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I am trying to install the RADammi package on R 3.6 using "devtools", however I receive this error:

Installing package into ‘C:/Users/taham/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)

ERROR: dependencies 'Biostrings', 'IRanges' are not available for package 'RADami' * removing 'C:/Users/taham/Documents/R/win-library/3.6/RADami'

Error: Failed to install 'unknown package' from URL: (converted from warning) installation of package > ‘C:/Users/taham/AppData/Local/Temp/RtmpycMnQ2/remotes11246cb38f0/RADami’ had non-zero exit status.

It is an old package that has been removed from CRAN https://rdrr.io/cran/RADami/

how should I install it?

update: I finally could manage to install the two dependencies using below command:

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("Biostrings")

BiocManager::install("IRanges")

I have downloaded the zip archived RADami file and tried to install the package, I receive this fetal error again:

install.packages("C:/Users/taham/Downloads/RADami_1.1-2.tar.gz", repos = NULL, type = "source")

Installing package into ‘C:/Users/taham/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)

  • installing source package 'RADami' ...

** package 'RADami' successfully unpacked and MD5 sums checked

** using staged installation

** R

** data

** inst

** byte-compile and prepare package for lazy loading

Error: objects 'c.phylo', 'c.multiPhylo' are not exported by 'namespace:ape' Execution halted

ERROR: lazy loading failed for package 'RADami'

  • removing 'C:/Users/taham/Documents/R/win-library/3.6/RADami'

Warning in install.packages :

installation of package ‘C:/Users/taham/Downloads/RADami_1.1-2.tar.gz’ had non-> zero exit status

I get the same error when using devtools

Masse
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  • Does this answer your question? [How do I install a package that has been archived from CRAN?](https://stackoverflow.com/questions/24194409/how-do-i-install-a-package-that-has-been-archived-from-cran) – Jaccar Jan 29 '20 at 14:55
  • not really, I have already downloaded the latest archived zip file, but now my problem is in installing the dependencies, being 'BioString', before manually installing the actual package – Masse Jan 29 '20 at 14:59
  • Do you have package ‘ape’ installed? – Allan Cameron Jan 30 '20 at 11:17
  • I think I do; > library(ape) Attaching package: ‘ape’ The following object is masked from ‘package:Biostrings’: complement The following objects are masked from ‘package:hierfstat’: pcoa, varcomp – Masse Jan 30 '20 at 11:25

2 Answers2

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It sounds like you need to first install "IRanges" and "Biostrings" from BioConductor:

library(devtools)
install_bioc("IRanges")
install_bioc("Biostrings")

Though these have other dependencies such as "S4Vector" which you may need to install manually also.

Then you should be able to install RADami:

install_url("https://cran.r-project.org/src/contrib/Archive/RADami/RADami_1.0-3.tar.gz")
Allan Cameron
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  • I could manage somehow to install 'IRanges' but for 'Biostrings', it doesn't work. I tried both : install_bioc("BioStrings") and if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") – Masse Jan 29 '20 at 14:44
  • @Masse what error does install_bioc("BioStrings") give you? – Allan Cameron Jan 29 '20 at 14:47
  • Downloading Bioconductor repo https://git.bioconductor.org/packages/BioStrings Error in git2r::clone(url, bundle, credentials = x$credentials, progress = FALSE) : Error in 'git2r_clone': remote error: FATAL: R any packages/BioStrings nobody DENIED by fallthru (or you mis-spelled the reponame) – Masse Jan 29 '20 at 14:51
  • @Masse I think it should be `install_bioc("Biostrings")` (without the capital) - my bad. – Allan Cameron Jan 29 '20 at 14:59
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I also had this issue with installing from the CRAN archive, but was successfully able to install it from the developer's Github. In R:

library(devtools)
install_github("andrew-hipp/RADami")
Katherine Silliman
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