flowCore install missing a dependency?
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Robert Baer ▴ 70
@robert-baer-4660
Last seen 16 months ago
United States

Trying to install and use flowCore on R 3.6.0 seems to produce a dependency issue:

BiocManager::install("flowCore")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'flowCore'
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/flowCore_1.50.0.zip'
Content type 'application/zip' length 8983028 bytes (8.6 MB)
downloaded 8.6 MB

package ‘flowCore’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\rbaer\AppData\Local\Temp\RtmpsBV8Ru\downloaded_packages
> library(flowCore)
Error: package or namespace load failed for ‘flowCore’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘robustbase’
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] usethis_1.5.0  devtools_2.0.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1          compiler_3.6.0      BiocManager_1.30.4  prettyunits_1.0.2  
 [5] remotes_2.0.4       tools_3.6.0         digest_0.6.19       pkgbuild_1.0.3     
 [9] pkgload_1.0.2       memoise_1.1.0       lattice_0.20-38     rlang_0.3.4        
[13] graph_1.62.0        cli_1.1.0           rstudioapi_0.10     curl_3.3           
[17] parallel_3.6.0      mvtnorm_1.0-10      cluster_2.0.9       withr_2.1.2        
[21] desc_1.2.0          fs_1.3.1            grid_3.6.0          stats4_3.6.0       
[25] rprojroot_1.3-2     glue_1.3.1          Biobase_2.44.0      R6_2.4.0           
[29] processx_3.3.1      sessioninfo_1.1.1   callr_3.2.0         corpcor_1.6.9      
[33] magrittr_1.5        backports_1.1.4     ps_1.3.0            matrixStats_0.54.0 
[37] BiocGenerics_0.30.0 MASS_7.3-51.4       assertthat_0.2.1    crayon_1.3.4       
>
flowCore Installation dependency • 486 views
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Entering edit mode

Hi,

It seems that robustbase is not needed by flowCore. https://bioconductor.org/packages/release/bioc/html/flowCore.html FlowCore depends on rrcov which depends on robustbase. https://cran.r-project.org/web/packages/rrcov/index.html

Please report if rrcov is installed or not on your session.

To solve your issue, I would say you have to install robustbase and/or rrcov.

Mike will answer you certainly. NB: I am still on R3.5.1, and I have both rrcov and robustbase.

Best.

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Entering edit mode

Well FWIW, installing robustbase DID solve my issue per se, but I thought it worth reporting because it seemed like this was not intended workflow. Unfortunately, my sessionInfo is all the information I still have of my situation when I experienced the problem.

Today rrcov IS on my package list, but I can't speak to when the error occurred..

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Entering edit mode
Jake Wagner ▴ 280
@jake-wagner-19995
Last seen 11 months ago

Mike re-opened an issue related to this: https://github.com/RGLab/flowCore/issues/23. I'll be moving the classes and methods that necessitate these dependencies over to flowStats and I'll post here and to that issue when that's complete.

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Entering edit mode

After a few recent commits linked at the issue above, the rrcov dependency (among others) is removed from flowCore and those changes will be incorporated in to the next Bioconductor release.

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