[Bioc-devel] Unable to reproduce chimeraviz 3.9 build failure (test failure)

[Pages, Herve]

Hi Stian,

This is likely related to an issue with the recently updated 
org.Hs.eg.db package. The issue was reported on this list 2 days ago:

https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014956.html

A fix for org.Hs.eg.db is on its way. Hopefully it will make the current 
test failure in chimeraviz go away. Stay tuned.

Sorry for the inconvenience,

H.


On 4/24/19 11:15, Stian Lågstad wrote:
> Hi,
>
> The most recent build of chimeraviz failed due to a test failure:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_chimeraviz_malbec2-2Dchecksrc.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=MdK9hl5VGKOQ5L01KOENKtzhbQfHSKF2JXKXYYLu0Es&s=RzrEQTeEfet8-fmPrU92HU5kJ7UxZxY-DFlO2Q84X80&e=.
> That the test in question should suddenly fail surprises me, and I'm unable
> to reproduce this locally. Does anyone have ideas as to how I can dig
> deeper into this?
>
> Thank you!
>
> Here's an excerpt from build log in case it disappears when the new build
> is done:
> ```
> * checking tests ...
>    Running ‘testthat.R’
>   ERROR
> Running the tests in ‘tests/testthat.R’ failed.
> Last 13 lines of output:
>
>    >
>    > test_check("chimeraviz")
>    ── 1. Failure: get_ensembl_ids gets the correct Ensembl gene ids for a
> fusion ob
>    fusion using gene_upstream@ensembl_id not equal to
> `correct_ensembl_id_upstream`.
>    Lengths differ: 2 is not 1
>
>    ══ testthat results
> ═══════════════════════════════════════════════════════════
>    OK: 170 SKIPPED: 0 FAILED: 1
>    1. Failure: get_ensembl_ids gets the correct Ensembl gene ids for a
> fusion object (@test_utilities.R#217)
>
>    Error: testthat unit tests failed
> ```
>
-- 
Hervé Pagès

Program in Computational Biology
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