From mboxrd@z Thu Jan 1 00:00:00 1970 From: zimoun Subject: bug#39885: Bioconductor URI, fallback and time-machine Date: Tue, 3 Mar 2020 16:59:03 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="000000000000aa3660059ff5625d" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:51287) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j99xj-0003XL-T6 for bug-guix@gnu.org; Tue, 03 Mar 2020 11:00:05 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j99xi-0004pV-IB for bug-guix@gnu.org; Tue, 03 Mar 2020 11:00:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33905) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j99xi-0004pM-Ei for bug-guix@gnu.org; Tue, 03 Mar 2020 11:00:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1j99xi-0000Gm-Bh for bug-guix@gnu.org; Tue, 03 Mar 2020 11:00:02 -0500 Sender: "Debbugs-submit" Resent-Message-ID: Received: from eggs.gnu.org ([2001:470:142:3::10]:51176) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j99wz-00031a-KH for bug-guix@gnu.org; Tue, 03 Mar 2020 10:59:18 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j99wy-0004eG-3x for bug-guix@gnu.org; Tue, 03 Mar 2020 10:59:17 -0500 Received: from mail-qv1-xf30.google.com ([2607:f8b0:4864:20::f30]:34213) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j99wx-0004ds-T3 for bug-guix@gnu.org; Tue, 03 Mar 2020 10:59:16 -0500 Received: by mail-qv1-xf30.google.com with SMTP id o18so1906342qvf.1 for ; Tue, 03 Mar 2020 07:59:15 -0800 (PST) List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+gcggb-bug-guix=m.gmane-mx.org@gnu.org Sender: "bug-Guix" To: 39885@debbugs.gnu.org, me@tobias.gr, rekado@elephly.net --000000000000aa3660059ff5625d Content-Type: text/plain; charset="UTF-8" Dear, Currently, the URI scheme (see 'bioconductor-uri' in guix/build-system/r.scm) is: https://bioconductor.org/packages/release/data//src/contrib/-.tar.gz which leads to 2 issues: 1. when Bioconductor updates their release, some package versions are updated too, and so, the upstream return 404. 2. for this reason 1., the "guix time-machine" is broken for all the Bioconductor packages, at least if Berlin or SWH does not have a substitute; which is not expected for 'annotation' packages. However, the Bioconductor archive still serves the old release, i.e., https://bioconductor.org/packages/3.x/data//src/contrib/-.tar.gz The ways to fix the both issues are: a) Add the Bioconductor release (known at packaging time) to all the packages; provide as argument to 'bioconductor-uri'. b) Add more URLs to fallback. As discussed on IRC, Tobias seems more inclined with the option a) and I am more in favour of option b. Attached, a quick patch showing the option b). Please also consider #36805 which was never merged or closed. http://issues.guix.gnu.org/issue/36805 All the best, simon --000000000000aa3660059ff5625d Content-Type: text/x-patch; charset="US-ASCII"; name="0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch" Content-Disposition: