package or namespace load failed for dada2 in latest conda environment

Technical Support
1

Hi,

I've successfully installed qiime2 amplicon within a conda environment on linux following the instructions here, but dada2 is unable to load when I run this command:

qiime dada2 denoise-paired \
  --i-demultiplexed-seqs output/test_demux-paired-end.qza \
  --p-trim-left-f 17 \
  --p-trim-left-r 24 \
  --p-trunc-len-f 290 \
  --p-trunc-len-r 290 \
  --p-n-threads 0 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza \
  --o-denoising-stats stats-dada2.qza

It produces this error:

R version 4.3.3 (2024-02-29) 
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’:
 Functions found when exporting methods from the namespace ‘SparseArray’ which are not S4 generic: ‘crossprod’, ‘tcrossprod’
8: stop(msg, call. = FALSE, domain = NA)
7: value[[3L]](cond)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
4: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
3: library(dada2)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w, 
       classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(library(dada2))
Traceback (most recent call last):
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_dada2/_denoise.py", line 353, in denoise_paired
    run_commands([cmd])
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_dada2/_denoise.py", line 38, in run_commands
    subprocess.run(cmd, check=True)
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/subprocess.py", line 526, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmp74nc0hac/forward', '--input_directory_reverse', '/tmp/tmp74nc0hac/reverse', '--output_path', '/tmp/tmp74nc0hac/output.tsv.biom', '--output_track', '/tmp/tmp74nc0hac/track.tsv', '--filtered_directory', '/tmp/tmp74nc0hac/filt_f', '--filtered_directory_reverse', '/tmp/tmp74nc0hac/filt_r', '--truncation_length', '290', '--truncation_length_reverse', '290', '--trim_left', '17', '--trim_left_reverse', '24', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '0', '--learn_min_reads', '1000000']' returned non-zero exit status 1.

When I tried library(dada2) on the command line, I found these warnings. I think the first one suggests this version of R might be too out-of-date for dada2:

In addition: Warning messages:
1: package ‘dada2’ was built under R version 4.4.1
2: no function found corresponding to methods exports from ‘GenomicRanges’ for: ‘terminators’
3: multiple methods tables found for ‘sort’

I could tinker with package versions in the yaml file, but suspect I'd just break even more dependencies, so I'm feeling stuck here. Any suggestions?

This issue is similar to this one, but in this case I've verified that the version of R is consistent (4.3.3).

My qiime version is q2cli version 2024.10.1, running conda 24.9.2 on Ubuntu 20.04.6 LTS (GNU/Linux 5.15.0-1073-azure x86_64).

Thanks!
Scott

1 Like
2

Hi @sklasek, You definitely shouldn't have to tinker with the environment file to get this to work. Were there any issues when you ran the install? Any chance you have the exact command that you ran? Before we dive in to more intensive debugging, it might be worth you deactivating all conda environments and then running the Linux install command again to see if it works. If you try that and still get a failure, could you reply with the command that you ran and the results of running qiime info?

Thanks!

UPDATE before re-installing, it may help to run these two commands:

conda update conda
conda clean --all

Another update, after getting some feedback from @lizgehret - if you're still running into issues in the fresh install, could you also please include the output of running conda list in your reply?

1 Like
5

Hi @gregcaporaso,

Thanks for the quick reply. Unfortunately running conda update conda and conda clean --all did not work for me.

I then reinstalled like this (same command as I followed last time):

conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml

I ran the same command, and got the same error.

`qiime dada2 denoise-paired \
  --i-demultiplexed-seqs output/test_demux-paired-end.qza \
  --p-trim-left-f 17 \
  --p-trim-left-r 24 \
  --p-trunc-len-f 290 \
  --p-trunc-len-r 290 \
  --p-n-threads 0 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza \
  --o-denoising-stats stats-dada2.qza
Plugin error from dada2:
  An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-o_kmaw0u.log
`

Full contents of the debug log file:

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada.R --input_directory /tmp/tmpjhkcv0x8/forward --input_directory_reverse /tmp/tmpjhkcv0x8/reverse --output_path /tmp/tmpjhkcv0x8/output.tsv.biom --output_track /tmp/tmpjhkcv0x8/track.tsv --filtered_directory /tmp/tmpjhkcv0x8/filt_f --filtered_directory_reverse /tmp/tmpjhkcv0x8/filt_r --truncation_length 290 --truncation_length_reverse 290 --trim_left 17 --trim_left_reverse 24 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2 --min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 0 --learn_min_reads 1000000

R version 4.3.3 (2024-02-29) 
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’:
 Functions found when exporting methods from the namespace ‘SparseArray’ which are not S4 generic: ‘crossprod’, ‘tcrossprod’
8: stop(msg, call. = FALSE, domain = NA)
7: value[[3L]](cond)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
4: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
3: library(dada2)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w, 
       classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(library(dada2))
Traceback (most recent call last):
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_dada2/_denoise.py", line 353, in denoise_paired
    run_commands([cmd])
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_dada2/_denoise.py", line 38, in run_commands
    subprocess.run(cmd, check=True)
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/subprocess.py", line 526, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpjhkcv0x8/forward', '--input_directory_reverse', '/tmp/tmpjhkcv0x8/reverse', '--output_path', '/tmp/tmpjhkcv0x8/output.tsv.biom', '--output_track', '/tmp/tmpjhkcv0x8/track.tsv', '--filtered_directory', '/tmp/tmpjhkcv0x8/filt_f', '--filtered_directory_reverse', '/tmp/tmpjhkcv0x8/filt_r', '--truncation_length', '290', '--truncation_length_reverse', '290', '--trim_left', '17', '--trim_left_reverse', '24', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allow_one_off', 'False', '--num_threads', '0', '--learn_min_reads', '1000000']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 530, in __call__
    results = self._execute_action(
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 602, in _execute_action
    results = action(**arguments)
  File "<decorator-gen-49>", line 2, in denoise_paired
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 299, in bound_callable
    outputs = self._callable_executor_(
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 570, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_dada2/_denoise.py", line 366, in denoise_paired
    raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

My conda list output:

