Question: flowCore install missing a dependency?
0
gravatar for Robert Baer
4 weeks ago by
Robert Baer70
United States
Robert Baer70 wrote:

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       
>
ADD COMMENTlink modified 4 weeks ago by Jake Wagner100 • written 4 weeks ago by Robert Baer70

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.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by SamGG190

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..

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Robert Baer70
Answer: flowCore install missing a dependency?
1
gravatar for Jake Wagner
4 weeks ago by
Jake Wagner100
Jake Wagner100 wrote:

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.

ADD COMMENTlink written 4 weeks ago by Jake Wagner100

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.

ADD REPLYlink written 27 days ago by Jake Wagner100
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