Issue regarding 'hdf5r' when installing about powsimr

[bvieth]

Dear Sander,

up until now I have not updated to R version 3.5.

However, concerning your issue, I just encountered the same while installing another package depending on hdf5r. On my Ubuntu machine, I needed to run the following command in my terminal: sudo apt-get install libhdf5-dev to be able to install hdf5r in R. Once you have installed that, the installation of Seurat should run smoothly as well.

Feel free to contact me again if you need any further assistance.

Kind regards
Beate

[swvanderlaan]

Hi,

I google some further and figured it is actually the hdf5r installation in R which throws the error. Seems I'm not alone: hhoeflin/hdf5r#97. But now it's fixed by doing:

wget https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.5/hdf5r_1.0.0.tgz
R CMD INSTALL hdf5r_1.0.0.tgz

After that I could install Seurat without issue. Oh, and powsimR...

library(devtools)
install_github("bvieth/powsimR", build_vignettes = FALSE, dependencies = FALSE)
Downloading GitHub repo bvieth/powsimR@master
from URL https://api.github.com/repos/bvieth/powsimR/zipball/master
Installing powsimR
'/usr/local/Cellar/r/3.5.0_1/lib/R/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/tmp/RtmpgWjvGs/devtoolse0085cb8d2f5/bvieth-powsimR-f3e43ef'  \
  --library='/usr/local/lib/R/3.5/site-library' --install-tests

* installing *source* package ‘powsimR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘DECENT::lrTest’ by ‘MAST::lrTest’ when loading ‘powsimR’
Warning: replacing previous import ‘parallel::makeCluster’ by ‘snow::makeCluster’ when loading ‘powsimR’
Warning: replacing previous import ‘parallel::stopCluster’ by ‘snow::stopCluster’ when loading ‘powsimR’
Warning: replacing previous import ‘penalized::predict’ by ‘stats::predict’ when loading ‘powsimR’
Warning: replacing previous import ‘zinbwave::glmWeightedF’ by ‘zingeR::glmWeightedF’ when loading ‘powsimR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘DECENT::lrTest’ by ‘MAST::lrTest’ when loading ‘powsimR’
Warning: replacing previous import ‘parallel::makeCluster’ by ‘snow::makeCluster’ when loading ‘powsimR’
Warning: replacing previous import ‘parallel::stopCluster’ by ‘snow::stopCluster’ when loading ‘powsimR’
Warning: replacing previous import ‘penalized::predict’ by ‘stats::predict’ when loading ‘powsimR’
Warning: replacing previous import ‘zinbwave::glmWeightedF’ by ‘zingeR::glmWeightedF’ when loading ‘powsimR’
* DONE (powsimR)

I am a happy man.

Thanks!

Sander

[swvanderlaan]

Dear Beate,

Thing is I am on macOS High Sierra with home-brew. And I have got h5py installed via python and hdf5 installed via brew. I can't seem to find the development version of hdf5 for brew. Do you have another idea?

Thanks and best,

Sander

[bvieth]

Dear Sander,

A colleague tried it out on her MacBook and found that you need to run the following:
brew tap homebrew/science
brew install homebrew/science/hdf5 --enable-cxx

I hope this helps!

Beate

[swvanderlaan]

Hi,

That doesn't work with the latest version of homebrew...

Any other suggestions...?

Thanks

Sander

swvanderlaan@Sanders-MacBook ~
$ brew tap homebrew/science
Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated.

swvanderlaan@Sanders-MacBook ~
$ brew install hdf5 --enable-cxx
Warning: hdf5 1.10.2_1 is already installed and up-to-date
To reinstall 1.10.2_1, run `brew reinstall hdf5`

swvanderlaan@Sanders-MacBook ~
$ brew reinstall hdf5 --enable-cxx
==> Reinstalling hdf5
Warning: hdf5: this formula has no --enable-cxx option so it will be ignored!
==> Downloading https://homebrew.bintray.com/bottles/hdf5-1.10.2_1.high_sierra.bottle.tar.gz
Already downloaded: /Users/swvanderlaan/Library/Caches/Homebrew/hdf5-1.10.2_1.high_sierra.bottle.tar.gz
==> Pouring hdf5-1.10.2_1.high_sierra.bottle.tar.gz
Warning: hdf5 dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
🍺  /usr/local/Cellar/hdf5/1.10.2_1: 261 files, 15MB

swvanderlaan@Sanders-MacBook ~
$ brew info hdf5
hdf5: stable 1.10.2 (bottled)
File format designed to store large amounts of data
https://www.hdfgroup.org/HDF5
/usr/local/Cellar/hdf5/1.10.2_1 (261 files, 15MB) *
  Poured from bottle on 2018-07-04 at 12:15:49
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/hdf5.rb
==> Dependencies
Build: autoconf ✔, automake ✔, libtool ✔
Required: gcc ✔, szip ✔
==> Options
--with-mpi
	Enable parallel support

[bvieth]

Hello Sander,

unfortunately I have no other ideas how to deal with this issue. However, I can tell you that there are certain R packages that we could not install on our linux cluster running centOS with the new R version 3.5 either, eg haven.
As far as I know hdf5r is a dependency of Seurat. I can package a R version of powsimR for you without the functionality of Seurat, ie imputation using lasso.

Kind regards
Beate

[bvieth]

Hey Sander,

great that it worked out for you in the end. Feel free to message me again if have any further questions.

Kind regards
Beate