# packages in environment at /home/sklasek/qdd/miniconda3/envs/qiime2-amplicon-2024.10:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.11               hd590300_1    conda-forge
altair                    5.4.1              pyhd8ed1ab_1    conda-forge
anyio                     4.6.2.post1        pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argcomplete               3.5.1              pyhd8ed1ab_0    conda-forge
argh                      0.31.3             pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310ha75aee5_5    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
astor                     0.8.1              pyh9f0ad1d_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
atpublic                  5.0                pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     24.2.0             pyh71513ae_0    conda-forge
bcrypt                    4.2.0           py310h505e2c1_1    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bibtexparser              1.4.2              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.43                 h4bf12b8_2    conda-forge
bioconductor-ancombc      2.4.0             r43hdfd78af_0    bioconda
bioconductor-beachmat     2.18.0            r43hf17093f_1    bioconda
bioconductor-biobase      2.62.0            r43ha9d7317_2    bioconda
bioconductor-biocbaseutils 1.4.0             r43hdfd78af_0    bioconda
bioconductor-biocgenerics 0.48.1            r43hdfd78af_2    bioconda
bioconductor-biocneighbors 1.20.0            r43hf17093f_1    bioconda
bioconductor-biocparallel 1.36.0            r43hf17093f_2    bioconda
bioconductor-biocsingular 1.18.0            r43hf17093f_1    bioconda
bioconductor-biomformat   1.30.0            r43hdfd78af_0    bioconda
bioconductor-biostrings   2.70.1            r43ha9d7317_2    bioconda
bioconductor-bluster      1.12.0            r43hf17093f_1    bioconda
bioconductor-dada2        1.30.0            r43hf17093f_0    bioconda
bioconductor-data-packages 20231203             hdfd78af_0    bioconda
bioconductor-decipher     2.30.0            r43ha9d7317_1    bioconda
bioconductor-decontam     1.22.0            r43hdfd78af_0    bioconda
bioconductor-delayedarray 0.28.0            r43ha9d7317_2    bioconda
bioconductor-delayedmatrixstats 1.24.0            r43hdfd78af_0    bioconda
bioconductor-dirichletmultinomial 1.44.0            r43hee7dd41_1    bioconda
bioconductor-genomeinfodb 1.38.1            r43hdfd78af_1    bioconda
bioconductor-genomeinfodbdata 1.2.11            r43hdfd78af_1    bioconda
bioconductor-genomicalignments 1.38.0            r43ha9d7317_1    bioconda
bioconductor-genomicranges 1.54.1            r43ha9d7317_2    bioconda
bioconductor-iranges      2.36.0            r43ha9d7317_2    bioconda
bioconductor-matrixgenerics 1.14.0            r43hdfd78af_3    bioconda
bioconductor-mia          1.10.0            r43hdfd78af_0    bioconda
bioconductor-multiassayexperiment 1.28.0            r43hdfd78af_0    bioconda
bioconductor-multtest     2.58.0            r43ha9d7317_1    bioconda
bioconductor-phyloseq     1.46.0            r43hdfd78af_0    bioconda
bioconductor-rhdf5        2.46.1            r43hf17093f_1    bioconda
bioconductor-rhdf5filters 1.14.1            r43hf17093f_1    bioconda
bioconductor-rhdf5lib     1.24.0            r43ha9d7317_2    bioconda
bioconductor-rhtslib      2.4.0             r43ha9d7317_2    bioconda
bioconductor-rsamtools    2.18.0            r43hf17093f_2    bioconda
bioconductor-s4arrays     1.2.0             r43ha9d7317_2    bioconda
bioconductor-s4vectors    0.40.2            r43ha9d7317_2    bioconda
bioconductor-scaledmatrix 1.10.0            r43hdfd78af_0    bioconda
bioconductor-scater       1.30.1            r43hdfd78af_0    bioconda
bioconductor-scuttle      1.12.0            r43hf17093f_1    bioconda
bioconductor-shortread    1.60.0            r43hf17093f_1    bioconda
bioconductor-singlecellexperiment 1.24.0            r43hdfd78af_0    bioconda
bioconductor-sparsearray  1.2.2             r43ha9d7317_2    bioconda
bioconductor-sparsematrixstats 1.14.0            r43hf17093f_1    bioconda
bioconductor-summarizedexperiment 1.32.0            r43hdfd78af_0    bioconda
bioconductor-treeio       1.26.0            r43hdfd78af_1    bioconda
bioconductor-treesummarizedexperiment 2.10.0            r43hdfd78af_0    bioconda
bioconductor-xvector      0.42.0            r43ha9d7317_2    bioconda
bioconductor-zlibbioc     1.48.0            r43ha9d7317_2    bioconda
biom-format               2.1.15          py310h2372a71_1    conda-forge
biopython                 1.84            py310hc51659f_0    conda-forge
blast                     2.16.0               hc155240_2    bioconda
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
bowtie2                   2.5.4                h7071971_4    bioconda
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
brotli-python             1.1.0           py310hf71b8c6_2    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.2               heb4867d_0    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py310h8deb56e_0    conda-forge
chardet                   5.2.0           py310hff52083_2    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
clustalw                  2.1                 h4ac6f70_10    bioconda
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
conda-pack                0.7.0              pyh6c4a22f_0    conda-forge
contourpy                 1.3.0           py310h3788b33_2    conda-forge
cryptography              43.0.3          py310h6c63255_0    conda-forge
curl                      8.8.0                he654da7_1    conda-forge
cutadapt                  4.9             py310h7c593f9_2    bioconda
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
deblur                    1.1.1              pyhdfd78af_0    bioconda
debugpy                   1.8.7           py310hf71b8c6_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dendropy                  5.0.1              pyhdfd78af_0    bioconda
dill                      0.3.9              pyhd8ed1ab_0    conda-forge
dnaio                     1.2.2           py310h7c593f9_0    bioconda
dnspython                 2.7.0              pyhff2d567_0    conda-forge
emperor                   1.0.4           py310hff52083_3    conda-forge
entrez-direct             22.4                 he881be0_0    bioconda
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.1.0              pyhd8ed1ab_0    conda-forge
expat                     2.6.3                h5888daf_0    conda-forge
fastcluster               1.2.6           py310h89e8f5a_4    conda-forge
fasttree                  2.1.11               h031d066_4    bioconda
filelock                  3.16.1             pyhd8ed1ab_0    conda-forge
flufl.lock                8.1.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.54.1          py310h89163eb_1    conda-forge
formulaic                 1.0.2              pyhd8ed1ab_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
frictionless              5.5.0              pyh1a96a4e_0    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
gawk                      5.3.1                hcd3d067_0    conda-forge
gcc_impl_linux-64         14.2.0               h6b349bd_1    conda-forge
gettext                   0.22.5               he02047a_3    conda-forge
gettext-tools             0.22.5               he02047a_3    conda-forge
gffutils                  0.10.1             pyh864c0ab_1    bioconda
gfortran_impl_linux-64    14.2.0               hc73f493_1    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
glib                      2.80.2               hf974151_0    conda-forge
