QIIME2 2023.2 Installation error on *Linux*

Technical Support
1

Hi all!
I encountered an error when trying to install version 2023.2 on Linux. I have come across similar topics in the Qiime2 forum, but they seem to be focused on Mac. I currently have version 2022.2 installed, and I have never experienced any issues with installing QIIME2 before.
I appreciate any help
Pat

(base) pat@nzxt:~$ conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

  • jupyter_client=8.0.3
  • r-ggrepel=0.9.3
  • r-rcpp=1.0.10
  • pygments=2.14.0
  • r-vctrs=0.5.2
  • krb5=1.20.1
  • r-rmarkdown=2.20
  • r-mass=7.3_58.2
  • r-jsonlite=1.8.4
  • beautifulsoup4=4.11.2
  • r-htmlwidgets=1.6.1
  • r-expm=0.999_7
  • altair=4.2.2
  • nbconvert-pandoc=7.2.9
  • python-fastjsonschema=2.16.3
  • libxkbcommon=1.5.0
  • libsndfile=1.2.0
  • perl-parent=0.241
  • r-dorng=1.8.6
  • r-stringi=1.7.12
  • importlib_resources=5.12.0
  • gstreamer=1.21.3
  • r-colorspace=2.1_0
  • nbconvert=7.2.9
  • r-foreign=0.8_84
  • r-sp=1.6_0
  • r-formatr=1.14
  • pyrsistent=0.19.3
  • exceptiongroup=1.1.0
  • r-bibtex=0.5.1
  • r-osqp=0.6.0.8
  • r-dplyr=1.1.0
  • libudev1=253
  • pango=1.50.13
  • r-tinytex=0.44
  • r-png=0.1_8
  • libhwloc=2.9.0
  • r-igraph=1.4.1
  • r-gargle=1.3.0
  • r-forcats=1.0.0
  • bleach=6.0.0
  • r-matrixstats=0.63.0
  • stack_data=0.6.2
  • yq=3.1.1
  • cryptography=39.0.0
  • r-jpeg=0.1_10
  • pytz=2022.7.1
  • contourpy=1.0.7
  • r-lubridate=1.9.2
  • platformdirs=3.0.0
  • r-nlme=3.1_162
  • r-rbibutils=2.2.13
  • r-bh=1.81.0_1
  • mysql-libs=8.0.32
  • r-vroom=1.6.1
  • r-fs=1.6.1
  • r-fansi=1.0.4
  • libtool=2.4.7
  • binutils_impl_linux-64=2.40
  • gst-plugins-base=1.21.3
  • r-ggplot2=3.4.1
  • attrs=22.2.0
  • nspr=4.35
  • nbconvert-core=7.2.9
  • r-dtplyr=1.3.0
  • r-bslib=0.4.2
  • debugpy=1.6.6
  • jupyter_server_terminals=0.4.4
  • networkx=3.0
  • r-yulab.utils=0.0.6
  • jedi=0.18.2
  • r-dbplyr=2.3.1
  • r-utf8=1.2.3
  • r-formula=1.2_5
  • libnghttp2=1.51.0
  • r-tidyr=1.3.0
  • fontconfig=2.14.2
  • ijson=3.2.0.post0
  • r-desctools=0.99.48
  • r-timechange=0.2.0
  • nbformat=5.7.3
  • r-hmisc=4.8_0
  • r-energy=1.7_11
  • mistune=2.0.5
  • websocket-client=1.5.1
  • r-sass=0.4.5
  • r-tidytree=0.4.2
  • r-broom=1.0.3
  • pytest=7.2.1
  • r-purrr=1.0.1
  • r-emmeans=1.8.4_1
  • nss=3.88
  • ca-certificates=2022.12.7
  • r-codetools=0.2_19
  • lz4=4.3.2
  • wrapt=1.15.0
  • ld_impl_linux-64=2.40
  • libpq=15.1
  • r-openssl=2.0.5
  • r-rmpfr=0.9_1
  • r-stringr=1.5.0
  • r-cachem=1.0.7
  • r-digest=0.6.31
  • r-ggbeeswarm=0.7.1
  • r-data.table=1.14.8
  • wcwidth=0.2.6
  • mysql-common=8.0.32
  • setuptools=67.4.0
  • requests=2.28.2
  • libclang13=15.0.7
  • r-highr=0.10
  • r-rcppparallel=5.1.6
  • jack=1.9.22
  • r-evaluate=0.20
  • r-rsqlite=2.2.20
  • asttokens=2.2.1
  • perl-extutils-makemaker=7.66
  • r-readxl=1.4.2
  • r-gsl=2.1_8
  • r-xfun=0.37
  • r-statmod=1.5.0
  • r-pkgmaker=0.32.8
  • r-knitr=1.42
  • traitlets=5.9.0
  • r-httr=1.4.5
  • r-ape=5.7
  • r-yaml=2.3.7
  • natsort=8.3.0
  • harfbuzz=6.0.0
  • r-boot=1.3_28.1
  • sip=6.7.7
  • jupyter_server=2.3.0
  • libgpg-error=1.46
  • seaborn-base=0.12.2
  • r-isoband=0.2.7
  • r-htmltools=0.5.4
  • pyzmq=25.0.0
  • nbclient=0.7.2
  • ipykernel=6.21.2
  • r-survival=3.5_3
  • xyzservices=2023.2.0
  • libllvm15=15.0.7
  • zipp=3.15.0
  • r-gmp=0.7_1
  • libclang=15.0.7
  • iniconfig=2.0.0
  • r-class=7.3_21
  • r-fastmap=1.1.1
  • mpg123=1.31.2
  • r-rcurl=1.98_1.10
  • markupsafe=2.1.2
  • prometheus_client=0.16.0
  • r-cli=3.6.0
  • r-ade4=1.7_22
  • r-readr=2.1.4
  • r-e1071=1.7_13
3

Hello @PatoUru, can you post the content of your .condarc file here? There could be some channel overrides in there causing this issue. Another potential cause is an overly aggressive firewall particularly if you are attempting to install on a system behind an institutional firewall.

1 Like
4

Thank you @Oddant1 for your quickly response! This computer is from our lab, it is not institutional.
Should I make any changes to the firewall?

$ cat ~/.condarc
channels:

  • conda-forge
  • bioconda
  • defaults
  • ursky
    channel_priority: strict
5

I recreated your .condarc and was able to install QIIME 2 2023.2 fine also on Linux, so I do not think there are any problems there (it didn't look like a problem anyway after you posted it, but I figured it would be better to check).

You say this is a lab machine, but are you connected to institutional wifi/ethernet for your internet connection? If so, it is still possible that an institutional firewall is blocking this in which case you will most likely need to talk to IT about it. If you are comfortable with temporarily disabling the firewall on your machine then attempting to install QIIME 2 again and turning the firewall back on after you can try that. There isn't any real risk associated with doing that; however, if the firewall is in the network not on your machine this will not help.

If you are on a network that is unadministered (a home network for instance) then I am currently unsure of what would cause this.

6

Yes, we are connected to the institutional Ethernet!
After disabling the firewall on our machine ($ sudo ufw disable), we have the same error. So, I will reach out to the IT department. I will provide an update as soon as I have news!
Pat

7

Hi @Oddant1!
I finally found what the problem was! I reinstalled Conda and everything was solved!
Thank you so much for your help
Pat

9

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