +427,14 @@ (define-public r-bsgenome-hsapiens-ucsc-hg19
(version "1.4.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Hsapiens.UCSC.hg19_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
+ version 'annotation))
(sha256
(base32
"1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
--
cgit v1.2.3
From 717d7cda9dbbae3ca6b7101c6e499d0e12718fcf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:32:48 +0100
Subject: gnu: r-genelendatabase: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-genelendatabase)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4132973418..9f79be3874 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -474,11 +474,7 @@ (define-public r-genelendatabase
(source
(origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/experiment/src/contrib"
- "/geneLenDataBase_" version ".tar.gz"))
+ (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
(sha256
(base32
"03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
--
cgit v1.2.3
From f2580a13856705d30b6d979c9c51df9f5ceda783 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:33:09 +0100
Subject: gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9f79be3874..86d4735d2d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -497,21 +497,14 @@ (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
(version "3.2.2")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
+ version 'annotation))
(sha256
(base32
"1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
(properties
`((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-genomicfeatures" ,r-genomicfeatures)))
(home-page
--
cgit v1.2.3
From d78db088623fcfbefc40dafe11d2ecf042842a41 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:33:35 +0100
Subject: gnu: r-txdb-hsapiens-ucsc-hg38-knowngene: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg38-knowngene)[source]:
Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 86d4735d2d..ca4b57c3fd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -522,12 +522,8 @@ (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
(version "3.4.6")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
+ version 'annotation))
(sha256
(base32
"12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
--
cgit v1.2.3
From 1afdf41b4984dfe09807583a0ee38bdff3579fa2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:33:54 +0100
Subject: gnu: r-txdb-mmusculus-ucsc-mm9-knowngene: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm9-knowngene)[source]:
Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ca4b57c3fd..42a3f7bb23 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -547,12 +547,8 @@ (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
(version "3.2.2")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://bioconductor.org/packages/"
- "release/data/annotation/src/contrib"
- "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
+ version 'annotation))
(sha256
(base32
"16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
--
cgit v1.2.3
From c271d9902553771119c292a92caffe06253c895f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:34:13 +0100
Subject: gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene)[source]:
Use bioconductor-uri.
[arguments]: Enable substitution.
---
gnu/packages/bioconductor.scm | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 42a3f7bb23..262618cf9e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -573,21 +573,14 @@ (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(version "3.4.7")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "TxDb.Mmusculus.UCSC.mm10.knownGene_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
+ version 'annotation))
(sha256
(base32
"04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)
("r-genomicfeatures" ,r-genomicfeatures)
--
cgit v1.2.3
From 6aca4054e06c78cbbd5ae4c90b4c4b5fd5dc1866 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:34:47 +0100
Subject: gnu: r-fdb-infiniummethylation-hg19: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-fdb-infiniummethylation-hg19)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 262618cf9e..c76bd42765 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -626,12 +626,8 @@ (define-public r-fdb-infiniummethylation-hg19
(version "2.2.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "FDb.InfiniumMethylation.hg19_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
+ version 'annotation))
(sha256
(base32
"0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
--
cgit v1.2.3
From 25f567a85a984febeb52a0d989344a1741194650 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:35:08 +0100
Subject: gnu: r-illuminahumanmethylationepicmanifest: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-illuminahumanmethylationepicmanifest)[source]:
Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c76bd42765..69e628bdce 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -654,12 +654,8 @@ (define-public r-illuminahumanmethylationepicmanifest
(version "0.3.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "IlluminaHumanMethylationEPICmanifest_"
- version ".tar.gz"))
+ (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
+ version 'annotation))
(sha256
(base32
"0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
--
cgit v1.2.3
From eed2766a45b1aa3278fff7f915a6f717b57a8ab7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:35:26 +0100
Subject: gnu: r-do-db: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-do-db)[source]: Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69e628bdce..42eb829ada 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -676,11 +676,7 @@ (define-public r-do-db
(version "2.9")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "DO.db_" version ".tar.gz"))
+ (uri (bioconductor-uri "DO.db" version 'annotation))
(sha256
(base32
"10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
--
cgit v1.2.3
From ced61edf5d1aed33afc4ea24e6040e8d6b706430 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:35:44 +0100
Subject: gnu: r-abadata: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-abadata)[source]: Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 42eb829ada..2bd98e8746 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -753,11 +753,7 @@ (define-public r-abadata
(version "1.12.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "ABAData_" version ".tar.gz"))
+ (uri (bioconductor-uri "ABAData" version 'experiment))
(sha256
(base32
"1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
--
cgit v1.2.3
From b86f77469b7e312aaa23e0959aab3fb2eecc9a13 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:35:59 +0100
Subject: gnu: r-arrmdata: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-arrmdata)[source]: Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2bd98e8746..f2a9b22e28 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -786,11 +786,7 @@ (define-public r-arrmdata
(version "1.18.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "ARRmData_" version ".tar.gz"))
+ (uri (bioconductor-uri "ARRmData" version 'experiment))
(sha256
(base32
"0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
--
cgit v1.2.3
From 545e67ac032abf4f44025234e465f17ae03531fb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:36:15 +0100
Subject: gnu: r-hsmmsinglecell: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-hsmmsinglecell)[source]: Use
bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f2a9b22e28..de12213561 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -806,11 +806,7 @@ (define-public r-hsmmsinglecell
(version "1.2.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "HSMMSingleCell_" version ".tar.gz"))
+ (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
(sha256
(base32
"1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
--
cgit v1.2.3
From 41728d234b9e27e69cef4451fd7826b6f779b476 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 4 Dec 2019 09:36:34 +0100
Subject: gnu: r-all: Use bioconductor-uri.
* gnu/packages/bioconductor.scm (r-all)[source]: Use bioconductor-uri.
---
gnu/packages/bioconductor.scm | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
(limited to 'gnu/packages/bioconductor.scm')
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index de12213561..5c191a2c0b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -835,11 +835,7 @@ (define-public r-all
(version "1.26.0")
(source (origin
(method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/experiment/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/experiment/src/contrib/"
- "ALL_" version ".tar.gz"))
+ (uri (bioconductor-uri "ALL" version 'experiment))
(sha256
(base32
"1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
--
cgit v1.2.3