glib-tools                2.80.2               hb6ce0ca_0    conda-forge
globus-sdk                3.46.0             pyhd8ed1ab_0    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
graphlib-backport         1.0.3              pyhd8ed1ab_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.24.4               h9ad1361_0    conda-forge
gstreamer                 1.24.4               haf2f30d_0    conda-forge
gxx_impl_linux-64         14.2.0               h2c03514_1    conda-forge
h5py                      3.11.0          nompi_py310h60e0fe6_103    conda-forge
harfbuzz                  8.5.0                hfac3d4d_0    conda-forge
hdf5                      1.14.3          nompi_hdf9ad27_105    conda-forge
hdmedians                 0.14.2          py310h261611a_6    conda-forge
hmmer                     3.4                  hdbdd923_2    bioconda
htslib                    1.21                 h5efdd21_0    bioconda
humanize                  4.11.0             pyhd8ed1ab_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.10               pyhd8ed1ab_0    conda-forge
ijson                     3.3.0              pyhd8ed1ab_0    conda-forge
importlib-metadata        8.5.0              pyha770c72_0    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
interface_meta            1.3.0              pyhd8ed1ab_0    conda-forge
iow                       1.0.5           py310hc31ed2c_5    bioconda
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.21.0             pyh707e725_0    conda-forge
ipython_genutils          0.2.0              pyhd8ed1ab_1    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_0    conda-forge
iqtree                    2.3.6                hdbdd923_0    bioconda
isa-l                     2.31.0               h4bc722e_2    conda-forge
isodate                   0.7.2              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
jq                        1.7.1                hd590300_0    conda-forge
jsonlines                 3.0.0              pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0           py310hff52083_1    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   3.10.0              he073ed8_18    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.7           py310h3788b33_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libasprintf               0.22.5               he8f35ee_3    conda-forge
libasprintf-devel         0.22.5               he8f35ee_3    conda-forge
libblas                   3.9.0           25_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
libbrotlidec              1.1.0                hb9d3cd8_2    conda-forge
libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcap                    2.69                 h0f662aa_0    conda-forge
libcblas                  3.9.0           25_linux64_openblas    conda-forge
libclang-cpp15            15.0.7          default_h127d8a8_5    conda-forge
libclang13                18.1.7          default_h087397f_0    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libcurl                   8.8.0                hca28451_1    conda-forge
libdeflate                1.20                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.6.3                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.3                h59595ed_0    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-devel_linux-64     14.2.0             h41c2201_101    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgcrypt                 1.11.0               h4ab18f5_1    conda-forge
libgettextpo              0.22.5               he02047a_3    conda-forge
libgettextpo-devel        0.22.5               he02047a_3    conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran-ng            14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libglib                   2.80.2               hf974151_0    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libgpg-error              1.50                 h4f305b6_0    conda-forge
libhwloc                  2.11.1          default_hecaa2ac_1000    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libidn2                   2.3.7                hd590300_0    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           25_linux64_openblas    conda-forge
liblapacke                3.9.0           25_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libllvm15                 15.0.7               hb3ce162_4    conda-forge
libllvm18                 18.1.7               hb77312f_0    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libogg                    1.3.5                h4ab18f5_0    conda-forge
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
libpq                     16.4                 h2d7952a_3    conda-forge
libprotobuf               3.20.3               h3eb15da_0    conda-forge
libsanitizer              14.2.0               h2a3dede_1    conda-forge
libsndfile                1.2.2                hc60ed4a_1    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-devel_linux-64  14.2.0             h41c2201_101    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libsystemd0               256.7                h2774228_1    conda-forge
libtiff                   4.6.0                h1dd3fc0_3    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxkbcommon              1.7.0                h662e7e4_0    conda-forge
libxml2                   2.12.7               hc051c1a_1    conda-forge
libxslt                   1.1.39               h76b75d6_0    conda-forge
libzlib                   1.2.13               h4ab18f5_6    conda-forge
llvmlite                  0.42.0          py310h1b8f574_1    conda-forge
lxml                      5.2.2           py310h6a33d3d_0    conda-forge
lz4                       4.3.3           py310hb259640_1    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
mafft                     7.526                h4bc722e_0    conda-forge
make                      4.4.1                hb9d3cd8_2    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_0    conda-forge
marko                     2.1.2              pyhd8ed1ab_0    conda-forge
markupsafe                3.0.2           py310h89163eb_0    conda-forge
matplotlib                3.8.4           py310hff52083_2    conda-forge
matplotlib-base           3.8.4           py310hef631a5_2    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
mpfr                      4.2.1                h90cbb55_3    conda-forge
mpg123                    1.32.8               hc50e24c_0    conda-forge
mpi                       1.0.1                   mvapich    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
muscle                    3.8.1551             h7d875b9_6    bioconda
mysql-common              8.3.0                hf1915f5_4    conda-forge
mysql-libs                8.3.0                hca2cd23_4    conda-forge
narwhals                  1.10.0             pyhd8ed1ab_0    conda-forge
natsort                   8.4.0              pyhd8ed1ab_0    conda-forge
nbclassic                 1.1.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncbi-datasets-pylib       16.6.1             pyhdfd78af_0    bioconda
ncbi-vdb                  3.1.1                h4ac6f70_2    bioconda
ncurses                   6.5                  he02047a_1    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nlopt                     2.8.0           py310h151153b_2    conda-forge
notebook                  6.5.5              pyha770c72_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
nspr                      4.36                 h5888daf_0    conda-forge
nss                       3.100                hca3bf56_0    conda-forge