attachment; filename="0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch" Content-Transfer-Encoding: base64 Content-ID: X-Attachment-Id: f_k7c2u5mz0 RnJvbSA4N2U3M2UwMjIwMmZlNWUzNDJkNjhmMWZiMTdlZmRkNDQyNTczN2NkIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiB6aW1vdW4gPHppbW9uLnRvdXRvdW5lQGdtYWlsLmNvbT4KRGF0 ZTogVHVlLCAzIE1hciAyMDIwIDE2OjUzOjM5ICswMTAwClN1YmplY3Q6IFtQQVRDSF0gYnVpbGQt c3lzdGVtOiByOiBVc2UgQmlvY29uZHVjdG9yIG9sZCByZWxlYXNlcyB0byBmYWxsYmFjay4KCiog Z3VpeC9idWlsZC1zeXN0ZW0vci5zY20gKGJpb2NvbmR1Y3Rvci11cmkpOiBFeHRlbmQgdGhlIGZh bGxiYWNrIGxpc3QuCi0tLQogZ3VpeC9idWlsZC1zeXN0ZW0vci5zY20gfCAyMSArKysrKysrKysr KystLS0tLS0tLS0KIDEgZmlsZSBjaGFuZ2VkLCAxMiBpbnNlcnRpb25zKCspLCA5IGRlbGV0aW9u cygtKQoKZGlmZiAtLWdpdCBhL2d1aXgvYnVpbGQtc3lzdGVtL3Iuc2NtIGIvZ3VpeC9idWlsZC1z eXN0ZW0vci5zY20KaW5kZXggMmQzMjg3NjRiMC4uODYzOGUxYjg4OCAxMDA2NDQKLS0tIGEvZ3Vp eC9idWlsZC1zeXN0ZW0vci5zY20KKysrIGIvZ3VpeC9idWlsZC1zeXN0ZW0vci5zY20KQEAgLTU0 LDE1ICs1NCwxOCBAQCByZWxlYXNlIGNvcnJlc3BvbmRpbmcgdG8gTkFNRSBhbmQgVkVSU0lPTi4i CiAgICAgICAgICAgICAgICAgICAgICAgICAgKCdhbm5vdGF0aW9uICIvZGF0YS9hbm5vdGF0aW9u IikKICAgICAgICAgICAgICAgICAgICAgICAgICAoJ2V4cGVyaW1lbnQgIi9kYXRhL2V4cGVyaW1l bnQiKQogICAgICAgICAgICAgICAgICAgICAgICAgIChfICIvYmlvYyIpKSkpCi0gICAgKGxpc3Qg KHN0cmluZy1hcHBlbmQgImh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNl IgotICAgICAgICAgICAgICAgICAgICAgICAgIHR5cGUtdXJsLXBhcnQKLSAgICAgICAgICAgICAg ICAgICAgICAgICAiL3NyYy9jb250cmliLyIKLSAgICAgICAgICAgICAgICAgICAgICAgICBuYW1l ICJfIiB2ZXJzaW9uICIudGFyLmd6IikKLSAgICAgICAgICA7OyBUT0RPOiB1c2UgJWJpb2NvbmR1 Y3Rvci12ZXJzaW9uIGZyb20gKGd1aXggaW1wb3J0IGNyYW4pCi0gICAgICAgICAgKHN0cmluZy1h cHBlbmQgImh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy8zLjEwIgotICAgICAgICAg ICAgICAgICAgICAgICAgIHR5cGUtdXJsLXBhcnQKLSAgICAgICAgICAgICAgICAgICAgICAgICAi L3NyYy9jb250cmliL0FyY2hpdmUvIgotICAgICAgICAgICAgICAgICAgICAgICAgIG5hbWUgIl8i IHZlcnNpb24gIi50YXIuZ3oiKSkpKQorICAgIChhcHBlbmQgKGxpc3QgKHN0cmluZy1hcHBlbmQg Imh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNlIgorICAgICAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgdHlwZS11cmwtcGFydAorICAgICAgICAgICAgICAgICAgICAg ICAgICAgICAgICAgIi9zcmMvY29udHJpYi8iCisgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFyLmd6IikpCisgICAgICAgICAgICAobWFwIChsYW1i ZGEgKHJlbGVhc2UpCisgICAgICAgICAgICAgICAgICAgKHN0cmluZy1hcHBlbmQgImh0dHBzOi8v YmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy8iCisgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICAgcmVsZWFzZQorICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIHR5cGUtdXJs LXBhcnQKKyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAiL3NyYy9jb250cmliLyIK KyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFy Lmd6IikpCisgICAgICAgICAgICAgICAgIChsaXN0IChAQCAoZ3VpeCBpbXBvcnQgY3JhbikgJWJp b2NvbmR1Y3Rvci12ZXJzaW9uKQorICAgICAgICAgICAgICAgICAgICAgICAiMy45IiAiMy44IiAi My43IikpKSkpCiAKIChkZWZpbmUgJXItYnVpbGQtc3lzdGVtLW1vZHVsZXMKICAgOzsgQnVpbGQt c2lkZSBtb2R1bGVzIGltcG9ydGVkIGJ5IGRlZmF1bHQuCi0tIAoyLjI1LjAKCg== --000000000000aa3660059ff5625d--