Bioconductor Single Package Builder - Build History

===============================

 R CMD BUILD

===============================

* checking for file ‘SimBu/DESCRIPTION’ ... OK
* preparing ‘SimBu’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘SimBu_0.99.2.tar.gz’

===============================

 BiocCheckGitClone('SimBu')

===============================

─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: SimBu
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2627/b79c1b2d8323feb77cb09a6d9803245a3e100113/SimBu
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2627/b79c1b2d8323feb77cb09a6d9803245a3e100113/SimBu.Rcheck’
* using R version 4.2.0 RC (2022-04-19 r82224)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SimBu/DESCRIPTION’ ... OK
* this is package ‘SimBu’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘SimBu’ can be installed ... [3s/3s] NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2627/b79c1b2d8323feb77cb09a6d9803245a3e100113/SimBu.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'dataset.Rd':
  \examples lines wider than 100 characters:
     ds <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset")

Rd file 'dataset_h5ad.Rd':
  \examples lines wider than 100 characters:
                                    cell_id_col = 'ID',                  # this will use the 'ID' column of the metadata as cell identifiers
                                    cell_type_col = 'cell_type',         # this will use the 'cell-type' column of the metadata as cell type ... [TRUNCATED]
                                    cells_in_obs = TRUE)                 # in case your cell information is stored in the var layer, switch  ... [TRUNCATED]

Rd file 'dataset_merge.Rd':
  \examples lines wider than 100 characters:
     ds1 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset1")
     ds2 <- SimBu::dataset(annotation = annotation, count_matrix = counts, tpm_matrix = tpm, name = "test_dataset2")

Rd file 'dataset_sfaira.Rd':
  \examples lines wider than 100 characters:
     ds <- SimBu::dataset_sfaira(sfaira_id = 'homosapiens_lungparenchyma_2019_10x3v2_madissoon_001_10.1186/s13059-019-1906-x',

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [223s/278s] ERROR
Running examples in ‘SimBu-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataset_h5ad
> ### Title: Build SummarizedExperiment using a h5ad file for the counts
> ### Aliases: dataset_h5ad
> 
> ### ** Examples
> 
> h5 <- system.file('extdata', 'anndata.h5ad', package='SimBu')
> ds_h5ad <- SimBu::dataset_h5ad(h5ad_file_counts = h5,
+                                name = "h5ad_dataset",
+                                cell_id_col = 'ID',                  # this will use the 'ID' column of the metadata as cell identifiers
+                                cell_type_col = 'cell_type',         # this will use the 'cell-type' column of the metadata as cell type info
+                                cells_in_obs = TRUE)                 # in case your cell information is stored in the var layer, switch to FALSE
PREFIX=/home/pkgbuild/.cache/R/basilisk/1.8.0/0
Unpacking payload ...