numba                     0.59.1          py310h7dc5dd1_0    conda-forge
numpy                     1.26.4          py310hb13e2d6_0    conda-forge
oniguruma                 6.9.9                hd590300_0    conda-forge
openjdk                   22.0.1               hb622114_0    conda-forge
openjpeg                  2.5.2                h488ebb8_0    conda-forge
openssl                   3.3.2                hb9d3cd8_0    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.2           py310hf9f9076_1    conda-forge
pandoc                    3.5                  ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.54.0               h84a9a3c_0    conda-forge
paramiko                  3.5.0              pyhd8ed1ab_0    conda-forge
parsl                     2024.4.15          pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pasta                     1.9.2           py310h2eb23f3_1    bioconda
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pbzip2                    1.1.13               h1fcc475_2    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.43                hcad00b1_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
perl-archive-tar          2.40            pl5321hdfd78af_0    bioconda
perl-carp                 1.50            pl5321hd8ed1ab_0    conda-forge
perl-common-sense         3.75            pl5321hd8ed1ab_0    conda-forge
perl-compress-raw-bzip2   2.201           pl5321hbf60520_0    conda-forge
perl-compress-raw-zlib    2.202           pl5321hadc24fc_0    conda-forge
perl-encode               3.21            pl5321hb9d3cd8_1    conda-forge
perl-exporter             5.74            pl5321hd8ed1ab_0    conda-forge
perl-exporter-tiny        1.002002        pl5321hd8ed1ab_0    conda-forge
perl-extutils-makemaker   7.70            pl5321hd8ed1ab_0    conda-forge
perl-io-compress          2.201           pl5321hdbdd923_2    bioconda
perl-io-zlib              1.14            pl5321hdfd78af_0    bioconda
perl-json                 4.10            pl5321hdfd78af_1    bioconda
perl-json-xs              4.03            pl5321h4ac6f70_3    bioconda
perl-list-moreutils       0.430           pl5321hdfd78af_0    bioconda
perl-list-moreutils-xs    0.430           pl5321h031d066_3    bioconda
perl-parent               0.242           pl5321hd8ed1ab_0    conda-forge
perl-pathtools            3.75            pl5321h166bdaf_0    conda-forge
perl-scalar-list-utils    1.63            pl5321hb9d3cd8_1    conda-forge
perl-storable             3.15            pl5321hb9d3cd8_0    conda-forge
perl-types-serialiser     1.01            pl5321hdfd78af_0    bioconda
petl                      1.7.15             pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pigz                      2.8                  h2797004_0    conda-forge
pillow                    10.3.0          py310hf73ecf8_0    conda-forge
pip                       24.2               pyh8b19718_1    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_0    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_0    conda-forge
ply                       3.11               pyhd8ed1ab_2    conda-forge
prank                     170427               h4ac6f70_0    bioconda
prometheus_client         0.21.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.48             pyha770c72_0    conda-forge
protobuf                  3.20.3          py310heca2aa9_1    conda-forge
psutil                    6.1.0           py310ha75aee5_0    conda-forge
pthread-stubs             0.4               hb9d3cd8_1002    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio-client         17.0                 hb77b528_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pyfaidx                   0.8.1.3            pyhdfd78af_0    bioconda
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyhmmer                   0.10.15         py310h7c593f9_0    bioconda
pyjwt                     2.9.0              pyhd8ed1ab_1    conda-forge
pymongo                   4.10.1          py310hf71b8c6_0    conda-forge
pynacl                    1.5.0           py310h2372a71_3    conda-forge
pynndescent               0.5.13             pyhff2d567_0    conda-forge
pyparsing                 3.2.0              pyhd8ed1ab_1    conda-forge
pyqt                      5.15.9          py310h04931ad_5    conda-forge
pyqt5-sip                 12.12.2         py310hc6cd4ac_5    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    8.3.3              pyhd8ed1ab_0    conda-forge
python                    3.10.14         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-isal               1.7.1           py310ha75aee5_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-slugify            8.0.4              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python-zlib-ng            0.5.1           py310h62b3d1f_0    conda-forge
python_abi                3.10                    5_cp310    conda-forge
pytz                      2024.2             pyhd8ed1ab_0    conda-forge
pyvcf3                    1.0.3              pyhdfd78af_0    bioconda
pyyaml                    6.0.2           py310ha75aee5_1    conda-forge
pyzmq                     24.0.1          py310h330234f_1    conda-forge
q2-alignment              2024.10.0       py310h500e9c1_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-composition            2024.10.0       py310h3f7cb81_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-cutadapt               2024.10.0       py310h29f0b32_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-dada2                  2024.10.0       py310hf76d30f_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-deblur                 2024.10.0       py310h918c320_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-demux                  2024.10.0       py310h06caff7_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-diversity              2024.10.0       py310hd625f91_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-diversity-lib          2024.10.0       py310h4f88c15_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-emperor                2024.10.0       py310h3e5d6d3_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-feature-classifier     2024.10.0       py310h84e6bf9_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-feature-table          2024.10.0       py310hb384b8f_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-fragment-insertion     2024.10.0       py310h6c9ea3d_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-longitudinal           2024.10.0       py310ha66dc25_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-metadata               2024.10.0       py310h39bade1_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-mystery-stew           2024.10.0       py310hfc1c045_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-phylogeny              2024.10.0       py310h050f5c7_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-quality-control        2024.10.0       py310h1ccb9e7_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-quality-filter         2024.10.0       py310h3a6f734_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-sample-classifier      2024.10.0       py310hf367180_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-stats                  2024.10.0       py310h2597699_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-taxa                   2024.10.0       py310h41e678c_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-types                  2024.10.0       py310h1f36736_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-vizard                 2024.10.0       py310hd98517b_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2-vsearch                2024.10.0       py310hb216672_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2cli                     2024.10.1       py310h2c1950c_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2galaxy                  2024.10.0       py310hf370668_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
