I had no issue using flowCust on a new shiny application following previous advice:
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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'citation()' on how to cite R or R packages in publications.
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> install.packages("BiocManager")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/BiocManager_1.30.4.tgz'
Content type 'application/x-gzip' length 288867 bytes (282 KB)
==================================================
downloaded 282 KB
The downloaded binary packages are in
/var/folders/16/ryy1sf5n4qvg1fcqrh5x3qs00000gn/T//RtmphKvTpP/downloaded_packages
> BiocManager::install("flowClust")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'BiocVersion', 'flowClust'
also installing the dependencies ‘DEoptimR’, ‘robustbase’, ‘mvtnorm’, ‘pcaPP’, ‘latticeExtra’, ‘RColorBrewer’, ‘hexbin’, ‘IDPmisc’, ‘rrcov’, ‘matrixStats’, ‘BiocGenerics’, ‘Biobase’, ‘graph’, ‘ellipse’, ‘flowViz’, ‘flowCore’, ‘clue’, ‘corpcor’, ‘mnormt’
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/DEoptimR_1.0-8.tgz'
Content type 'application/x-gzip' length 39837 bytes (38 KB)
==================================================
downloaded 38 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/robustbase_0.93-5.tgz'
Content type 'application/x-gzip' length 3243644 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/mvtnorm_1.0-10.tgz'
Content type 'application/x-gzip' length 262314 bytes (256 KB)
==================================================
downloaded 256 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/pcaPP_1.9-73.tgz'
Content type 'application/x-gzip' length 653808 bytes (638 KB)
==================================================
downloaded 638 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/latticeExtra_0.6-28.tgz'
Content type 'application/x-gzip' length 2198048 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/RColorBrewer_1.1-2.tgz'
Content type 'application/x-gzip' length 53161 bytes (51 KB)
==================================================
downloaded 51 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/hexbin_1.27.3.tgz'
Content type 'application/x-gzip' length 931571 bytes (909 KB)
==================================================
downloaded 909 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/IDPmisc_1.1.19.tgz'
Content type 'application/x-gzip' length 789042 bytes (770 KB)
==================================================
downloaded 770 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rrcov_1.4-7.tgz'
Content type 'application/x-gzip' length 1692875 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/matrixStats_0.54.0.tgz'
Content type 'application/x-gzip' length 1923009 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/BiocGenerics_0.30.0.tgz'
Content type 'application/x-gzip' length 637480 bytes (622 KB)
==================================================
downloaded 622 KB
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/Biobase_2.44.0.tgz'
Content type 'application/x-gzip' length 2358426 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/graph_1.62.0.tgz'
Content type 'application/x-gzip' length 1654323 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/ellipse_0.4.1.tgz'
Content type 'application/x-gzip' length 71606 bytes (69 KB)
==================================================
downloaded 69 KB
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/flowViz_1.48.0.tgz'
Content type 'application/x-gzip' length 1566845 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/flowCore_1.50.0.tgz'
Content type 'application/x-gzip' length 8232769 bytes (7.9 MB)
==================================================
downloaded 7.9 MB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/clue_0.3-57.tgz'
Content type 'application/x-gzip' length 1035861 bytes (1011 KB)
==================================================
downloaded 1011 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/corpcor_1.6.9.tgz'
Content type 'application/x-gzip' length 115169 bytes (112 KB)
==================================================
downloaded 112 KB
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/mnormt_1.5-5.tgz'
Content type 'application/x-gzip' length 106148 bytes (103 KB)
==================================================
downloaded 103 KB
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/BiocVersion_3.9.0.tgz'
Content type 'application/x-gzip' length 5513 bytes
==================================================
downloaded 5513 bytes
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/flowClust_3.22.0.tgz'
Content type 'application/x-gzip' length 1548500 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
The downloaded binary packages are in
/var/folders/16/ryy1sf5n4qvg1fcqrh5x3qs00000gn/T//RtmphKvTpP/downloaded_packages
Update old packages: 'cluster', 'digest', 'e1071', 'mime', 'nlme', 'openssl', 'rgdal'
Update all/some/none? [a/s/n]:
n
> shiny::runApp()
Loading required package: shiny
Attaching package: ‘flowClust’
The following object is masked from ‘package:graphics’:
box
The following object is masked from ‘package:base’:
Map
Listening on http://127.0.0.1:6125
Registered S3 method overwritten by 'openssl':
method from
print.bytes Rcpp
> setRepositories()
--- Please select repositories for use in this session ---
1: + CRAN
2: BioC software
3: BioC annotation
4: BioC experiment
5: CRAN (extras)
6: Omegahat
7: R-Forge
8: rforge.net
Enter one or more numbers separated by spaces, or an empty line to cancel
1: 1 2
And then deploying.