Consider adding cytominer on conda

gwaybio commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

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

to the environment.yml file

hkhawar commented 5 years ago

Great

gwaybio commented 5 years ago

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 commented 5 years ago

Screen Shot 2019-07-01 at 4 03 02 PM

hkhawar commented 5 years ago

Should I add these packages in environment file?

hkhawar commented 5 years ago

It didn't work even by setting Dependencies=FALSE

gwaybio commented 5 years ago

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 commented 5 years ago

Screen Shot 2019-07-01 at 4 11 28 PM

hkhawar commented 5 years ago

It complains about incompatibility

gwaybio commented 5 years ago

not surprisingly! Try removing r-tinytex

edit - can also remove r-xfun

hkhawar commented 5 years ago

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 commented 5 years ago

:tada: :tada:

cytomining / cytominer

Consider adding cytominer on conda #132

ERROR: dependency ‘caret’ is not available for package ‘cytominer’ ─ removing ‘/private/var/folders/zz/vvqfkgdj22b0z3h50yjvw3fjzzgfxt/T/Rtmp2idUAH/Rinst1611e334d39df/cytominer’