q2templates               2024.10.0       py310h2690626_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
qiime2                    2024.10.1       py310h0fb5ea9_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
qt-main                   5.15.8              hc9dc06e_21    conda-forge
r-abind                   1.4_5           r43hc72bb7e_1006    conda-forge
r-ade4                    1.7_22            r43h0d28552_2    conda-forge
r-ape                     5.8               r43hb424bfc_1    conda-forge
r-askpass                 1.2.1             r43h2b5f3a1_0    conda-forge
r-assertthat              0.2.1             r43hc72bb7e_5    conda-forge
r-backports               1.5.0             r43hb1dbf0f_1    conda-forge
r-base                    4.3.3                hf0d99cb_1    conda-forge
r-base64enc               0.1_3           r43hb1dbf0f_1007    conda-forge
r-beeswarm                0.4.0             r43hdb488b9_4    conda-forge
r-bh                      1.84.0_0          r43hc72bb7e_1    conda-forge
r-bibtex                  0.5.1             r43hc72bb7e_2    conda-forge
r-bit                     4.5.0             r43h2b5f3a1_0    conda-forge
r-bit64                   4.5.2             r43h2b5f3a1_0    conda-forge
r-bitops                  1.0_9             r43h2b5f3a1_0    conda-forge
r-blob                    1.2.4             r43hc72bb7e_2    conda-forge
r-boot                    1.3_31            r43hc72bb7e_0    conda-forge
r-broom                   1.0.7             r43hc72bb7e_0    conda-forge
r-bslib                   0.8.0             r43hc72bb7e_0    conda-forge
r-cachem                  1.1.0             r43hb1dbf0f_1    conda-forge
r-cairo                   1.6_2             r43h4dc26e9_0    conda-forge
r-callr                   3.7.6             r43hc72bb7e_1    conda-forge
r-cellranger              1.1.0           r43hc72bb7e_1007    conda-forge
r-checkmate               2.3.2             r43hdb488b9_0    conda-forge
r-class                   7.3_22            r43hb1dbf0f_2    conda-forge
r-cli                     3.6.3             r43h0d4f4ea_1    conda-forge
r-clipr                   0.8.0             r43hc72bb7e_3    conda-forge
r-cluster                 2.1.6             r43hbcb9c34_1    conda-forge
r-codetools               0.2_20            r43hc72bb7e_1    conda-forge
r-colorspace              2.1_1             r43hdb488b9_0    conda-forge
r-conflicted              1.2.0             r43h785f33e_2    conda-forge
r-cpp11                   0.5.0             r43hc72bb7e_0    conda-forge
r-crayon                  1.5.3             r43hc72bb7e_1    conda-forge
r-curl                    5.2.1             r43h6b349a7_1    conda-forge
r-cvxr                    1.0_13            r43h93ab643_1    conda-forge
r-data.table              1.15.2            r43h029312a_0    conda-forge
r-dbi                     1.2.3             r43hc72bb7e_1    conda-forge
r-dbplyr                  2.5.0             r43hc72bb7e_1    conda-forge
r-deldir                  2.0_4             r43hbcb9c34_1    conda-forge
r-desctools               0.99.57           r43he59cc3e_0    conda-forge
r-digest                  0.6.37            r43h0d4f4ea_0    conda-forge
r-doparallel              1.0.17            r43hc72bb7e_3    conda-forge
r-dorng                   1.8.6             r43hc72bb7e_2    conda-forge
r-dplyr                   1.1.4             r43h0d4f4ea_1    conda-forge
r-dqrng                   0.3.2             r43h0d4f4ea_1    conda-forge
r-dtplyr                  1.3.1             r43hc72bb7e_2    conda-forge
r-e1071                   1.7_16            r43h93ab643_0    conda-forge
r-ecosolver               0.5.5             r43hdb488b9_2    conda-forge
r-ellipsis                0.3.2             r43hb1dbf0f_3    conda-forge
r-energy                  1.7_12            r43h93ab643_0    conda-forge
r-evaluate                1.0.1             r43hc72bb7e_0    conda-forge
r-exact                   3.3               r43hc72bb7e_0    conda-forge
r-expm                    1.0_0             r43h61c59f8_0    conda-forge
r-fansi                   1.0.6             r43hb1dbf0f_1    conda-forge
r-farver                  2.1.2             r43ha18555a_1    conda-forge
r-fastmap                 1.2.0             r43ha18555a_1    conda-forge
r-fnn                     1.1.4.1           r43h93ab643_0    conda-forge
r-fontawesome             0.5.2             r43hc72bb7e_1    conda-forge
r-forcats                 1.0.0             r43hc72bb7e_2    conda-forge
r-foreach                 1.5.2             r43hc72bb7e_3    conda-forge
r-foreign                 0.8_87            r43hb1dbf0f_1    conda-forge
r-formatr                 1.14              r43hc72bb7e_2    conda-forge
r-formula                 1.2_5             r43hc72bb7e_2    conda-forge
r-frictionless            1.2.0             r43hc72bb7e_0    conda-forge
r-fs                      1.6.4             r43ha18555a_1    conda-forge
r-futile.logger           1.4.3           r43hc72bb7e_1006    conda-forge
r-futile.options          1.0.1           r43hc72bb7e_1005    conda-forge
r-gargle                  1.5.2             r43h785f33e_1    conda-forge
r-gbrd                    0.4.12            r43hc72bb7e_1    conda-forge
r-generics                0.1.3             r43hc72bb7e_3    conda-forge
r-getopt                  1.20.4            r43ha770c72_1    conda-forge
r-ggbeeswarm              0.7.2             r43hc72bb7e_2    conda-forge
r-ggplot2                 3.5.1             r43hc72bb7e_1    conda-forge
r-ggrastr                 1.0.2             r43hc72bb7e_2    conda-forge
r-ggrepel                 0.9.6             r43h93ab643_0    conda-forge
r-gld                     2.6.6             r43hdb488b9_2    conda-forge
r-glue                    1.8.0             r43h2b5f3a1_0    conda-forge
r-gmp                     0.7_5             r43h93ab643_0    conda-forge
r-googledrive             2.1.1             r43hc72bb7e_2    conda-forge
r-googlesheets4           1.1.1             r43h785f33e_2    conda-forge
r-gridextra               2.3             r43hc72bb7e_1006    conda-forge
r-gsl                     2.1_8             r43h9e4e80d_2    conda-forge
r-gtable                  0.3.6             r43hc72bb7e_0    conda-forge
r-gtools                  3.9.5             r43hb1dbf0f_1    conda-forge
r-haven                   2.5.4             r43h0d4f4ea_1    conda-forge
r-here                    1.0.1             r43hc72bb7e_3    conda-forge
r-highr                   0.11              r43hc72bb7e_1    conda-forge
r-hmisc                   5.1_3             r43hc4980d5_1    conda-forge
r-hms                     1.1.3             r43hc72bb7e_2    conda-forge
r-htmltable               2.4.3             r43hc72bb7e_0    conda-forge
r-htmltools               0.5.8.1           r43ha18555a_1    conda-forge
r-htmlwidgets             1.6.4             r43h785f33e_3    conda-forge
r-httr                    1.4.7             r43hc72bb7e_1    conda-forge
r-httr2                   1.0.5             r43hc72bb7e_0    conda-forge
r-hwriter                 1.3.2.1           r43hc72bb7e_3    conda-forge
r-ids                     1.0.1             r43hc72bb7e_4    conda-forge
r-igraph                  2.0.3             r43h510f1ce_1    conda-forge
r-interp                  1.1_6             r43ha936806_1    conda-forge
