Error installing Empress

[OliverAshton1]

Hello

I am trying to install empress into qiime2 2021.11 on Windows 10 WSL (Ubuntu 20.04.3 LTS (GNU/Linux 5.10.60.1-microsoft-standard-WSL2 x86_64)), versions attached. I have attached a copy of the full error below. The rest of Qiime2 works fine for me.

Any help is appreciated.
Oliver

Empress Error.txt

Versions.txt

[fedarko]

Hi @OliverAshton1,

Thanks for the detailed report. I just checked, and was able to install Empress using pip into a new QIIME 2 2021.11 environment (with the same software versions as you've listed in Versions.txt) on a Linux computer. This, together with the exact error message you got, implies that things are going wrong when installing the iow library into your system.

The origin of the installation error seems to occur when trying to build one of iow's dependencies (line 81 of your error message file):

  ar -csru libbitarr.a bit_array.o
  make: ar: No such file or directory
  make: *** [Makefile:25: libbitarr.a] Error 127

From what I can tell, the reason you're running into this problem is that the ar command (which creates / extracts certain types of archives) is not installed on your system (and it looks like it is installed on my Linux system already, so this would explain why I don't encounter this problem when installing Empress).

It seems like ar is part of the binutils package, so I think that installing binutils should then allow you to install Empress. Long story short, could you please try installing binutils, and then try re-installing Empress? I'm not very familiar with WSL, but from some googling I think something like

sudo apt-get install binutils

should do the trick for installing binutils in WSL.

Let us know if this works out!

[OliverAshton1]

Hi @fedarko

As you recommended I used:

conda activate qiime2-2021.11
sudo apt-get install binutils
pip install empress
qiime dev refresh-cache
qiime empress --help

binutils installed 6 new packages, then Empress installed first time, on both my PCs that showed the error.
Many thanks for your quick reply!

Oliver

[fedarko]

Fantastic, thanks @OliverAshton1! Glad that worked.

I just created a new issue (#553): we'll add this information to EMPress' documentation to help other people who run into this problem in the future, since I imagine that other WSL users may also encounter this.