Closed semiller10 closed 11 months ago
@semiller10 , Meren already fixed this problem. Please see the following section from the installation page:
We are in the process of updating our installation page to be split into different pages by OS so that the solutions to errors like these are more obvious :)
Perfect, should have caught that.
Same error in anvio-8 installation on Mac OSX (pip install anvio-8.tar.gz), can be fixed in the same way, Thanks.
Thanks for letting us know, @ChunqiJIANG.
I will make those export statements a mandatory step for macos installation page to avoid further confusion.
Hi, meren
One more thing may need fixation on the installation page (not only Mac OSX I think):
command 'anvi-setup-kegg-kofams’ at Setup key resource can not be found in anvio v8, seems should be 'anvi-setup-kegg-data’.
Hope to be helpful.
On Sep 29, 2023, at 16:41, A. Murat Eren (Meren) @.***> wrote:
Thanks for letting us know, @ChunqiJIANG https://github.com/ChunqiJIANG.
I will make those export statements a mandatory step for macos installation page to avoid further confusion.
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command 'anvi-setup-kegg-kofams’ at Setup key resource can not be found in anvio v8, seems should be 'anvi-setup-kegg-data’.
I just fixed this one. Thanks @ChunqiJIANG
FYI, I just got the same "ERROR: Failed building wheel for datrie" on our server running a very fresh installation of Ubuntu 22.04, and had to do a separate "mamba install datrie" before installing anvio. Not sure how common this is, but it may be worth including in 'common problems'.
Is this for v8
or anvio-dev
, @ac-simpson? And how did you solve the issue? By updating the environment variables for CC/CCX?
On an HPC, adding the export CC and export CXX commands before pip install anvio-8.tar.gz
did not fix the issue, but as @ac-simpson suggested running mamba install datrie
before pip installation did.
I had the same issue on Fedora 40 using micromamba. The micromamba install datrie
fixed the issue.
Short description of the problem
In
anvio-dev
installation,pip
failed to build thedatrie
package, a dependency ofsnakemake
.anvi'o version
System info
macOS: 13.5.2 (22G91)
Detailed description of the issue
anvio-dev
installation withpython 3.10
failed at the commandpip install -r requirements.txt
with failure to builddatrie
. I think that I fixed the problem by installing the package usingmamba
rather thanpip
:mamba install datrie
. Therefore, I suggest thatdatrie
be installed bymamba
earlier in the installation instructions.For the record, here was the full error message following the instructions.