Seurat: Suerat Installation erroring out

[rarvindk]

R_studio_341_2.txt

Hello Suerat Team,

We are trying to install “Suerat” package on one of the HPC environment. We are constantly running into errors. I’m attaching a txt file with the capture of the screen while installing the Seurat package with in R 3.4.1. Could pls let us know if there is anything we are missing or your assistance is greatly appreciated.

[romanhaa]

My personal advice is to use either conda environments or (better) containers. I can't really tell what the problem is from the txt file you uploaded, but there could be all sorts of library incompatibilities that are hard to overcome on HPC if you are not an admin (I've had my experience with this). So, check out conda environments which are easy to set up and overcome most library problems. However, some libraries kept making trouble, including cairo. I used conda environment quite extensively for a while on our HPC but eventually switched to Docker + Singularity because it gives me full control. Since then, I've had 0 issues installing any R package. In a nutshell, you create your Docker container on your local machine and then convert that to a Singularity image (not necessary if you have a Docker license for Linux machines I think).

Hope this helps.

[rarvindk]

Hello,

Thanks for your time and support. Greatly appreciate you assist. This is
the client environment and we have very limited authority to change the
environment for now. I'll check on condo environment and see what best
assist can I provide.

-Arvind

On Wed, Jul 18, 2018 at 8:48 PM, Roman [e-mail] wrote:

My personal advice is to use either conda environments or (better)
containers. I can't really tell what the problem is from the txt file you
uploaded, but there could be all sorts of library incompatibilities that
are hard to overcome on HPC if you are not an admin (I've had my experience
with this). So, check out conda environments which are easy to set up and
overcome most library problems. However, some libraries kept making
trouble, including cairo. I used conda environment quite extensively for
a while on our HPC but eventually switched to Docker + Singularity because
it gives me full control. Since then, I've had 0 issues installing any R
package. In a nutshell, you create your Docker container on your local
machine and then convert that to a Singularity image (not necessary if you
have a Docker license for Linux machines I think).

Hope this helps.

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[HenrikBengtsson]

We ran into the same problem where we / users couldn't easily install hdf5r due to lacking or outdated hdf5 system libraries.
If you don't need to read 10X HDF5 files using Seurat::Read10X_h5() then a workaround is to install the fake hdf5r package that I've created - see https://github.com/UCSF-TI/fake-hdf5r

To Seurat devels: By moving hdf5r from Imports to Suggests and update Seurat::Read10X_h5() to:

  requireNamespace("hdf5r", quietly = TRUE) || stop("Please install the 'hdf5r' package")
  infile <- hdf5r::H5File$new(filename)

you'll make 'hdf5r' optional and help users with this particular issue.

[sunnyzwu]

Others and myself also encountered this problem trying to update seurat on our HPC systems. Thanks @HenrikBengtsson, did the trick!

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[HenrikBengtsson]

Ping

[evolvedmicrobe]

Ping as well, if it would be useful to rebase @HenrikBengtsson changes on to a newer branch, I'd be happy to help with that. The HDF5 format is great when it works, but it seems it's a bridge too far for typical users.

[andrewwbutler]

Agreed. We have moved hdf5r from Imports to Suggests on therelease/3.0 branch.

[HenrikBengtsson]

Did you see my other pull requests?

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.