Warning: unable to access index for repository BioCsoft = https://bioconductor.org/packages/3.8/bioc/src/contrib:
scheme not supported in URL 'BioCsoft = https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
It seems the solution provided some weeks ago does not work anymore...
Child Task 622891518 failed: Error parsing manifest: Unable to determine package source for Bioconductor package flowClust: Repository must be specified
Execution halted
Actually flowClust has always been in in bioconductor (now in Release 3.9).
See: https://bioconductor.org/packages/release/bioc/html/flowClust.html
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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.
Thank you
Now it works just fine
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