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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data FLAMES
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* checking for file ‘FLAMES/DESCRIPTION’ ... OK
* preparing ‘FLAMES’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘FLAMES_vignette.Rmd’ using rmarkdown
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.25.0/FLAMES/2.7.0/flames_env/lib/python3.11/site-packages (24.0)
Collecting pip
  Using cached pip-26.1.1-py3-none-any.whl.metadata (4.6 kB)
Collecting wheel
  Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in /home/biocbuild/.cache/R/basilisk/1.25.0/FLAMES/2.7.0/flames_env/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
  Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.2-py3-none-any.whl (100 kB)
Installing collected packages: setuptools, pip, packaging, wheel
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 24.0
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed packaging-26.2 pip-26.1.1 setuptools-82.0.1 wheel-0.47.0
Collecting numpy==2.1.1
  Using cached numpy-2.1.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (62 kB)
Collecting scipy==1.14.1
  Using cached scipy-1.14.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (60 kB)
Collecting pysam==0.22.1
  Using cached pysam-0.22.1-cp311-cp311-manylinux_2_28_aarch64.whl.metadata (1.5 kB)
Collecting cutadapt==4.9
  Using cached cutadapt-4.9-cp311-cp311-linux_aarch64.whl
Collecting tqdm==4.66.5
  Using cached tqdm-4.66.5-py3-none-any.whl.metadata (57 kB)
Collecting pandas==2.2.3
  Using cached pandas-2.2.3-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.whl.metadata (89 kB)
Collecting pgzip==0.3.5
  Using cached pgzip-0.3.5-py3-none-any.whl.metadata (4.6 kB)
Collecting fast-edit-distance==1.2.2
  Using cached fast_edit_distance-1.2.2-cp311-cp311-linux_aarch64.whl
Collecting blaze2==2.5.1
  Using cached blaze2-2.5.1-py3-none-any.whl.metadata (13 kB)
Collecting matplotlib==3.9.1
  Using cached matplotlib-3.9.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB)
Collecting dnaio>=1.2.0 (from cutadapt==4.9)
  Using cached dnaio-1.2.4-cp311-cp311-linux_aarch64.whl
Collecting xopen>=1.6.0 (from cutadapt==4.9)
  Using cached xopen-2.0.2-py3-none-any.whl.metadata (15 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.2.3)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.2.3)
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Collecting tzdata>=2022.7 (from pandas==2.2.3)
  Using cached tzdata-2026.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting cython (from fast-edit-distance==1.2.2)
  Using cached cython-3.2.4-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl.metadata (7.5 kB)
Collecting contourpy>=1.0.1 (from matplotlib==3.9.1)
  Using cached contourpy-1.3.3-cp311-cp311-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl.metadata (5.5 kB)
Collecting cycler>=0.10 (from matplotlib==3.9.1)
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Collecting fonttools>=4.22.0 (from matplotlib==3.9.1)
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Collecting kiwisolver>=1.3.1 (from matplotlib==3.9.1)
  Using cached kiwisolver-1.5.0-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl.metadata (5.1 kB)
Requirement already satisfied: packaging>=20.0 in /home/biocbuild/.cache/R/basilisk/1.25.0/FLAMES/2.7.0/flames_env/lib/python3.11/site-packages (from matplotlib==3.9.1) (26.2)
Collecting pillow>=8 (from matplotlib==3.9.1)
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Collecting pyparsing>=2.3.1 (from matplotlib==3.9.1)
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Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas==2.2.3)
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting isal>=1.6.1 (from xopen>=1.6.0->cutadapt==4.9)
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Collecting zlib-ng>=0.4.1 (from xopen>=1.6.0->cutadapt==4.9)
  Using cached zlib_ng-1.0.0-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl.metadata (6.8 kB)
WARNING: The candidate selected for download or install is a yanked version: 'matplotlib' candidate (version 3.9.1 at https://files.pythonhosted.org/packages/54/7e/4f8f44fcc65a8cfa6303d3469d8973d6a2ba019a9627af9a9ae545f718d6/matplotlib-3.9.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/matplotlib/) (requires-python:>=3.9))
Reason for being yanked: The Windows wheels, under some conditions, caused segfaults in unrelated user code.  Due to this we deleted the Windows wheels to prevent these segfaults, however this caused greater disruption as pip then began to try (and fail) to build 3.9.1 from the sdist on Windows which impacted far more users.  Yanking the whole release is the only tool available to eliminate these failures without changes to on the user side.  The sdist, OSX wheel, and manylinux wheels are all functional and there are no critical bugs in the release.   Downstream packagers should not yank their builds of Matplotlib 3.9.1.  See https://github.com/matplotlib/matplotlib/issues/28551 for details.
Using cached numpy-2.1.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (14.0 MB)
Using cached scipy-1.14.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (35.6 MB)
Using cached pysam-0.22.1-cp311-cp311-manylinux_2_28_aarch64.whl (24.5 MB)
Using cached tqdm-4.66.5-py3-none-any.whl (78 kB)
Using cached pandas-2.2.3-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.whl (15.6 MB)
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Using cached blaze2-2.5.1-py3-none-any.whl (45.7 MB)
Using cached matplotlib-3.9.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (8.2 MB)
Using cached contourpy-1.3.3-cp311-cp311-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl (329 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.62.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl (5.1 MB)
Using cached kiwisolver-1.5.0-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl (1.2 MB)
Using cached pillow-12.2.0-cp311-cp311-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl (6.4 MB)
Using cached pyparsing-3.3.2-py3-none-any.whl (122 kB)
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Using cached zlib_ng-1.0.0-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl (111 kB)
Using cached cython-3.2.4-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl (3.2 MB)
Installing collected packages: pytz, zlib-ng, tzdata, tqdm, six, pysam, pyparsing, pillow, pgzip, numpy, kiwisolver, isal, fonttools, cython, cycler, xopen, scipy, python-dateutil, fast-edit-distance, contourpy, pandas, matplotlib, dnaio, cutadapt, blaze2