r-irlba                   2.3.5.1           r43h0d28552_3    conda-forge
r-isoband                 0.2.7             r43ha18555a_3    conda-forge
r-iterators               1.0.14            r43hc72bb7e_3    conda-forge
r-jpeg                    0.1_10            r43had62be2_6    conda-forge
r-jquerylib               0.1.4             r43hc72bb7e_3    conda-forge
r-jsonlite                1.8.9             r43h2b5f3a1_0    conda-forge
r-knitr                   1.48              r43hc72bb7e_0    conda-forge
r-labeling                0.4.3             r43hc72bb7e_1    conda-forge
r-lambda.r                1.2.4             r43hc72bb7e_4    conda-forge
r-lattice                 0.22_6            r43hb1dbf0f_1    conda-forge
r-latticeextra            0.6_30            r43hc72bb7e_3    conda-forge
r-lazyeval                0.2.2             r43hb1dbf0f_5    conda-forge
r-lifecycle               1.0.4             r43hc72bb7e_1    conda-forge
r-lme4                    1.1_35.5          r43h0d4f4ea_1    conda-forge
r-lmertest                3.1_3             r43hc72bb7e_3    conda-forge
r-lmom                    3.2               r43hb67ce94_0    conda-forge
r-lubridate               1.9.3             r43hdb488b9_1    conda-forge
r-magrittr                2.0.3             r43hb1dbf0f_3    conda-forge
r-mass                    7.3_60.0.1        r43hb1dbf0f_1    conda-forge
r-matrix                  1.6_5             r43he966344_1    conda-forge
r-matrixstats             1.4.1             r43h2b5f3a1_0    conda-forge
r-memoise                 2.0.1             r43hc72bb7e_3    conda-forge
r-mgcv                    1.9_1             r43h0d28552_1    conda-forge
r-mime                    0.12              r43hb1dbf0f_3    conda-forge
r-minqa                   1.2.8             r43ha936806_0    conda-forge
r-modelr                  0.1.11            r43hc72bb7e_2    conda-forge
r-multcomp                1.4_26            r43hc72bb7e_0    conda-forge
r-munsell                 0.5.1             r43hc72bb7e_1    conda-forge
r-mvtnorm                 1.3_1             r43h9ad1c49_0    conda-forge
r-nlme                    3.1_165           r43hbcb9c34_1    conda-forge
r-nloptr                  2.1.1             r43h9b87a3a_1    conda-forge
r-nnet                    7.3_19            r43hb1dbf0f_2    conda-forge
r-numderiv                2016.8_1.1        r43hc72bb7e_6    conda-forge
r-openssl                 2.2.2             r43he8289e2_0    conda-forge
r-optparse                1.7.5             r43hc72bb7e_1    conda-forge
r-osqp                    0.6.3.3           r43h0d4f4ea_1    conda-forge
r-permute                 0.9_7             r43hc72bb7e_3    conda-forge
r-pheatmap                1.0.12            r43hc72bb7e_5    conda-forge
r-pillar                  1.9.0             r43hc72bb7e_2    conda-forge
r-pixmap                  0.4_13            r43hc72bb7e_1    conda-forge
r-pkgconfig               2.0.3             r43hc72bb7e_4    conda-forge
r-pkgmaker                0.32.10           r43hc72bb7e_2    conda-forge
r-plogr                   0.2.0           r43hc72bb7e_1006    conda-forge
r-plyr                    1.8.9             r43ha18555a_1    conda-forge
r-png                     0.1_8             r43h21f035c_2    conda-forge
r-prettyunits             1.2.0             r43hc72bb7e_1    conda-forge
r-processx                3.8.4             r43hb1dbf0f_1    conda-forge
r-progress                1.2.3             r43hc72bb7e_1    conda-forge
r-proxy                   0.4_27            r43hb1dbf0f_3    conda-forge
r-ps                      1.8.0             r43h2b5f3a1_0    conda-forge
r-purrr                   1.0.2             r43hdb488b9_1    conda-forge
r-r6                      2.5.1             r43hc72bb7e_3    conda-forge
r-ragg                    1.3.3             r43h9aa3752_0    conda-forge
r-rappdirs                0.3.3             r43hb1dbf0f_3    conda-forge
r-rbibutils               2.3               r43h2b5f3a1_0    conda-forge
r-rcolorbrewer            1.1_3             r43h785f33e_3    conda-forge
r-rcpp                    1.0.13_1          r43h93ab643_0    conda-forge
r-rcppannoy               0.0.22            r43ha18555a_1    conda-forge
r-rcppeigen               0.3.4.0.2         r43hb79369c_0    conda-forge
r-rcpphnsw                0.6.0             r43h0d4f4ea_1    conda-forge
r-rcppml                  0.3.7             r43h0d4f4ea_2    conda-forge
r-rcppparallel            5.1.9             r43h93ab643_1    conda-forge
r-rcppprogress            0.4.2             r43hc72bb7e_4    conda-forge
r-rcpptoml                0.2.2             r43ha18555a_2    conda-forge
r-rcurl                   1.98_1.16         r43h6b349a7_0    conda-forge
r-rdpack                  2.6.1             r43hc72bb7e_0    conda-forge
r-readr                   2.1.5             r43h0d4f4ea_1    conda-forge
r-readxl                  1.4.3             r43he58e087_1    conda-forge
r-registry                0.5_1             r43hc72bb7e_5    conda-forge
r-rematch                 2.0.0             r43hc72bb7e_1    conda-forge
r-rematch2                2.1.2             r43hc72bb7e_4    conda-forge
r-reprex                  2.1.1             r43hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r43h0d4f4ea_4    conda-forge
r-reticulate              1.36.0            r43ha503ecb_0    conda-forge
r-rlang                   1.1.4             r43ha18555a_1    conda-forge
r-rmarkdown               2.28              r43hc72bb7e_0    conda-forge
r-rmpfr                   0.9_5             r43h3d92cb3_2    conda-forge
r-rngtools                1.5.2             r43hc72bb7e_3    conda-forge
r-rootsolve               1.8.2.4           r43hc4980d5_1    conda-forge
r-rpart                   4.1.23            r43hb1dbf0f_1    conda-forge
r-rprojroot               2.0.4             r43hc72bb7e_1    conda-forge
r-rsqlite                 2.3.7             r43h93ab643_1    conda-forge
r-rstudioapi              0.17.1            r43hc72bb7e_0    conda-forge
r-rsvd                    1.0.5             r43hc72bb7e_2    conda-forge
r-rtsne                   0.17              r43h4387864_1    conda-forge
r-rvest                   1.0.4             r43hc72bb7e_1    conda-forge
r-sandwich                3.1_1             r43hc72bb7e_0    conda-forge
r-sass                    0.4.9             r43ha18555a_1    conda-forge
r-scales                  1.3.0             r43hc72bb7e_1    conda-forge
r-scs                     3.2.4             r43h02ebe12_2    conda-forge
r-selectr                 0.4_2             r43hc72bb7e_4    conda-forge
r-sitmo                   2.0.2             r43h0d4f4ea_3    conda-forge
r-snow                    0.4_4             r43hc72bb7e_3    conda-forge
r-sp                      2.1_4             r43hdb488b9_1    conda-forge
r-stringi                 1.8.4             r43ha8ce623_2    conda-forge
r-stringr                 1.5.1             r43h785f33e_1    conda-forge
r-survival                3.7_0             r43hdb488b9_1    conda-forge
r-sys                     3.4.3             r43h2b5f3a1_0    conda-forge
r-systemfonts             1.1.0             r43h38d38ca_1    conda-forge
r-textshaping             0.4.0             r43h024d615_0    conda-forge
r-th.data                 1.1_2             r43hc72bb7e_2    conda-forge
r-tibble                  3.2.1             r43hdb488b9_3    conda-forge
r-tidyr                   1.3.1             r43h0d4f4ea_1    conda-forge
r-tidyselect              1.2.1             r43hc72bb7e_1    conda-forge
r-tidytree                0.4.6             r43hc72bb7e_1    conda-forge
