METACLUSTER installation error

[anani-a-missinou]

Hi Dear METACLUSTER developer,

I’m a Ph.D. student in France on Brassica napus (rapeseed) specialized metabolites against pathogens. I want to apply your strategy “METACLUSTER—an R package for context-specific expression analysis of metabolic gene clusters” on my data. Your tool can help us to concise your data to highlight relevant biosynthesis pathways activated during plant infection.

I tried to install METACLUSTER using the following script:

*************** SCRIPT *******************************
install.packages("devtools")
library(devtools)
install.packages(mvtnorm)
install_github("https://github.com/mbanf/METACLUSTER")
install_github("METACLUSTER","mbanf")

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**************** ERROR MESSAGE *******************

version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 4.3
year 2017
month 11
day 30
svn rev 73796
language R
version.string R version 3.4.3 (2017-11-30)
nickname Kite-Eating Tree

install_github("https://github.com/mbanf/METACLUSTER")
Downloading GitHub repo mbanf/METACLUSTER@master
Skipping 3 packages not available: mvtnorm, plotrix, multtest
Installing 20 packages: foreach, doParallel, pheatmap, metap, iterators, Rdpack, TFisher, mutoss, bibtex, gbRd, sn, mvtnorm, mnormt, numDeriv, plotrix, multtest, multcomp, TH.data, sandwich, zoo
Error: Failed to install 'METACLUSTER' from GitHub:
(converted from warning) packages ‘mvtnorm’, ‘plotrix’, ‘multtest’ are not available (for R version 3.4.3)

---

Please, help me to avoid this error.

Thank you. Anani

[mbanf]

Dear Anani,

Sorry for being able to answer just now. What you're experiencing is that some of the dependencies (here, mvtnorm, plotrix, multtest) have been removed from CRAN into the bioconductor repository. so here is what you need to do (we have also updated the description accordingly):

• upgrade R to Version 3.6.1 or 3.6.2

• install devtools

• install METACLUSTER from github, providing bioconductor as an additional repo

install_github("https://github.com/mbanf/METACLUSTER", build_vignettes=TRUE,
repos=c("http://cran.rstudio.org", "http://bioconductor.org/packages/release/bioc"),
dependencies=TRUE)

Let me know if this works out.

Best,

Michael