Discussion:
01/01: gnu: bedtools: Update to 2.27.0.
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Mark H Weaver
2017-12-08 05:57:44 UTC
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Hi,

***@elephly.net (Ricardo Wurmus) writes:

> rekado pushed a commit to branch master
> in repository guix.
>
> commit 0d9824cc127f045d32c22d0c75df46d97cb61624
> Author: Ricardo Wurmus <***@elephly.net>
> Date: Wed Dec 6 19:12:16 2017 +0100
>
> gnu: bedtools: Update to 2.27.0.
>
> * gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
> [arguments]: Remove custom "install" phase; specify prefix.

The standard 'install' phase seems to have failed on Hydra:

https://hydra.gnu.org/build/2389354

--8<---------------cut here---------------start------------->8---
starting phase `install'
make: *** No rule to make target 'install'. Stop.
phase `install' failed after 0.0 seconds
builder for `/gnu/store/fq59s5x7kxn8sq9wl62334bacpjgj1b3-bedtools-2.18.0.drv' failed with exit code 1
@ build-failed /gnu/store/fq59s5x7kxn8sq9wl62334bacpjgj1b3-bedtools-2.18.0.drv - 1 builder for `/gnu/store/fq59s5x7kxn8sq9wl62334bacpjgj1b3-bedtools-2.18.0.drv' failed with exit code 1
--8<---------------cut here---------------end--------------->8---

Any idea what happened here?

Mark
Mark H Weaver
2017-12-08 18:06:56 UTC
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Hi Ricardo,

Ricardo Wurmus <***@elephly.net> writes:

> Mark H Weaver <***@netris.org> writes:
>
>> ***@elephly.net (Ricardo Wurmus) writes:
>>
>>> rekado pushed a commit to branch master
>>> in repository guix.
>>>
>>> commit 0d9824cc127f045d32c22d0c75df46d97cb61624
>>> Author: Ricardo Wurmus <***@elephly.net>
>>> Date: Wed Dec 6 19:12:16 2017 +0100
>>>
>>> gnu: bedtools: Update to 2.27.0.
>>>
>>> * gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
>>> [arguments]: Remove custom "install" phase; specify prefix.
>>
>> The standard 'install' phase seems to have failed on Hydra:
>>
>> https://hydra.gnu.org/build/2389354
>>
>> --8<---------------cut here---------------start------------->8---
>> starting phase `install'
>> make: *** No rule to make target 'install'. Stop.
>> phase `install' failed after 0.0 seconds
>> builder for `/gnu/store/fq59s5x7kxn8sq9wl62334bacpjgj1b3-bedtools-2.18.0.drv' failed with exit code 1
>> @ build-failed
>> /gnu/store/fq59s5x7kxn8sq9wl62334bacpjgj1b3-bedtools-2.18.0.drv - 1
>> builder for
>> `/gnu/store/fq59s5x7kxn8sq9wl62334bacpjgj1b3-bedtools-2.18.0.drv'
>> failed with exit code 1
>> --8<---------------cut here---------------end--------------->8---
>
> “builder for … 2.18.0”? This should be version 2.27.0 and worked fine
> on at least three machines here.

I see now that there's a 'bedtools-2.18' package that inherits from the
main 'bedtools'. 'bedtools-2.18', apparently needed by 'ribotaper', was
broken by your changes to 'bedtools'.

Mark
Ricardo Wurmus
2017-12-09 12:02:00 UTC
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Mark H Weaver <***@netris.org> writes:

>> “builder for … 2.18.0”? This should be version 2.27.0 and worked fine
>> on at least three machines here.
>
> I see now that there's a 'bedtools-2.18' package that inherits from the
> main 'bedtools'. 'bedtools-2.18', apparently needed by 'ribotaper', was
> broken by your changes to 'bedtools'.

Thank you. This is now fixed with commit 83b9d121a.

--
Ricardo

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