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Extracting : wheel-0.34.2-py37_0.conda:   3%|▎         | 1/35 [00:00<00:05,  6.19it/s]  
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Extracting : ruamel_yaml-0.15.87-py37h7b6447c_0.conda:   9%|▊         | 3/35 [00:00<00:05,  6.19it/s]
Extracting : ruamel_yaml-0.15.87-py37h7b6447c_0.conda:  11%|█▏        | 4/35 [00:00<00:03,  8.10it/s]
Extracting : pycosat-0.6.3-py37h7b6447c_0.conda:  11%|█▏        | 4/35 [00:00<00:03,  8.10it/s]      
Extracting : readline-8.0-h7b6447c_0.conda:  14%|█▍        | 5/35 [00:00<00:03,  8.10it/s]     
Extracting : setuptools-46.4.0-py37_0.conda:  17%|█▋        | 6/35 [00:00<00:03,  8.10it/s]
Extracting : yaml-0.1.7-had09818_2.conda:  20%|██        | 7/35 [00:00<00:03,  8.10it/s]   
Extracting : pysocks-1.7.1-py37_0.conda:  23%|██▎       | 8/35 [00:00<00:03,  8.10it/s] 
Extracting : libffi-3.3-he6710b0_1.conda:  26%|██▌       | 9/35 [00:00<00:03,  8.10it/s]
Extracting : zlib-1.2.11-h7b6447c_3.conda:  29%|██▊       | 10/35 [00:00<00:03,  8.10it/s]
Extracting : tqdm-4.46.0-py_0.conda:  31%|███▏      | 11/35 [00:00<00:02,  8.10it/s]      
Extracting : tk-8.6.8-hbc83047_0.conda:  34%|███▍      | 12/35 [00:00<00:02,  8.10it/s]
Extracting : requests-2.23.0-py37_0.conda:  37%|███▋      | 13/35 [00:00<00:02,  8.10it/s]
Extracting : openssl-1.1.1g-h7b6447c_0.conda:  40%|████      | 14/35 [00:00<00:02,  8.10it/s]
Extracting : chardet-3.0.4-py37_1003.conda:  43%|████▎     | 15/35 [00:00<00:02,  8.10it/s]  
Extracting : xz-5.2.5-h7b6447c_0.conda:  46%|████▌     | 16/35 [00:00<00:02,  8.10it/s]    
Extracting : xz-5.2.5-h7b6447c_0.conda:  49%|████▊     | 17/35 [00:00<00:01, 11.24it/s]
Extracting : ca-certificates-2020.1.1-0.conda:  49%|████▊     | 17/35 [00:00<00:01, 11.24it/s]
Extracting : ncurses-6.2-he6710b0_1.conda:  51%|█████▏    | 18/35 [00:00<00:01, 11.24it/s]    
Extracting : sqlite-3.31.1-h62c20be_1.conda:  54%|█████▍    | 19/35 [00:00<00:01, 11.24it/s]
Extracting : certifi-2020.4.5.1-py37_0.conda:  57%|█████▋    | 20/35 [00:00<00:01, 11.24it/s]
Extracting : six-1.14.0-py37_0.conda:  60%|██████    | 21/35 [00:00<00:01, 11.24it/s]        
Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:  63%|██████▎   | 22/35 [00:00<00:01, 11.24it/s]
Extracting : libedit-3.1.20181209-hc058e9b_0.conda:  66%|██████▌   | 23/35 [00:00<00:01, 11.24it/s]
Extracting : pyopenssl-19.1.0-py37_0.conda:  69%|██████▊   | 24/35 [00:00<00:00, 11.24it/s]        
Extracting : pip-20.0.2-py37_3.conda:  71%|███████▏  | 25/35 [00:00<00:00, 11.24it/s]      
Extracting : ld_impl_linux-64-2.33.1-h53a641e_7.conda:  74%|███████▍  | 26/35 [00:00<00:00, 11.24it/s]
Extracting : conda-package-handling-1.6.1-py37h7b6447c_0.conda:  77%|███████▋  | 27/35 [00:00<00:00, 11.24it/s]
Extracting : python-3.7.7-hcff3b4d_5.conda:  80%|████████  | 28/35 [00:00<00:00, 11.24it/s]                    
Extracting : python-3.7.7-hcff3b4d_5.conda:  83%|████████▎ | 29/35 [00:00<00:00, 13.93it/s]
Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  83%|████████▎ | 29/35 [00:00<00:00, 13.93it/s]
Extracting : cryptography-2.9.2-py37h1ba5d50_0.conda:  86%|████████▌ | 30/35 [00:00<00:00, 13.93it/s]
Extracting : idna-2.9-py_1.conda:  89%|████████▊ | 31/35 [00:00<00:00, 13.93it/s]                    
Extracting : _libgcc_mutex-0.1-main.conda:  91%|█████████▏| 32/35 [00:00<00:00, 13.93it/s]
Extracting : pycparser-2.20-py_0.conda:  94%|█████████▍| 33/35 [00:00<00:00, 13.93it/s]   
Extracting : conda-4.8.3-py37_0.tar.bz2:  97%|█████████▋| 34/35 [00:00<00:00, 13.93it/s]
                                                                                        
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/pkgbuild/.cache/R/basilisk/1.8.0/0

