# Bioconductor version error

**URL:** <https://travis-ci.community/t/bioconductor-version-error/3332>\
**Category:** R\
**Created:** [May 7, 2019, 2:09am UTC](https://travis-ci.community/t/bioconductor-version-error/3332 "2019-05-07T02:09:47Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![kevinwang09](https://avatars.discourse-cdn.com/v4/letter/k/b4bc9f/32.png) [@kevinwang09](https://travis-ci.community/u/kevinwang09)\
**Post date:** [May 7, 2019, 2:09am UTC](https://travis-ci.community/t/bioconductor-version-error/3332/1 "2019-05-07T02:09:47Z")

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@jeroen, @jimhester  
Hi,  
I am the maintainer of this `scMerge` package for Bioconductor. The issue that I am having is that Travis seems to be using Bioconductor version 3.8 rather than the newly released 3.9 ([https://travis-ci.org/SydneyBioX/scMerge/jobs/529095216](https://travis-ci.org/SydneyBioX/scMerge/jobs/529095216)). This caused an installation error for a dependent BioC package `M3Drop` (`scMerge` requires `M3Drop` version \>= 1.9.4).

I am unsure if this is a bug or not.

Thanks

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**Author:** ![native-api](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/native-api/32/430_2.png) [@native-api](https://travis-ci.community/u/native-api)\
**Post date:** [May 11, 2019, 6:39am UTC](https://travis-ci.community/t/bioconductor-version-error/3332/2 "2019-05-11T06:39:58Z")

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Looking through the code that generates download URLs [suggests](http://mtweb.cs.ucl.ac.uk/mus/bin/install_R/R-3.1.1/src/library/tools/R/utils.R) that “3.8” comes from the `R_BIOC_VERSION` envvar.

According to [https://bioconductor.org/install/](https://bioconductor.org/install/), you can install the latest Bioconductor version with

```auto
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

```

Maybe it’s sufficient to set the envvar: the logic suggests that it may be calling the above code in any case.

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**Author:** ![xrobin](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/xrobin/32/1843_2.png) [@xrobin](https://travis-ci.community/u/xrobin)\
**Post date:** [May 22, 2019, 11:51am UTC](https://travis-ci.community/t/bioconductor-version-error/3332/3 "2019-05-22T11:51:25Z")

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I am being hit by this too for a package of mine: [https://travis-ci.org/xrobin/xavamess/jobs/535684539](https://travis-ci.org/xrobin/xavamess/jobs/535684539)

Did you manage to solve the issue?  
I don’t set the `R_BIOC_VERSION` variable anywhere, nor do I install or load BiocManager anywhere… I assume that’s done in a setup script?

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<div class="post-metadata">

**Author:** ![kevinwang09](https://avatars.discourse-cdn.com/v4/letter/k/b4bc9f/32.png) [@kevinwang09](https://travis-ci.community/u/kevinwang09)\
**Post date:** [May 22, 2019, 12:20pm UTC](https://travis-ci.community/t/bioconductor-version-error/3332/4 "2019-05-22T12:20:21Z")

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I managed to get around this problem by writing up a short R script in the travis.yml file. But I think this is only a short-term patch. [https://travis-ci.org/SydneyBioX/scMerge/builds/534666350/config](https://travis-ci.org/SydneyBioX/scMerge/builds/534666350/config)

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<div class="post-metadata">

**Author:** ![native-api](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/native-api/32/430_2.png) [@native-api](https://travis-ci.community/u/native-api)\
**Post date:** [May 26, 2019, 9:44am UTC](https://travis-ci.community/t/bioconductor-version-error/3332/6 "2019-05-26T09:44:55Z")

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> <https://github.com/travis-ci/travis-build/pull/1710>

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<div class="post-metadata">

**Author:** ![native-api](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/native-api/32/430_2.png) [@native-api](https://travis-ci.community/u/native-api)\
**Post date:** [June 12, 2019, 8:28pm UTC](https://travis-ci.community/t/bioconductor-version-error/3332/7 "2019-06-12T20:28:33Z")

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@LiNk-NY [has stated](https://github.com/travis-ci/travis-build/pull/1710#issuecomment-501337886) that this was an upstream problem – they had an issue updating the `BiocManager` package at CRAN.

So this should be working now without any workarounds. You may need to clear your cache.

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<div class="post-metadata">

**Author:** ![xrobin](https://sea1.discourse-cdn.com/flex015/user_avatar/travis-ci.community/xrobin/32/1843_2.png) [@xrobin](https://travis-ci.community/u/xrobin)\
**Post date:** [June 14, 2019, 7:38am UTC](https://travis-ci.community/t/bioconductor-version-error/3332/8 "2019-06-14T07:38:34Z")

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@native-api it’s working now, thanks a lot!  
By the way I didn’t have to clean the cache - however I had done it previously, so not sure about it.