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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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installation error around hdf5r #37

Open trptyrphe11 opened 5 years ago

trptyrphe11 commented 5 years ago

Hi, I was trying to install SingleR and got the following error message:

configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed.

However, I already have Seurat development version (3.0) installed and worked fine. Is there any workaround or ultimate solution? Thanks.

dviraran commented 5 years ago

This is very weird. hdf5 is not required by SingleR, and not loaded by it. I didn't do a lot of testing with Seurat v3.0, but I did install it with SingleR and it did work. Does this issue come already in the installation of SingleR?

trptyrphe11 commented 5 years ago

Would singleR reinstall Seurat package if it already exists (I think Seurat uses hdf5r package but required a lower system version and that's why it worked before when I was installing Seurat)? Thanks.

dviraran commented 5 years ago

No, there is no reason why it would do that.

yilingmialiu commented 5 years ago

I have the same issue while installing SingleR from GitHub source, do you find an answer to solve this?

dviraran commented 5 years ago

If you are using macOS you probably need to upgrade your hdf5 version. If you are using Homebrew, try in the terminal:

brew install hdf5
yilingmialiu commented 5 years ago

Thank you so much for your reply. I am using cluster with Red Hat Enterprise Linux 6 the current operating system and I don't have root permission. Seems like the hdf5 is a dependency by Seurat and I have Seurat run pretty well in my cluster, so can I install SingleR while avoid the need of hdf5?

dviraran commented 5 years ago

I guess what happens is that while trying to install SingleR, it identifies that Seurat needs to be updated (not to version 3, just the current version in CRAN), but in the new version, they require a newer version of hdf5.

You can try using the install_github flags dependencies=F or upgrade = 'ask'.