Error when running exploBATCH

lrd9 commented 4 years ago

I got a very weird error when running exploBATCH. Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install Dose this mean that some dependency packages should be installed from Bioconductor and is not in my session? Thanks in advance!

syspremed commented 4 years ago

Thanks for highlighting this issue.

This is a problem associated with R version 3.5 and above. In exploBatch we are installing all dependence packages using "https://bioconductor.org/biocLite.R") but this has been deprecated now. For R version 3.5+ you install using BiocManager::install(). We are going to update this exploBATCH asap.

Thanks.

birkiy commented 4 years ago

Hi it still gives the same error, even if I downloaded with the following code, BioManager::install("exploBATCH") I use 3.9 Bioconductor, 3.6 R.

Separately, can you provide a valid tutorial for an analysis?

syspremed commented 4 years ago

It will continue giving the same error since within exploBATCH we are installing all dependencies using "https://bioconductor.org/biocLite.R". So we need to change that asap. The manual will also be updated with these changes.

Thanks.

camilla0801 commented 4 years ago

I wanted to install it viaBiocManager::install() but it says: Warning in install.packages : package ‘exploBatch’ is not available (for R version 4.0.0) is there any way to install it in R4.0.0?

gnyamundanda commented 4 years ago

Hi

I am forwarding your query to Gift Nyamundanda.

On Fri, Aug 28, 2020 at 3:10 PM camilla0801 notifications@github.com wrote:

I wanted to install it via BiocManager::install() but it says ``` Warning in install.packages : package ‘exploBatch’ is not available (for R version 4.0.0)

is there any way to install it in R4.0.0?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/syspremed/exploBATCH/issues/3#issuecomment-682597285, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACEXFITEIV4W3AEAWWNOI5TSC63FPANCNFSM4KZPWMGQ .

mickaelleclercq commented 4 years ago

Run this code before executing ExploBatch:

  installed<-installed.packages()[,1] 
  required<-c("mvtnorm","mclust","sva","stats","ggplot2","RColorBrewer",
              "rARPACK","RcppArmadillo","RcppEigen","Rcpp","parallel",
              "foreach","doParallel","doMC","compiler","devtools")
  toinstall<-required[!(required %in% installed)]
  if(length(toinstall) != 0){
    if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    BiocManager::install(toinstall)
  }
  lapply(required, require, character.only = TRUE)
  requirfMM<-c("fMM","exploBATCHcolon","exploBATCHbreast")
  toinstallfMM<-requirfMM[!(requirfMM %in% installed)]
  if(length(toinstallfMM) != 0){
      install_github("syspremed/fMM")
      install_github("syspremed/exploBATCHbreast")
      install_github("syspremed/exploBATCHcolon")
  }

JPGranizo commented 3 years ago

Hi! I have the same problem. When running exploBATCH I get the Error message Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install It seems like the error still hasn't been fixed. It is a shame, as the exploBATCH package looks very attractive.

I followed the steps by @mickaelleclercq to install all dependencies manually. I also run into a problem here, as two packages can't be installed:

(1) package "doMC" is apparently a MacOS / UNIX based package only, so it is not possible to install on a Windows PC. What is the solution here? (2) The package from install_github("syspremed/fMM") can not be installed. An error is showing up: Error : (converted from warning) C:/Users/JPGranizo/AppData/Local/Temp/RtmpwvntxY/Rbuild4b7874205a8e/fMM/man/fMM-package.Rd:24: All text must be in a section ERROR: installing Rd objects failed for package 'fMM' removing C:/Users/JPGranizo/Documents/R/win-library/4.0/fMM Error: Failed to install fMM from GitHub: (converted from warning) installation of package C:/Users/JPGranizo/AppData/Local/Temp/RtmpSW1Dvq/file4e085d642ded/fMM_1.0.tar.gz had non-zero exit status

I would really appreciate any help to get exploBATCH up an running!! Thank you in advance!

Here are my Systeminformation version R version 4.0.3 (2020-10-10) os Windows 10 x64 system x86_64, mingw32 ui RStudio

syspremed / exploBATCH

Error when running exploBATCH #3