r-tidyverse               2.0.0             r43h785f33e_2    conda-forge
r-timechange              0.3.0             r43ha18555a_1    conda-forge
r-tinytex                 0.53              r43hc72bb7e_0    conda-forge
r-tzdb                    0.4.0             r43ha18555a_2    conda-forge
r-utf8                    1.2.4             r43hb1dbf0f_1    conda-forge
r-uuid                    1.2_1             r43hdb488b9_0    conda-forge
r-uwot                    0.1.16            r43h0d4f4ea_1    conda-forge
r-vctrs                   0.6.5             r43h0d4f4ea_1    conda-forge
r-vegan                   2.6_8             r43h9ad1c49_0    conda-forge
r-vipor                   0.4.7             r43hc72bb7e_1    conda-forge
r-viridis                 0.6.5             r43hc72bb7e_1    conda-forge
r-viridislite             0.4.2             r43hc72bb7e_2    conda-forge
r-vroom                   1.6.5             r43h0d4f4ea_1    conda-forge
r-withr                   3.0.1             r43hc72bb7e_0    conda-forge
r-xfun                    0.48              r43h93ab643_0    conda-forge
r-xml2                    1.3.6             r43h8194278_2    conda-forge
r-xtable                  1.8_4             r43hc72bb7e_6    conda-forge
r-yaml                    2.3.10            r43hdb488b9_0    conda-forge
r-yulab.utils             0.1.7             r43hc72bb7e_0    conda-forge
r-zoo                     1.8_12            r43hb1dbf0f_2    conda-forge
raxml                     8.2.13               h031d066_2    bioconda
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
rescript                  2024.10.0       py310h5c81cde_0    https://packages.qiime2.org/qiime2/2024.10/amplicon/released
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986                   2.0.0              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rich                      13.9.3             pyhd8ed1ab_0    conda-forge
rpds-py                   0.20.0          py310h505e2c1_1    conda-forge
rpsbproc                  0.5.0                h6a68c12_1    bioconda
samtools                  1.21                 h50ea8bc_0    bioconda
scikit-bio                0.6.0           py310h1f7b6fc_4    conda-forge
scikit-learn              1.4.2           py310h981052a_1    conda-forge
scipy                     1.13.0          py310h93e2701_1    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
sepp                      4.5.5           py310h9ee0642_0    bioconda
setproctitle              1.3.3           py310ha75aee5_1    conda-forge
setuptools                75.1.0             pyhd8ed1ab_0    conda-forge
shellingham               1.5.4              pyhd8ed1ab_0    conda-forge
simpleeval                0.9.13             pyhd8ed1ab_1    conda-forge
simplejson                3.19.3          py310ha75aee5_1    conda-forge
sip                       6.7.12          py310hc6cd4ac_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
sortmerna                 2.0                  he860b03_4    bioconda
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.14.4          py310hf462985_0    conda-forge
stringcase                1.2.0              pyhd8ed1ab_1    conda-forge
sysroot_linux-64          2.17                h4a8ded7_18    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tapi                      1300.6.5             h5888daf_0    conda-forge
tbb                       2021.13.0            h84d6215_0    conda-forge
tblib                     3.0.0              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
text-unidecode            1.3                pyhd8ed1ab_1    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tinycss2                  1.4.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tktable                   2.10                 h8bc8fbc_6    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.2              pyhd8ed1ab_0    conda-forge
tomlkit                   0.13.2             pyha770c72_0    conda-forge
tornado                   6.4.1           py310ha75aee5_1    conda-forge
tqdm                      4.66.5             pyhd8ed1ab_0    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typeguard                 4.3.0              pyhd8ed1ab_1    conda-forge
typer                     0.12.5             pyhd8ed1ab_0    conda-forge
typer-slim                0.12.5             pyhd8ed1ab_0    conda-forge
typer-slim-standard       0.12.5               hd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20241003     pyhff2d567_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
tzlocal                   2.1                pyh9f0ad1d_0    conda-forge
umap-learn                0.5.6           py310hff52083_1    conda-forge
unicodedata2              15.1.0          py310ha75aee5_1    conda-forge
unifrac                   1.3             py310h1425a21_0    bioconda
unifrac-binaries          1.4                  h1d423cb_0    bioconda
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   1.26.19            pyhd8ed1ab_0    conda-forge
validators                0.34.0             pyhd8ed1ab_0    conda-forge
vsearch                   2.22.1               h6a68c12_2    bioconda
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.8.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wget                      1.21.4               hda4d442_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0          py310ha75aee5_1    conda-forge
xcb-util                  0.4.0                hd590300_1    conda-forge
xcb-util-image            0.4.0                h8ee46fc_1    conda-forge
xcb-util-keysyms          0.4.0                h8ee46fc_1    conda-forge
xcb-util-renderutil       0.3.9                hd590300_1    conda-forge
xcb-util-wm               0.4.1                h8ee46fc_1    conda-forge
xkeyboard-config          2.42                 h4ab18f5_0    conda-forge
xmltodict                 0.14.2             pyhd8ed1ab_0    conda-forge
xopen                     2.0.2              pyh707e725_1    conda-forge
xorg-fixesproto           5.0               hb9d3cd8_1003    conda-forge
xorg-inputproto           2.3.2             hb9d3cd8_1003    conda-forge
xorg-kbproto              1.0.7             hb9d3cd8_1003    conda-forge
xorg-libice               1.1.1                hb9d3cd8_1    conda-forge
xorg-libsm                1.2.4                he73a12e_1    conda-forge
xorg-libx11               1.8.9                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hb9d3cd8_1    conda-forge
xorg-libxdmcp             1.1.5                hb9d3cd8_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h4bc722e_1    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxt                1.3.0                hd590300_1    conda-forge
xorg-libxtst              1.2.5                h4bc722e_0    conda-forge
xorg-recordproto          1.14.2            hb9d3cd8_1003    conda-forge
xorg-renderproto          0.11.1            hb9d3cd8_1003    conda-forge
xorg-xextproto            7.3.0             hb9d3cd8_1004    conda-forge
xorg-xf86vidmodeproto     2.3.1             hb9d3cd8_1005    conda-forge
xorg-xproto               7.0.31            hb9d3cd8_1008    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yq                        3.4.3              pyhd8ed1ab_0    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.20.2             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h4ab18f5_6    conda-forge
zlib-ng                   2.2.2                h5888daf_0    conda-forge
zstandard                 0.23.0          py310ha39cb0e_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Please let me know if you need anything more from me!
Scott