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - ca-certificates==2020.1.1=0
    - certifi==2020.4.5.1=py37_0
    - cffi==1.14.0=py37he30daa8_1
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.1=py37h7b6447c_0
    - conda==4.8.3=py37_0
    - cryptography==2.9.2=py37h1ba5d50_0
    - idna==2.9=py_1
    - ld_impl_linux-64==2.33.1=h53a641e_7
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.3=he6710b0_1
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.2=he6710b0_1
    - openssl==1.1.1g=h7b6447c_0
    - pip==20.0.2=py37_3
    - pycosat==0.6.3=py37h7b6447c_0
    - pycparser==2.20=py_0
    - pyopenssl==19.1.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.7=hcff3b4d_5
    - readline==8.0=h7b6447c_0
    - requests==2.23.0=py37_0
    - ruamel_yaml==0.15.87=py37h7b6447c_0
    - setuptools==46.4.0=py37_0
    - six==1.14.0=py37_0
    - sqlite==3.31.1=h62c20be_1
    - tk==8.6.8=hbc83047_0
    - tqdm==4.46.0=py_0
    - urllib3==1.25.8=py37_0
    - wheel==0.34.2=py37_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/linux-64::certifi-2020.4.5.1-py37_0
  cffi               pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.8.3-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0
  idna               pkgs/main/noarch::idna-2.9-py_1
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_1
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
  pip                pkgs/main/linux-64::pip-20.0.2-py37_3
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
  pycparser          pkgs/main/noarch::pycparser-2.20-py_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
  readline           pkgs/main/linux-64::readline-8.0-h7b6447c_0
  requests           pkgs/main/linux-64::requests-2.23.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
  setuptools         pkgs/main/linux-64::setuptools-46.4.0-py37_0
  six                pkgs/main/linux-64::six-1.14.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.46.0-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.25.8-py37_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2

  added / updated specs:
    - python=3.9


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            2_gnu          23 KB  conda-forge
    bzip2-1.0.8                |       h7f98852_4         484 KB  conda-forge
    ca-certificates-2021.10.8  |       ha878542_0         139 KB  conda-forge
    ld_impl_linux-64-2.36.1    |       hea4e1c9_2         667 KB  conda-forge
    libffi-3.4.2               |       h7f98852_5          57 KB  conda-forge
    libgcc-ng-11.2.0           |      h1d223b6_16         902 KB  conda-forge
    libgomp-11.2.0             |      h1d223b6_16         428 KB  conda-forge
    libnsl-2.0.0               |       h7f98852_0          31 KB  conda-forge
    libuuid-2.32.1             |    h7f98852_1000          28 KB  conda-forge
    libzlib-1.2.11             |    h166bdaf_1014          60 KB  conda-forge
    ncurses-6.3                |       h27087fc_1        1002 KB  conda-forge
    openssl-3.0.3              |       h166bdaf_0         2.9 MB  conda-forge
    pip-22.0.4                 |     pyhd8ed1ab_0         1.5 MB  conda-forge
    python-3.9.12              |h2660328_1_cpython        26.6 MB  conda-forge
    python_abi-3.9             |           2_cp39           4 KB  conda-forge
    readline-8.1               |       h46c0cb4_0         295 KB  conda-forge
    setuptools-62.1.0          |   py39hf3d152e_0         1.3 MB  conda-forge
    sqlite-3.38.5              |       h4ff8645_0         1.5 MB  conda-forge
    tk-8.6.12                  |       h27826a3_0         3.3 MB  conda-forge
    tzdata-2022a               |       h191b570_0         121 KB  conda-forge
    wheel-0.37.1               |     pyhd8ed1ab_0          31 KB  conda-forge
    xz-5.2.5                   |       h516909a_1         343 KB  conda-forge
    zlib-1.2.11                |    h166bdaf_1014          88 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        41.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  ca-certificates    conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_16
  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_16
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
  libzlib            conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
  ncurses            conda-forge/linux-64::ncurses-6.3-h27087fc_1
  openssl            conda-forge/linux-64::openssl-3.0.3-h166bdaf_0
  pip                conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.9.12-h2660328_1_cpython
  python_abi         conda-forge/linux-64::python_abi-3.9-2_cp39
  readline           conda-forge/linux-64::readline-8.1-h46c0cb4_0
  setuptools         conda-forge/linux-64::setuptools-62.1.0-py39hf3d152e_0
  sqlite             conda-forge/linux-64::sqlite-3.38.5-h4ff8645_0
  tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0
  tzdata             conda-forge/noarch::tzdata-2022a-h191b570_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2

  added / updated specs:
    - python=3.9


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.4.26  |       h06a4308_0         124 KB
    ------------------------------------------------------------
                                           Total:         124 KB

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2021.10.~ --> pkgs/main::ca-certificates-2022.4.26-h06a4308_0