Successfully installed blaze2-2.5.1 contourpy-1.3.3 cutadapt-4.9 cycler-0.12.1 cython-3.2.4 dnaio-1.2.4 fast-edit-distance-1.2.2 fonttools-4.62.1 isal-1.8.0 kiwisolver-1.5.0 matplotlib-3.9.1 numpy-2.1.1 pandas-2.2.3 pgzip-0.3.5 pillow-12.2.0 pyparsing-3.3.2 pysam-0.22.1 python-dateutil-2.9.0.post0 pytz-2026.2 scipy-1.14.1 six-1.17.0 tqdm-4.66.5 tzdata-2026.2 xopen-2.0.2 zlib-ng-1.0.0

Processed:   0%|          | 0/1 [00:00<?, ?gene_group/s]
Processed: 100%|██████████| 1/1 [00:00<00:00,  3.03gene_group/s]
Processed: 100%|██████████| 1/1 [00:00<00:00,  3.02gene_group/s]

Processed: 0Read [00:00, ?Read/s]
Processed: 2500.0Read [00:00, 347061.20Read/s]
[bam_sort_core] merging from 0 files and 8 in-memory blocks...

Processed:   0%|          | 0/1 [00:00<?, ?gene_group/s]
Processed: 100%|██████████| 1/1 [00:00<00:00,  2.58gene_group/s]
Processed: 100%|██████████| 1/1 [00:00<00:00,  2.57gene_group/s]

Processed: 0Read [00:00, ?Read/s]
Processed: 2500.0Read [00:00, 230304.41Read/s]
[bam_sort_core] merging from 0 files and 8 in-memory blocks...

Quitting from FLAMES_vignette.Rmd:117-131 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! object '.read_header' is not exported by 'namespace:nanonext'
---
Backtrace:
    ▆
 1. ├─FLAMES::example_pipeline("MultiSampleSCPipeline")
 2. │ └─FLAMES::MultiSampleSCPipeline(...)
 3. │   └─FLAMES:::normalize_controllers(controllers, names(steps))
 4. └─base::loadNamespace(x)
 5.   ├─base::namespaceImportFrom(...)
 6.   │ └─base::asNamespace(ns)
 7.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 8.     └─base::namespaceImportFrom(...)
 9.       └─base::importIntoEnv(impenv, impnames, ns, impvars)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'FLAMES_vignette.Rmd' failed with diagnostics:
object '.read_header' is not exported by 'namespace:nanonext'
--- failed re-building ‘FLAMES_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘FLAMES_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted