My colleagues in HPC support are having trouble installing this version as well. (I think on CentOS 8)
Feel free to split this into a new issue if it's unrelated.
Could not solve for environment specs
> The following packages are incompatible
> ├─ bioconductor-delayedmatrixstats 1.20.0** is not installable because it
> requires
> │ └─ r-matrixstats >=0.60.0 , which conflicts with any installable versions
> previously reported;
> ├─ bioconductor-phyloseq 1.42.0** is not installable because it requires
> │ └─ r-ade4 >=1.7-4 , which conflicts with any installable versions
> previously reported;
> ├─ bleach 6.0.0** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ c-ares 1.19.1** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ deblur 1.1.1** is not installable because it requires
> │ └─ scikit-bio >=0.5.0 , which conflicts with any installable versions
> previously reported;
> ├─ glpk 5.0** is not installable because it conflicts with any installable
> versions previously reported;
> ├─ jq 1.6** is not installable because it conflicts with any installable
> versions previously reported;
> ├─ libdb 6.2.32** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ libdeflate 1.17** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ munkres 1.1.4** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ paramiko 3.3.1** is not installable because it requires
> │ └─ pynacl >=1.5 , which conflicts with any installable versions
> previously reported;
> ├─ perl-carp 1.50** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ perl-compress-raw-zlib 2.202** is not installable because it conflicts
> with any installable versions previously reported;
> ├─ perl-exporter 5.74** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ perl-extutils-makemaker 7.70** is not installable because it conflicts
> with any installable versions previously reported;
> ├─ perl-parent 0.241** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ perl-scalar-list-utils 1.63** is not installable because it conflicts
> with any installable versions previously reported;
> ├─ q2-composition 2023.9.0** is not installable because it requires
> │ └─ biom-format 2.1.14.* , which conflicts with any installable versions
> previously reported;
> ├─ q2-dada2 2023.9.0** is not installable because it requires
> │ └─ r-optparse >=1.7.1 , which conflicts with any installable versions
> previously reported;
> ├─ q2-diversity 2023.9.0** is not installable because it requires
> │ └─ r-vegan >=2.5_3 , which conflicts with any installable versions
> previously reported;
> ├─ q2-emperor 2023.9.0** is not installable because it requires
> │ └─ emperor 1.0.3 , which conflicts with any installable versions
> previously reported;
> ├─ r-bh 1.81.0_1** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-bit 4.0.5** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-bit64 4.0.5** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-checkmate 2.2.0** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-data.table 1.14.8** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-deldir 1.0_9** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-digest 0.6.33** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-dorng 1.8.6** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-dplyr 1.1.3** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-e1071 1.7_13** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-fnn 1.1.3.2** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-futile.logger 1.4.3** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-futile.options 1.0.1** is not installable because it conflicts with
> any installable versions previously reported;
> ├─ r-ggplot2 3.4.3** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-ggrepel 0.9.3** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-htmltools 0.5.6** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-htmlwidgets 1.6.2** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-hwriter 1.3.2.1** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-jpeg 0.1_10** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-jsonlite 1.8.7** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-knitr 1.44** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-lambda.r 1.2.4** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-magrittr 2.0.3** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-permute 0.9_7** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-pheatmap 1.0.12** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-png 0.1_8** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-prettyunits 1.2.0** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-progress 1.2.2** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-proxy 0.4_27** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-rappdirs 0.3.3** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-rcppparallel 5.1.6** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-readr 2.1.4** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-rematch2 2.1.2** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-rmarkdown 2.25** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-rtsne 0.16** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-scales 1.2.1** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-snow 0.4_4** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-statmod 1.5.0** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-stringr 1.5.0** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-tibble 3.2.1** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-viridis 0.6.4** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ r-yaml 2.3.7** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ tqdm 4.66.1** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ urllib3 2.0.6** is not installable because it conflicts with any
> installable versions previously reported;
> ├─ xmltodict 0.13.0** is not installable because it conflicts with any
> installable versions previously reported;
> └─ xopen 1.7.0** is not installable because it conflicts with any
> installable versions previously reported.
Thanks for reporting this! Do you know when your colleagues attempted to install, and which distribution they were attempting to install (amplicon, shotgun, etc)?
Thanks for circling back! Hmm, this is interesting... we just had all of the 2023.9 distros installed on NAU's cluster without any issues. Can you have your HPC team provide you with the file output from the following command, while in their base conda environment?
conda list > base-env.txt
I suspect there may be conflicts coming from the base env, but want to take a closer look.
Another thing I'm wondering (sorry for creating a bunch of back and forth with your HPC team!) is which solver they are using. We used mamba to solve the 2023.9 environments (which is just using the libmamba solver under the hood) - so I'm wondering if they're still using the classic conda solver, which may explain these environments not solving.
If possible, can you request for them to update their conda instance and then attempt to re-install one of the 2023.9 environments and include the --solver= libmamba flag in their command?
Unfortunately, a mamba install doesn't work. I tried mamba first, but there are
many conflicts in the dependencies of qiime2/2023.9 (as listed in previous
replies), preventing installation.
We'll continue to discuss this problem internally and see if we can find a
solution. However, this seems like a bigger issue that the developers need to
address.
So we briefly explored this issue, but conda now utilizes the libmamba solver, which was the reasoning behind switching to mamba - and conda's next release will set the libmamba solver as the default, so we ultimately decided it would be best to stick with conda. Here's their release changelog with more details on this, in case you're interested: https://docs.conda.io/projects/conda/en/latest/release-notes.html
So it sounds like they tried a mamba install instead of using the libmamba solver within the newer version of conda. The language is definitely confusing with mamba, libmamba, and conda - but if they are amicable to this, I'd ask them to try updating their version of conda (~23.5.2 or later) and including the --solver=libmamba in their install command for QIIME 2 (example below):
- but if they are amicable to this, I'd ask them to try updating their version of conda (~23.5.2 or later) and including the --solver=libmamba in their install command for QIIME 2 (example below):