Consider adding cytominer on conda

[gwaybio]

@hkhawar and I were troubleshooting cytominer install. It was failing originally because of the issues described in #131 - we are trying to install in a conda environment, but are getting some errors.

[hkhawar]

ERROR: dependency ‘KernSmooth’ is not available for package ‘prodlim’

• removing ‘/Users/habbasi/anaconda3/envs/Target_ID/lib/R/library/prodlim’
  installation of package ‘prodlim’ had non-zero exit statusERROR: dependency ‘prodlim’ is not available for package ‘ipred’
• removing ‘/Users/habbasi/anaconda3/envs/Target_ID/lib/R/library/ipred’
  installation of package ‘ipred’ had non-zero exit statusERROR: dependency ‘ipred’ is not available for package ‘recipes’
• removing ‘/Users/habbasi/anaconda3/envs/Target_ID/lib/R/library/recipes’
  installation of package ‘recipes’ had non-zero exit statusERROR: dependency ‘recipes’ is not available for package ‘caret’
• removing ‘/Users/habbasi/anaconda3/envs/Target_ID/lib/R/library/caret’
  installation of package ‘caret’ had non-zero exit status
  The downloaded source packages are in
  ‘/private/var/folders/zz/vvqfkgdj22b0z3h50yjvw3fjzzgfxt/T/RtmpF3yNOJ/downloaded_packages’
  Updating HTML index of packages in '.Library'
  Making 'packages.html' ... done
  ✔ checking for file ‘/private/var/folders/zz/vvqfkgdj22b0z3h50yjvw3fjzzgfxt/T/RtmpF3yNOJ/remotes15d795582f191/cytomining-cytominer-3cde7f0/DESCRIPTION’ ...
  ─ preparing ‘cytominer’:
  ✔ checking DESCRIPTION meta-information ...
  ─ installing the package to build vignettes
  -----------------------------------
  ERROR: dependency ‘caret’ is not available for package ‘cytominer’
  ─ removing ‘/private/var/folders/zz/vvqfkgdj22b0z3h50yjvw3fjzzgfxt/T/Rtmp2idUAH/Rinst1611e334d39df/cytominer’
  -----------------------------------
  ERROR: package installation failed
  Error: Failed to install 'cytominer' from GitHub:
  System command error

[hkhawar]

name: Target_ID
channels:

• conda-forge
  dependencies:
• conda-forge::r-dplyr=0.7.6
• conda-forge::r-tidyr=0.8.1
• conda-forge::r-magrittr=1.5
• conda-forge::r-tibble=2.1.1
• conda-forge::r-docopt=0.6
• conda-forge::r-readr=1.1.1
• conda-forge::r-readxl=1.1.0
• conda-forge::r-ggplot2=3.0.0
• conda-forge::r-ggrepel=0.8.0
• conda-forge::r-optparse=1.6.0
• conda-forge::r-knitr=1.20
• conda-forge::r-devtools=2.0.2
• conda-forge::r-stringr=1.4.0

[gwaybio]

@hkhawar - I was able to install cytominer after adding:

- conda-forge::r-caret=6.0_84

to the environment.yml file

[hkhawar]

Great

[gwaybio]

I have a feeling that the installation using devtools

devtools::install_github("cytomining/cytominer", dependencies = TRUE, build_vignettes = TRUE)

will still break cytominer. Maybe you can try setting dependencies = FALSE. But this could also require more packages to add to environment.yml

[hkhawar]

[hkhawar]

Should I add these packages in environment file?

[hkhawar]

It didn't work even by setting Dependencies=FALSE

[gwaybio]

It didn't work even by setting Dependencies=FALSE

Great!

Try adding these packages to the environment.yml file. Warning! You may get caught in conda hell

[hkhawar]

[hkhawar]

It complains about incompatibility

[gwaybio]

not surprisingly! Try removing r-tinytex

edit - can also remove r-xfun

[hkhawar]

Removing r-tinytex and r-xfun packages from environment

Installing from CRAN using following below command worked for me

packageurl <- "https://cran.r-project.org/src/contrib/Archive/cytominer/cytominer_0.1.0.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

[gwaybio]

🎉 🎉