# Rescript: A plugin named 'longitudinal' could not be found.

**URL:** https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272
**Category:** User Support
**Tags:** rescript
**Created:** [November 14, 2023, 5:19am UTC](https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272 "2023-11-14T05:19:30Z")
**Posts on this page:** 5
**Page:** 1

<div class="post-metadata">

### Author: ![elizabeck](https://forum.qiime2.org/user_avatar/forum.qiime2.org/elizabeck/32/16933_2.png) [@elizabeck](https://forum.qiime2.org/u/elizabeck)
#### Post date: [November 14, 2023, 5:19am UTC](https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272/1 "2023-11-14T05:19:31Z")

</div>

Hello!  
I'm trying to run evaluate fit classifier, in qiime2 v. 2023.9. I've tried everything  
my script is:  
qiime rescript evaluate-fit-classifier  
--i-sequences ncbirefseqs.qza  
--i-taxonomy ncbirefseqstaxonomy.qza  
--o-classifier ncbirefseqsclassifier.qza  
--o-evaluation ncbirefseqsclassifierevaluation.qzv  
--o-observed-taxonomy ncbirefseqspredictedtaxonomy.qza  
--verbose

/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/rescript/cross\_validate.py:34: FutureWarning: Passing a set as an indexer is deprecated and will raise in a future version. Use a list instead.  
taxa = taxa.loc[seq\_ids]  
Validation: 0.44s  
/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/q2\_feature\_classifier/classifier.py:102: UserWarning: The TaxonomicClassifier artifact that results from this method was trained using scikit-learn version 0.24.1. It cannot be used with other versions of scikit-learn. (While the classifier may complete successfully, the results will be unreliable.)  
warnings.warn(warning, UserWarning)  
Training: 11.39s  
Classification: 10.96s  
Traceback (most recent call last):  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/context.py", line 53, in get\_action  
plugin\_obj = pm.plugins[plugin]  
KeyError: 'longitudinal'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/q2cli/commands.py", line 520, in **call**  
results = self.\_execute\_action(  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/q2cli/commands.py", line 586, in \_execute\_action  
results = action(\*\*arguments)  
File "", line 2, in evaluate\_fit\_classifier  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable  
outputs = self._callable\_executor_(  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in _callable\_executor_  
outputs = self.\_callable(scope.ctx, \*\*view\_args)  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/rescript/cross\_validate.py", line 53, in evaluate\_fit\_classifier  
evaluation, = \_eval([taxonomy], [observed\_taxonomy])  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred\_action  
return action\_obj.\_bind(  
File "", line 2, in evaluate\_classifications  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable  
outputs = self._callable\_executor_(  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in _callable\_executor_  
outputs = self.\_callable(scope.ctx, \*\*view\_args)  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/rescript/cross\_validate.py", line 169, in evaluate\_classifications  
volatility = ctx.get\_action('longitudinal', 'volatility')  
File "/home/elizabeth/miniconda3/envs/qiime2shot/lib/python3.8/site-packages/qiime2/sdk/context.py", line 55, in get\_action  
raise ValueError("A plugin named %r could not be found." % plugin)  
ValueError: A plugin named 'longitudinal' could not be found.

Plugin error from rescript:

A plugin named 'longitudinal' could not be found.

See above for debug info.

I've installed qiime2 twice, and I get the same error message, I don't know what to do now. 😭  
Can anybody help me, please? 🥹 👩‍💻

---

<div class="post-metadata">

### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [November 14, 2023, 11:09am UTC](https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272/2 "2023-11-14T11:09:29Z")

</div>

Hi @elizabeck ,

From the looks of things, I am guessing that you have installed the QIIME 2 shotgun metagenomics distribution, but now you are trying to build and evaluate an NCBI RefSeqs database (of 16S? or another marker gene?)

