andreaskapou/Melissa

which R version does Melissa support?

yeswzc opened this issue · 3 comments

yeswzc commented

Hi,
I am trying to install Melissa. However I get error of installing 'clues'.

✓  checking for file ‘/private/var/folders/k1/r_2p07k149vcpj8jzy87_z5c8718_r/T/RtmpewT8v9/remotes6b5e7a810992/andreaskapou-Melissa-4a869b5/DESCRIPTION’ ...
─  preparing ‘Melissa’:
✓  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
         -----------------------------------
   ERROR: dependency ‘clues’ is not available for package ‘Melissa’
─  removing ‘/private/var/folders/k1/r_2p07k149vcpj8jzy87_z5c8718_r/T/RtmpEJ0BYr/Rinst6bef5dcd1ad6/Melissa’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'Melissa' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr:
E> * checking for file ‘/private/var/folders/k1/r_2p07k149vcpj8jzy87_z5c8718_r/T/RtmpewT8v9/remotes6b5e7a810992/andreaskapou-Melissa-4a869b5/DESCRIPTION’ ... OK
E> * preparing ‘Melissa’:
E> * checking DESCRIPTION meta-information ... OK
E> * installing the package to build vignettes
E>       -----------------------------------
E> ERROR: dependency ‘clues’ is not available for package ‘Melissa’
E> * removing ‘/private/var/folders/k1/r_2p07k149vcpj8jzy87_z5c8718_r/T/RtmpEJ0BYr/Rinst6bef5dcd1ad6/Melissa’
E>       -----------------------------------
E> ERROR: package installation failed

And I also cannot install 'clues' by source code

install.packages("https://cran.r-project.org/src/contrib/Archive/clues/clues_0.6.2.2.tar.gz", type = "source", repos = NULL)
trying URL 'https://cran.r-project.org/src/contrib/Archive/clues/clues_0.6.2.2.tar.gz'
Content type 'application/x-gzip' length 572111 bytes (558 KB)
==================================================
downloaded 558 KB

* installing *source* package ‘clues’ ...
** package ‘clues’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran  -fPIC  -Wall -g -O2  -c  CH.f95 -o CH.o
make: gfortran: No such file or directory
make: *** [CH.o] Error 1
ERROR: compilation failed for package ‘clues’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/clues’
Warning in install.packages :
  installation of package ‘/var/folders/k1/r_2p07k149vcpj8jzy87_z5c8718_r/T//RtmpewT8v9/downloaded_packages/clues_0.6.2.2.tar.gz’ had non-zero exit status

So I think this might be a R version problem or some other issues. Could you tell me how to solve this, or which R version may solve this?
Thank you!

Mr-Pepe commented

Looks like you don't have gfortran installed on your system.

yeswzc commented

You are right. Thank you!

andreaskapou commented

Thanks for commenting on this Mr-Pepe. Looking again at the clues R package, it seems it is removed from CRAN repository: https://cran.r-project.org/web/packages/clues/index.html

So I updated Melissa to use the mclust package, which contains the same function to compute the Adjusted Rand Index.

Thanks to Mr-Pepe questions, I updated the package, fixing some bugs and also adding new functionality, such as imputing CpG met states by giving as input a directory of files.

These will not be available on Bioconductor yet. To get the latest functionality you should both install BPRMeth and Melissa. That is:

# Install BPRMeth 
devtools::install_github("andreaskapou/BPRMeth")
# Install Melissa
devtools::install_github("andreaskapou/Melissa")

The new vignettes can be found here:

  1. Data processing: https://rpubs.com/cakapourani/melissa-process
  2. Analysis with Melissa: https://rpubs.com/cakapourani/melissa-analysis
    where Section 5 contains the list of commands to go from binarised met files to imputed and clustered data.

Hope this helps.

Best,
Andreas