ggtree install
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bjarke ▴ 10
@bjarke-9149
Last seen 7 weeks ago
Denmark

When trying to install ggtree I get the error that get_aes_var’ is not exported by 'namespace:rvcheck'

```r

BiocManager::install("ggtree")

Error: object ‘get_aes_var’ is not exported by 'namespace:rvcheck'

sessionInfo( )

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_DK.UTF-8 LC_NUMERIC=C LC_TIME=en_DK.UTF-8 LC_COLLATE=en_DK.UTF-8 LC_MONETARY=en_DK.UTF-8
[6] LC_MESSAGES=en_DK.UTF-8 LC_PAPER=en_DK.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] magrittr_2.0.1 tidyselect_1.1.0 munsell_0.5.0 colorspace_2.0-2 R6_2.5.1 rlang_0.4.11 fansi_0.5.0
[8] dplyr_1.0.7 tools_3.6.3 grid_3.6.3 gtable_0.3.0 utf8_1.2.2 DBI_1.1.1 ellipsis_0.3.2
[15] assertthat_0.2.1 tibble_3.1.4 lifecycle_1.0.0 crayon_1.4.1 BiocManager_1.30.16 purrr_0.3.4 ggplot2_3.3.5
[22] vctrs_0.3.8 yulab.utils_0.0.2 glue_1.4.2 ggfun_0.0.4 compiler_3.6.3 pillar_1.6.2 rvcheck_0.2.0

ggtree rvcheck • 2.3k views
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For what it's worth, I didn't want to update my R version (4.0.5) so I downgraded rvcheck to v. 0.1.8 using:

devtools::install_version('rvcheck',version='0.1.8')

then I was able to install ggtree just fine with:

BiocManager::install("ggtree")

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Mike Smith ★ 5.2k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg / de.NBI

I think the easiest solution would be to update your version of R to the latest (4.1.1) and then reinstall the ggtree package.

The reason you're running into this error is because the latest version of rvcheck (0.2.0) has removed the get_aes_var function. The current ggtree version (3.0.4) is aware of this change, and doesn't look for it. However, because you're using an old version of R, you're using also using an old version of both Bioconductor and subsequently the ggtree package. This older version still thinks get_aes_var should be present, and then fails when it isn't.

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Excellent! Many thanks Mike.

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