The QIIME 2 shotgun metagenomics distribution includes RESCRIPt but does not include q2-longitudinal. This you can install in your environment with this command:

```auto
 conda install -c qiime2 q2-longitudinal

```

But before trying that you could just confirm that it is indeed not installed in your environment with this command (which should give an empty output):

```auto
conda list q2-longitudinal

```

Installing q2-longitudinal in your environment should resolve this error.

Good luck!

---

<div class="post-metadata">

### Author: ![elizabeck](https://forum.qiime2.org/user_avatar/forum.qiime2.org/elizabeck/32/16933_2.png) [@elizabeck](https://forum.qiime2.org/u/elizabeck)
#### Post date: [November 15, 2023, 12:43am UTC](https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272/3 "2023-11-15T00:43:27Z")

</div>

Hi!  
Yes, I have installed Qiime2 shotgun, and I run the script you gave me, and I got a error message:

conda install -c qiime2 q2-longitudinal  
Channels:

- qiime2
- defaults
- conda-forge
- bioconda
- [released](https://packages.qiime2.org/qiime2/2023.9/shotgun/released)  
Platform: linux-64  
Collecting package metadata (repodata.json): done  
Solving environment: | warning libmamba Added empty dependency for problem type SOLVER\_RULE\_UPDATE  
failed

LibMambaUnsatisfiableError: Encountered problems while solving:

- cannot install both pin-1-1 and pin-1-1
- package q2-longitudinal-2021.4.0-py38\_0 requires q2-feature-table 2021.4.\*, but none of the providers can be installed