Downloading and Extracting Packages

ca-certificates-2022 | 124 KB    |            |   0% 
ca-certificates-2022 | 124 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2

  added / updated specs:
    - anndata=0.7.6
    - h5py=3.2.1
    - hdf5=1.10.6
    - natsort=7.1.1
    - numpy=1.20.2
    - packaging=20.9
    - pandas=1.2.4
    - python[version='3.9.*,3.9.*']
    - scipy=1.6.3
    - sqlite=3.35.5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    anndata-0.7.6              |   py39hf3d152e_0         119 KB  conda-forge
    c-ares-1.18.1              |       h7f98852_0         113 KB  conda-forge
    cached-property-1.5.2      |       hd8ed1ab_1           4 KB  conda-forge
    cached_property-1.5.2      |     pyha770c72_1          11 KB  conda-forge
    h5py-3.2.1                 |nompi_py39h98ba4bc_100         1.3 MB  conda-forge
    hdf5-1.10.6                |nompi_h6a2412b_1114         3.1 MB  conda-forge
    keyutils-1.6.1             |       h166bdaf_0         115 KB  conda-forge
    krb5-1.19.3                |       h3790be6_0         1.4 MB  conda-forge
    libblas-3.9.0              |14_linux64_openblas          12 KB  conda-forge
    libcblas-3.9.0             |14_linux64_openblas          12 KB  conda-forge
    libcurl-7.83.0             |       h7bff187_0         342 KB  conda-forge
    libedit-3.1.20191231       |       he28a2e2_2         121 KB  conda-forge
    libev-4.33                 |       h516909a_1         104 KB  conda-forge
    libffi-3.3                 |       h58526e2_2          51 KB  conda-forge
    libgfortran-ng-11.2.0      |      h69a702a_16          23 KB  conda-forge
    libgfortran5-11.2.0        |      h5c6108e_16         1.7 MB  conda-forge
    liblapack-3.9.0            |14_linux64_openblas          12 KB  conda-forge
    libnghttp2-1.47.0          |       h727a467_0         808 KB  conda-forge
    libopenblas-0.3.20         |pthreads_h78a6416_0        10.1 MB  conda-forge
    libssh2-1.10.0             |       ha56f1ee_2         233 KB  conda-forge
    libstdcxx-ng-11.2.0        |      he4da1e4_16         4.2 MB  conda-forge
    natsort-7.1.1              |     pyhd8ed1ab_0          33 KB  conda-forge
    numpy-1.20.2               |   py39hdbf815f_0         5.8 MB  conda-forge
    openssl-1.1.1o             |       h166bdaf_0         2.1 MB  conda-forge
    packaging-20.9             |     pyh44b312d_0          35 KB  conda-forge
    pandas-1.2.4               |   py39h2531618_0         8.9 MB
    pyparsing-3.0.8            |     pyhd8ed1ab_0          79 KB  conda-forge
    python-3.9.5               |h49503c6_0_cpython        27.4 MB  conda-forge
    python-dateutil-2.8.2      |     pyhd8ed1ab_0         240 KB  conda-forge
    pytz-2022.1                |     pyhd8ed1ab_0         242 KB  conda-forge
    scipy-1.6.3                |   py39hee8e79c_0        20.7 MB  conda-forge
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge
    sqlite-3.35.5              |       h74cdb3f_0         1.4 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        90.9 MB

The following NEW packages will be INSTALLED:

  anndata            conda-forge/linux-64::anndata-0.7.6-py39hf3d152e_0
  c-ares             conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
  cached-property    conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
  cached_property    conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
  h5py               conda-forge/linux-64::h5py-3.2.1-nompi_py39h98ba4bc_100
  hdf5               conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.19.3-h3790be6_0
  libblas            conda-forge/linux-64::libblas-3.9.0-14_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-14_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-7.83.0-h7bff187_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_16
  libgfortran5       conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_16
  liblapack          conda-forge/linux-64::liblapack-3.9.0-14_linux64_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.47.0-h727a467_0
  libopenblas        conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
  libssh2            conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_16
  natsort            conda-forge/noarch::natsort-7.1.1-pyhd8ed1ab_0
  numpy              conda-forge/linux-64::numpy-1.20.2-py39hdbf815f_0
  packaging          conda-forge/noarch::packaging-20.9-pyh44b312d_0
  pandas             pkgs/main/linux-64::pandas-1.2.4-py39h2531618_0
  pyparsing          conda-forge/noarch::pyparsing-3.0.8-pyhd8ed1ab_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  scipy              conda-forge/linux-64::scipy-1.6.3-py39hee8e79c_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2022.4.26-~ --> conda-forge::ca-certificates-2021.10.8-ha878542_0