9

Hey @sklasek,

Jumping in for @gregcaporaso with a few more questions!

This is certainly an unusual error - here's the meat of it:

I found a similar thread regarding this type of error related to another R package (this was completely separate from QIIME 2): Bioconductor - Error : Function found is not S4 generic

What this made me wonder was whether or not you have an existing R installation on your machine (possibly within your BASE conda env) that's somehow overriding the version that's included in our QIIME 2 amplicon distribution.

  • Do you know whether or not you've installed R prior to your QIIME 2 installation?
  • Can you run conda deactivate and then provide the output of conda list?
  • Have you installed other versions of QIIME 2 in the past, and used dada2 successfully?
11

Hi @lizgehret,

Yes, I did install R prior to trying qiime2 installation. It turns out my base environment version of R appears to be 4.4.1, not 4.3.3 as on my qiime2 conda environment. I did install dada2 in the base version of R, so maybe this too-recent version is somehow leaking into my qiime conda environment. I just tried to re-download the appropriate version of dada2 for my conda environment using bioconductor:

    install.packages("BiocManager")
BiocManager::install("dada2", version = "3.18", force = TRUE)

but that failed with the same error.

qiime2-amplicon-2024.2 has been run successfully on this machine before I installed R 4.4.1. So to my understanding, this is consistent with the package leaking into the qiime2-amplicon-2024.10 conda environment.

Anyway, you asked for the conda list output of my base environment, here it is:

# packages in environment at /home/sklasek/qdd/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anaconda-anon-usage       0.4.4           py312hfc0e8ea_100
archspec                  0.2.3              pyhd3eb1b0_0
boltons                   23.0.0          py312h06a4308_0
brotli-python             1.0.9           py312h6a678d5_8
bzip2                     1.0.8                h5eee18b_6
c-ares                    1.19.1               h5eee18b_0
ca-certificates           2024.9.24            h06a4308_0
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312h1fdaa30_0
charset-normalizer        3.3.2              pyhd3eb1b0_0
conda                     24.9.2          py312h7900ff3_0    conda-forge
conda-content-trust       0.2.0           py312h06a4308_1
conda-libmamba-solver     24.9.0             pyhd3eb1b0_0
conda-package-handling    2.3.0           py312h06a4308_0
conda-package-streaming   0.10.0          py312h06a4308_0
cryptography              43.0.0          py312hdda0065_0
distro                    1.9.0           py312h06a4308_0
expat                     2.6.3                h6a678d5_0
fmt                       9.1.0                hdb19cb5_1
frozendict                2.4.2           py312h06a4308_0
gettext                   0.21.1               h27087fc_0    conda-forge
icu                       73.1                 h6a678d5_0
idna                      3.7             py312h06a4308_0
jsonpatch                 1.33            py312h06a4308_1
jsonpointer               2.1                pyhd3eb1b0_0
krb5                      1.20.1               h143b758_1
ld_impl_linux-64          2.40                 h12ee557_0
libarchive                3.7.4                hfab0078_0
libcurl                   8.9.1                h251f7ec_0
libedit                   3.1.20230828         h5eee18b_0
libev                     4.33                 h7f8727e_1
libexpat                  2.6.3                h5888daf_0    conda-forge
libffi                    3.4.4                h6a678d5_1
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libidn2                   2.3.7                hd590300_0    conda-forge
libmamba                  1.5.8                hfe524e5_3
libmambapy                1.5.8           py312h2dafd23_3
libnghttp2                1.57.0               h2d74bed_0
libnsl                    2.0.1                hd590300_0    conda-forge
libsolv                   0.7.24               he621ea3_1
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.0               h251f7ec_0
libstdcxx-ng              11.2.0               h1234567_1
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.13.1               hfdd30dd_2
libzlib                   1.2.13               h4ab18f5_6    conda-forge
lz4-c                     1.9.4                h6a678d5_1
menuinst                  2.1.2           py312h06a4308_0
ncurses                   6.4                  h6a678d5_0
openssl                   3.4.0                hb9d3cd8_0    conda-forge
packaging                 24.1            py312h06a4308_0
pcre2                     10.42                hebb0a14_1
pip                       24.2            py312h06a4308_0
platformdirs              3.10.0          py312h06a4308_0
pluggy                    1.0.0           py312h06a4308_1
pybind11-abi              5                    hd3eb1b0_0
pycosat                   0.6.6           py312h5eee18b_1
pycparser                 2.21               pyhd3eb1b0_0
pysocks                   1.7.1           py312h06a4308_0
python                    3.12.2          hab00c5b_0_cpython    conda-forge
python_abi                3.12                    5_cp312    conda-forge
readline                  8.2                  h5eee18b_0
reproc                    14.2.4               h6a678d5_2
reproc-cpp                14.2.4               h6a678d5_2
requests                  2.32.3          py312h06a4308_0
ruamel.yaml               0.18.6          py312h5eee18b_0
ruamel.yaml.clib          0.2.8           py312h5eee18b_0
setuptools                75.1.0          py312h06a4308_0
sqlite                    3.45.3               h5eee18b_0
tk                        8.6.14               h39e8969_0
tqdm                      4.66.5          py312he106c6f_0
truststore                0.8.0           py312h06a4308_0
tzdata                    2024b                h04d1e81_0
urllib3                   2.2.3           py312h06a4308_0
wget                      1.21.4               hda4d442_0    conda-forge
wheel                     0.44.0          py312h06a4308_0
xz                        5.4.6                h5eee18b_1
yaml-cpp                  0.8.0                h6a678d5_1
zlib                      1.2.13               h4ab18f5_6    conda-forge
zstandard                 0.23.0          py312h2c38b39_0
zstd                      1.5.6                hc292b87_0

Is it strange that I don't see any r-base info in this output?

Thanks in advance for any insight!

Scott

13

Confirmed, it was something involving the base version of R on my server being too recent for the qiime conda environment. I was able to delete the base R version

sudo apt-get remove r-base-core

and then the installation and dada2 command worked just fine. I suppose those without sudo privileges will have to complain to their sysadmins.

Thanks!
Scott

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