Could not solve for environment specs  
The following packages are incompatible  
├─ \_openmp\_mutex 4.5\*\* is requested and can be installed;  
├─ biom-format 2.1.14\*\* is requested and can be installed;  
├─ harfbuzz 6.0.0\*\* is installable with the potential options  
│ ├─ harfbuzz 6.0.0 would require  
│ │ └─ icu \>=70.1,\<71.0a0 , which can be installed;  
│ └─ harfbuzz 6.0.0 would require  
│ └─ icu \>=72.1,\<73.0a0 , which conflicts with any installable versions previously reported;  
├─ hdf5 1.14.0\*\* is requested and can be installed;  
├─ icu 70.1\*\* is requested and can be installed;  
├─ libffi 3.4.2\*\* is requested and can be installed;  
├─ libgfortran-ng 13.2.0\*\* is requested and can be installed;  
├─ libopenblas 0.3.24\*\* is installable and it requires  
│ └─ openblas \>=0.3.24,\<0.3.25.0a0 , which can be installed;  
├─ libzlib 1.2.13\*\* is installable with the potential options  
│ ├─ libzlib 1.2.13 would require  
│ │ └─ zlib 1.2.13 _\_4, which can be installed;  
│ └─ libzlib 1.2.13 would require  
│ └─ zlib 1.2.13 \_5, which can be installed;  
├─ ncurses 6.4_ is requested and can be installed;  
├─ numba 0.57.1\*\* is installable with the potential options  
│ ├─ numba 0.57.1 would require  
│ │ └─ numpy \>=1.21,!=1.22.0,!=1.22.1,!=1.22.2,\<1.25 , which can be installed;  
│ └─ numba 0.57.1 would require  
│ └─ \_openmp\_mutex \>=5.1 , which conflicts with any installable versions previously reported;  
├─ numpy 1.24.4\*\* is requested and can be installed;  
├─ pandas 1.5.3\*\* is requested and can be installed;  
├─ pin-1 is installable with the potential options  
│ ├─ pin-1 1, which can be installed;  
│ └─ pin-1 1 conflicts with any installable versions previously reported;  
├─ q2-feature-table 2023.9.0\*\* is requested and can be installed;  
└─ q2-longitudinal is not installable because there are no viable options  
├─ q2-longitudinal 2021.4.0 would require  
│ └─ q2-feature-table 2021.4.\* , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal 2019.10.0 would require  
│ └─ q2-types 2019.10.\* , which requires  
│ └─ matplotlib-base 3.1.0.\* , which requires  
│ └─ icu \>=58.2,\<59.0a0 , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal [2020.11.1|2020.8.0|2021.2.0] would require  
│ └─ matplotlib-base \<3.3 but there are no viable options  
│ ├─ matplotlib-base [2.2.3|2.2.4|...|3.2.2], which cannot be installed (as previously explained);  
│ ├─ matplotlib-base [2.1.2|2.2.4|...|3.2.2] would require  
│ │ └─ icu \>=64.2,\<65.0a0 , which conflicts with any installable versions previously reported;  
│ └─ matplotlib-base [2.2.5|3.2.2] would require  
│ └─ icu \>=67.1,\<68.0a0 , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal [2020.2.0|2020.6.0] would require  
│ └─ q2templates [2020.2.\* |2020.6.\*], which requires  
│ └─ pandas \<1 but there are no viable options  
│ ├─ pandas [0.20.3|0.21.0|...|0.25.3] conflicts with any installable versions previously reported;  
│ ├─ pandas [0.17.0|0.17.1|...|0.23.4] would require  
│ │ └─ python [3.5\* |\>=3.5,\<3.6.0a0] but there are no viable options  
│ │ ├─ python [3.4.5|3.5.1|3.5.2|3.5.3|3.5.4] would require  
│ │ │ └─ ncurses 5.9\* , which conflicts with any installable versions previously reported;  
│ │ ├─ python [3.5.4|3.5.5|3.5.6] would require  
│ │ │ └─ libffi [3.2.\* |\>=3.2.1,\<3.3.0a0 |\>=3.2.1,\<3.3a0], which conflicts with any installable versions previously reported;  
│ │ ├─ python 3.5.6 would require  
│ │ │ └─ libffi \>=3.3,\<3.4.0a0 , which conflicts with any installable versions previously reported;  
│ │ └─ python [3.5.4|3.5.5] would require  
│ │ └─ zlib 1.2.11 , which conflicts with any installable versions previously reported;  
│ ├─ pandas [0.17.0|0.17.1|...|0.19.2] would require  
│ │ └─ numpy 1.10\* but there are no viable options  
│ │ ├─ numpy [1.10.4|1.11.2|...|1.13.3] would require  
│ │ │ └─ openblas 0.2.19|0.2.19.\* , which conflicts with any installable versions previously reported;  
│ │ └─ numpy [1.10.4|1.11.0|1.11.1|1.11.2] would require  
│ │ └─ openblas [0.2.18\* |0.2.18|0.2.18.\*], which conflicts with any installable versions previously reported;  
│ ├─ pandas [0.17.0|0.17.1|...|0.20.3] would require  
│ │ └─ numpy 1.11\* but there are no viable options  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.1|1.13.3] would require  
│ │ │ ├─ libgfortran-ng [\>=7,\<8.0a0 |\>=7.2.0,\<8.0a0], which conflicts with any installable versions previously reported;  
│ │ │ ├─ libopenblas \>=0.2.20,\<0.2.21.0a0 , which requires  
│ │ │ │ └─ libgfortran-ng [\>=7,\<8.0a0 |\>=7.2.0,\<8.0a0], which conflicts with any installable versions previously reported;  
│ │ │ └─ numpy-base [1.11.3 py27h2b20989\_7|1.11.3 py27h2b20989\_8|...|1.11.3 py37h7cdd4dd\_9], which requires  
│ │ │ └─ libopenblas \>=0.2.20,\<0.2.21.0a0 , which cannot be installed (as previously explained);  