The following packages will be DOWNGRADED:

  libffi                                   3.4.2-h7f98852_5 --> 3.3-h58526e2_2
  openssl                                  3.0.3-h166bdaf_0 --> 1.1.1o-h166bdaf_0
  python                          3.9.12-h2660328_1_cpython --> 3.9.5-h49503c6_0_cpython
  sqlite                                  3.38.5-h4ff8645_0 --> 3.35.5-h74cdb3f_0



Downloading and Extracting Packages

pyparsing-3.0.8      | 79 KB     |            |   0% 
pyparsing-3.0.8      | 79 KB     | ########## | 100% 

packaging-20.9       | 35 KB     |            |   0% 
packaging-20.9       | 35 KB     | ########## | 100% 

python-3.9.5         | 27.4 MB   |            |   0% 
python-3.9.5         | 27.4 MB   | #5         |  15% 
python-3.9.5         | 27.4 MB   | ###5       |  36% 
python-3.9.5         | 27.4 MB   | #####6     |  57% 
python-3.9.5         | 27.4 MB   | #######5   |  76% 
python-3.9.5         | 27.4 MB   | #########6 |  97% 
python-3.9.5         | 27.4 MB   | ########## | 100% 

libgfortran-ng-11.2. | 23 KB     |            |   0% 
libgfortran-ng-11.2. | 23 KB     | ########## | 100% 

cached-property-1.5. | 4 KB      |            |   0% 
cached-property-1.5. | 4 KB      | ########## | 100% 

libcblas-3.9.0       | 12 KB     |            |   0% 
libcblas-3.9.0       | 12 KB     | ########## | 100% 

liblapack-3.9.0      | 12 KB     |            |   0% 
liblapack-3.9.0      | 12 KB     | ########## | 100% 

python-dateutil-2.8. | 240 KB    |            |   0% 
python-dateutil-2.8. | 240 KB    | ########## | 100% 

h5py-3.2.1           | 1.3 MB    |            |   0% 
h5py-3.2.1           | 1.3 MB    | ########## | 100% 

pandas-1.2.4         | 8.9 MB    |            |   0% 
pandas-1.2.4         | 8.9 MB    | 2          |   2% 
pandas-1.2.4         | 8.9 MB    | ######3    |  63% 
pandas-1.2.4         | 8.9 MB    | ########## | 100% 

c-ares-1.18.1        | 113 KB    |            |   0% 
c-ares-1.18.1        | 113 KB    | ########## | 100% 

libssh2-1.10.0       | 233 KB    |            |   0% 
libssh2-1.10.0       | 233 KB    | ########## | 100% 

hdf5-1.10.6          | 3.1 MB    |            |   0% 
hdf5-1.10.6          | 3.1 MB    | ########## | 100% 

scipy-1.6.3          | 20.7 MB   |            |   0% 
scipy-1.6.3          | 20.7 MB   | 6          |   6% 
scipy-1.6.3          | 20.7 MB   | #8         |  18% 
scipy-1.6.3          | 20.7 MB   | ###        |  30% 
scipy-1.6.3          | 20.7 MB   | ####1      |  41% 
scipy-1.6.3          | 20.7 MB   | #####2     |  53% 
scipy-1.6.3          | 20.7 MB   | ######3    |  64% 
scipy-1.6.3          | 20.7 MB   | #######6   |  76% 
scipy-1.6.3          | 20.7 MB   | ########7  |  88% 
scipy-1.6.3          | 20.7 MB   | #########9 | 100% 
scipy-1.6.3          | 20.7 MB   | ########## | 100% 

pytz-2022.1          | 242 KB    |            |   0% 
pytz-2022.1          | 242 KB    | ########## | 100% 

cached_property-1.5. | 11 KB     |            |   0% 
cached_property-1.5. | 11 KB     | ########## | 100% 

libev-4.33           | 104 KB    |            |   0% 
libev-4.33           | 104 KB    | ########## | 100% 

