Re: Broken URLs

[ludo@gnu.org (Ludovic Courtès)]

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

> Ludovic Courtès <ludo@gnu.org> writes:

[...]

>> gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: all the source URIs are unreachable:
>> gnu/packages/bioinformatics.scm:2627:5: sra-tools-2.4.5-5: URI https://github.com/ncbi/sra-tools/archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
>
> The tarball has been removed.  I’ll update it to the latest version.
>
>> gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: all the source URIs are unreachable:
>> gnu/packages/bioinformatics.scm:2419:5: ncbi-vdb-2.4.5-5: URI https://github.com/ncbi/ncbi-vdb        /archive/2.4.5-5.tar.gz not reachable: 404 ("Not Found")
>
> Same here.  The tarball was removed.  There are new versions out
> already, so I’ll take the opportunity to update it.

Aren’t these /archive URLs providing tarballs generated on the fly from
a Git tag?

Looking at <https://github.com/ncbi/ncbi-vdb/releases>, it seems that
this particular tag has been removed.

> From 01d547a6eedfb28d19551042f581e588dcc56fb5 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Nov 2015 11:14:00 +0100
> Subject: [PATCH 1/2] gnu: Add smithlab-cpp.
>
> * gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.

LGTM.

> From 534d7b73cda92b982f1338b1c9db420767d78066 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Nov 2015 11:14:48 +0100
> Subject: [PATCH 2/2] gnu: preseq: Update to 2.0.
>
> * gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
> [source]: Add file-name field, remove patches.
> [arguments]: Remove unused build phases, add make flags.
> [inputs]: Add smithlab-cpp.
> * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
> * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
>   file.
> * gnu-system.am (dist_patch_DATA): Remove them.

LGTM.

>> gnu/packages/java.scm:139:12: ant-1.9.4: all the source URIs are unreachable:
>> gnu/packages/java.scm:139:12: ant-1.9.4: URI https://www.apache.org/dist/ant/source/apache-ant-1.9.4-src.tar.gz not reachable: 404 ("Not Found")
>
> I don’t know why people do this but here again the tarballs have been
> removed and replaced with those for version 1.9.6.  Here’s another patch
> to update our ant package:

mirror://apache includes http://archive.apache.org/dist/, which is where
old archives go.  Could you use that one instead?

> From 212e56286c946b7a34d03819c20faa473cc42a9d Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 20 Nov 2015 11:23:18 +0100
> Subject: [PATCH] gnu: ant: Update to 1.9.6.
>
> * gnu/packages/java.scm (ant): Update to 1.9.6.

Upgrading is fine too.

Thank you!

Ludo’.