│ │ ├─ numpy [1.10.4|1.11.2|...|1.13.3], which cannot be installed (as previously explained);  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.1|1.13.2|1.13.3] would require  
│ │ │ └─ openblas [0.2.20|0.2.20.\* |\>=0.2.20,\<0.2.21.0a0] but there are no viable options  
│ │ │ ├─ openblas [0.2.20|0.3.3] would require  
│ │ │ │ ├─ libgfortran-ng \>=7,\<8.0a0 , which conflicts with any installable versions previously reported;  
│ │ │ │ ├─ libopenblas [0.3.3 h5a2b251\_1|0.3.3 h5a2b251\_2|0.3.3 h5a2b251\_3|\>=0.2.20,\<0.2.21.0a0], which cannot be installed (as previously explained);  
│ │ │ │ └─ openblas-devel \>=0.2.20,\<0.2.21.0a0 , which requires  
│ │ │ │ └─ libopenblas \>=0.2.20,\<0.2.21.0a0 , which cannot be installed (as previously explained);  
│ │ │ └─ openblas 0.2.20 conflicts with any installable versions previously reported;  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.3] would require  
│ │ │ ├─ libgfortran-ng \>=7,\<8.0a0 , which conflicts with any installable versions previously reported;  
│ │ │ └─ openblas \>=0.3.3,\<0.3.4.0a0 but there are no viable options  
│ │ │ ├─ openblas [0.2.20|0.3.3], which cannot be installed (as previously explained);  
│ │ │ └─ openblas 0.3.3 conflicts with any installable versions previously reported;  
│ │ ├─ numpy 1.11.3 would require  
│ │ │ ├─ libgfortran-ng \>=7,\<8.0a0 , which conflicts with any installable versions previously reported;  
│ │ │ ├─ libopenblas \>=0.3.2,\<0.3.3.0a0 , which conflicts with any installable versions previously reported;  
│ │ │ └─ numpy-base [1.11.3 py27h74e8950\_9|1.11.3 py35h74e8950\_9|1.11.3 py36h74e8950\_9|1.11.3 py37h74e8950\_9], which requires  
│ │ │ └─ libopenblas \>=0.3.2,\<0.3.3.0a0 , which conflicts with any installable versions previously reported;  
│ │ ├─ numpy [1.10.4|1.11.0|1.11.1|1.11.2], which cannot be installed (as previously explained);  
│ │ ├─ numpy 1.11.3 conflicts with any installable versions previously reported;  
│ │ ├─ numpy 1.11.3 would require  
│ │ │ └─ python 3.4\* , which cannot be installed (as previously explained);  
│ │ └─ numpy 1.11.3 would require  
│ │ └─ python 3.5\* , which cannot be installed (as previously explained);  
│ ├─ pandas [0.17.0|0.17.1|...|0.20.3] would require  
│ │ └─ python 3.4\* , which cannot be installed (as previously explained);  
│ ├─ pandas [0.19.2|0.20.0|0.20.1|0.20.2|0.20.3] would require  
│ │ └─ numpy 1.12\* , which cannot be installed (as previously explained);  
│ ├─ pandas [0.20.2|0.20.3] would require  
│ │ └─ numpy 1.13\* but there are no viable options  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.1|1.13.3], which cannot be installed (as previously explained);  
│ │ ├─ numpy 1.13.3 conflicts with any installable versions previously reported;  
│ │ ├─ numpy [1.10.4|1.11.2|...|1.13.3], which cannot be installed (as previously explained);  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.1|1.13.2|1.13.3], which cannot be installed (as previously explained);  
│ │ └─ numpy [1.11.3|1.12.1|1.13.3], which cannot be installed (as previously explained);  
│ └─ pandas [0.20.2|0.20.3] would require  
│ ├─ numpy 1.13\* but there are no viable options  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.1|1.13.3], which cannot be installed (as previously explained);  
│ │ ├─ numpy 1.13.3 conflicts with any installable versions previously reported;  
│ │ ├─ numpy [1.10.4|1.11.2|...|1.13.3], which cannot be installed (as previously explained);  
│ │ ├─ numpy [1.11.3|1.12.1|1.13.1|1.13.2|1.13.3], which cannot be installed (as previously explained);  
│ │ └─ numpy [1.11.3|1.12.1|1.13.3], which cannot be installed (as previously explained);  
│ └─ python 3.5\* , which cannot be installed (as previously explained);  
├─ q2-longitudinal [2021.11.0|2021.8.0] would require  
│ └─ q2-types [2021.11.\* |2021.8.\*], which requires  
│ └─ hdf5 1.10.6.\* , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal [2022.11.0|2022.11.1] would require  
│ └─ q2-types 2022.11.\* but there are no viable options  
│ ├─ q2-types [2022.11.1|2023.2.0|2023.5.0] would require  
│ │ └─ biom-format 2.1.12.\* , which conflicts with any installable versions previously reported;  
│ └─ q2-types 2022.11.0 would require  
│ └─ biom-format 2.1.13.\* , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal 2022.2.0 would require  
│ ├─ pandas 1.2.\* , which conflicts with any installable versions previously reported;  
│ └─ q2-feature-table 2022.2.\* , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal 2022.8.0 would require  
│ └─ q2-feature-table 2022.8.\* , which conflicts with any installable versions previously reported;  
├─ q2-longitudinal [2023.2.0|2023.5.0] would require  
│ └─ q2-types [2023.2.\* |2023.5.\*], which cannot be installed (as previously explained);  
└─ q2-longitudinal 2023.7.0 would require  
└─ q2-feature-table 2023.7.\* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:

