ERROR: dependencies ‘sf’, ‘spdep’ are not available for package ‘monocle3’

[xiaoli-gg]

My R version is 4.4.1.The way dowload monocle3 confused me long time.

ERROR: dependencies ‘sf’, ‘spdep’ are not available for package ‘monocle3’
* removing ‘/dssg/home/acct-chinamxj/chinamxj/R/x86_64-redhat-linux-gnu-library/4.4.1/monocle3’
Installation paths not writeable, unable to update packages
  path: /usr/local/lib/R/library
  packages:
    boot, foreign, MASS, Matrix, nlme, survival

[LGY692]

Have you solved it？

[xiaoli-gg]

No, I still have no idea to solve this error.

[HaikuoLi]

same issue

[um-pdavila]

Hi,

I think you are missing some devel packages. I just encountered the same "sf, spdep" error. I was missing the udunits2-devel package.

The following works on RHEL9, and should also work on RHEL8.

$ sudo subscription-manager repos --enable codeready-builder-for-rhel-9-$(arch)-rpms
$ sudo dnf install epel-release
$ sudo dnf install R freetype-devel libpng-devel libtiff-devel libjpeg-devel gdal gdal-devel hdf5 hdf5-devel proj proj-devel sqlite sqlite-devel geos geos-devel udunits2 udunits2-devel -y

$ R
> install.packages("devtools", Ncpus=8)

> BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats','limma', 'lme4', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment', 'batchelor', 'HDF5Array',  'terra', 'ggrastr'))

> devtools::install_github('cole-trapnell-lab/monocle3')

If the version of gdal or proj on RHEL8 is too old, I recommend using spack to build them.

[wenxiang688]

Maybe you can try to install these packages with biomanager first and then install monocle3 through github
BiocManager::install(c( 'sf', 'spdep'))
devtools::install_github('cole-trapnell-lab/monocle3')