Entering edit mode
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
>
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.
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..