- python 3.8.\* (labeled as 'pin-1')

So, I tried in qiime2 amplicon, I installed rescript with the following script:

```auto
conda install \
  -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -c defaults \
  qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier 'q2-types-genomics>2023.2' \
  "pandas>=0.25.3" xmltodict ncbi-datasets-pylib

```

and got this error message:

Channels:

- conda-forge
- bioconda
- qiime2
- [2023.5-tested](https://packages.qiime2.org/qiime2/2023.5/tested)
- defaults
- [released](https://packages.qiime2.org/qiime2/2023.9/amplicon/released)  
Platform: linux-64  
Collecting package metadata (repodata.json): done  
Solving environment: / warning libmamba Added empty dependency for problem type SOLVER\_RULE\_UPDATE  
failed

LibMambaUnsatisfiableError: Encountered problems while solving:

- cannot install both pin-1-1 and pin-1-1
- package q2-types-genomics-2023.5.0.dev0+1.g41f3d57-py38\_0 requires q2-types 2023.5.\*, but none of the providers can be installed

Could not solve for environment specs  
The following packages are incompatible  
├─ biom-format 2.1.14\*\* is requested and can be installed;  
├─ pin-1 is installable with the potential options  
│ ├─ pin-1 1, which can be installed;  
│ └─ pin-1 1 conflicts with any installable versions previously reported;  
└─ q2-types-genomics \>2023.2 is not installable because it requires  
└─ q2-types 2023.5.\* , which requires  
└─ biom-format 2.1.12.\* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:

- python 3.8.\* (labeled as 'pin-1')

Heeelp! 😭

---

<div class="post-metadata">

### Author: ![elizabeck](https://forum.qiime2.org/user_avatar/forum.qiime2.org/elizabeck/32/16933_2.png) [@elizabeck](https://forum.qiime2.org/u/elizabeck)
#### Post date: [November 15, 2023, 1:26am UTC](https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272/4 "2023-11-15T01:26:09Z")

</div>

Ok!  
I found the solution  
I installed rescript with mamba instead conda as suggested [here](https://forum.qiime2.org/t/rescript-problem-installing-dependencies/26258/13)

Thank you!  
Gracias! 👩‍💻

---

<div class="post-metadata">

### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [December 16, 2023, 7:26am UTC](https://forum.qiime2.org/t/rescript-a-plugin-named-longitudinal-could-not-be-found/28272/5 "2023-12-16T07:26:57Z")

</div>

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