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Question: Installation of CountClust fails
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gravatar for Daniel Bottomly
9 months ago by
United States
Daniel Bottomly20 wrote:

Hi:

I'm having an issue loading the release version of CountClust. See below for a reproducible example with error in yellow. I assume this is due to changes in the 'cowplot' CRAN package?

Thanks,

Dan

> source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

> biocLite("CountClust")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).

Installing package(s) ‘CountClust’

trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/CountClust_1.2.0.tgz'

Content type 'application/x-gzip' length 17561608 bytes (16.7 MB)

==================================================

downloaded 16.7 MB

The downloaded binary packages are in

    /var/folders/xf/6sc0vfxj5dj4_0dt0r9jm_jdnrv5h3/T//RtmpoKFL63/downloaded_packages

> library(CountClust)

Loading required package: ggplot2

Error : object ‘switch_axis_position’ is not exported by 'namespace:cowplot'

Error: package or namespace load failed for ‘CountClust’

> biocValid()

[1] TRUE

> sessionInfo()

R version 3.3.3 (2017-03-06)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X El Capitan 10.11.6

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] ggplot2_2.2.1        BiocInstaller_1.24.0

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.10     gtools_3.5.0     slam_0.1-40      grid_3.3.3       plyr_1.8.4       gtable_0.2.0     magrittr_1.5     scales_0.4.1     stringi_1.1.3    reshape2_1.4.2   lazyeval_0.2.0   cowplot_0.7.0    tools_3.3.3      stringr_1.2.0    munsell_0.4.3    colorspace_1.3-2 tibble_1.3.0    

ADD COMMENTlink written 9 months ago by Daniel Bottomly20

Try via devtools -> install_github("kkdey/Countclust") instead (they made some changes on the github version).

ADD REPLYlink written 9 months ago by joseph.bergenstrahle0
1

Yes, that does work for me.  However, it is unfortunate that the main Bioconductor version does not.

ADD REPLYlink written 9 months ago by Daniel Bottomly20
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