anndata-0.7.6        | 119 KB    |            |   0% 
anndata-0.7.6        | 119 KB    | ########## | 100% 

sqlite-3.35.5        | 1.4 MB    |            |   0% 
sqlite-3.35.5        | 1.4 MB    | ########## | 100% 

libffi-3.3           | 51 KB     |            |   0% 
libffi-3.3           | 51 KB     | ########## | 100% 

libedit-3.1.20191231 | 121 KB    |            |   0% 
libedit-3.1.20191231 | 121 KB    | ########## | 100% 

keyutils-1.6.1       | 115 KB    |            |   0% 
keyutils-1.6.1       | 115 KB    | ########## | 100% 

natsort-7.1.1        | 33 KB     |            |   0% 
natsort-7.1.1        | 33 KB     | ########## | 100% 

numpy-1.20.2         | 5.8 MB    |            |   0% 
numpy-1.20.2         | 5.8 MB    | ######6    |  66% 
numpy-1.20.2         | 5.8 MB    | ########## | 100% 

libcurl-7.83.0       | 342 KB    |            |   0% 
libcurl-7.83.0       | 342 KB    | ########## | 100% 

libnghttp2-1.47.0    | 808 KB    |            |   0% 
libnghttp2-1.47.0    | 808 KB    | ########## | 100% 

libopenblas-0.3.20   | 10.1 MB   |            |   0% 
libopenblas-0.3.20   | 10.1 MB   | ###7       |  38% 
libopenblas-0.3.20   | 10.1 MB   | #########3 |  94% 
libopenblas-0.3.20   | 10.1 MB   | ########## | 100% 

krb5-1.19.3          | 1.4 MB    |            |   0% 
krb5-1.19.3          | 1.4 MB    | ########## | 100% 

libstdcxx-ng-11.2.0  | 4.2 MB    |            |   0% 
libstdcxx-ng-11.2.0  | 4.2 MB    | ########## | 100% 

six-1.16.0           | 14 KB     |            |   0% 
six-1.16.0           | 14 KB     | ########## | 100% 

libgfortran5-11.2.0  | 1.7 MB    |            |   0% 
libgfortran5-11.2.0  | 1.7 MB    | ########## | 100% 

libblas-3.9.0        | 12 KB     |            |   0% 
libblas-3.9.0        | 12 KB     | ########## | 100% 

openssl-1.1.1o       | 2.1 MB    |            |   0% 
openssl-1.1.1o       | 2.1 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting sfaira==0.3.12
  Downloading sfaira-0.3.12-py2.py3-none-any.whl (409 kB)
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Collecting tables==3.7.0
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Requirement already satisfied: pandas in /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2/lib/python3.9/site-packages (from sfaira==0.3.12) (1.2.4)
Collecting boltons
  Downloading boltons-21.0.0-py2.py3-none-any.whl (193 kB)
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Collecting tensorflow
  Downloading tensorflow-2.8.0-cp39-cp39-manylinux2010_x86_64.whl (497.6 MB)
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Collecting dask
  Downloading dask-2022.5.0-py3-none-any.whl (1.1 MB)
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Collecting versioneer
  Downloading versioneer-0.22-py3-none-any.whl (42 kB)
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Collecting obonet
  Downloading obonet-0.3.0-py3-none-any.whl (7.9 kB)
Requirement already satisfied: anndata>=0.7.6 in /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2/lib/python3.9/site-packages (from sfaira==0.3.12) (0.7.6)
Collecting questionary>=1.8.1
  Downloading questionary-1.10.0-py3-none-any.whl (31 kB)
Collecting zarr
  Downloading zarr-2.11.3-py3-none-any.whl (153 kB)
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Collecting tqdm
  Downloading tqdm-4.64.0-py2.py3-none-any.whl (78 kB)
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Collecting click>=7.1.2
  Downloading click-8.1.3-py3-none-any.whl (96 kB)
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Collecting cookiecutter>=1.7.2
  Downloading cookiecutter-1.7.3-py2.py3-none-any.whl (34 kB)
Collecting numba
  Downloading numba-0.55.1-1-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
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Collecting seaborn
  Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
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Collecting flatten-dict
  Downloading flatten_dict-0.4.2-py2.py3-none-any.whl (9.7 kB)
Requirement already satisfied: numpy>=1.16.4 in /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2/lib/python3.9/site-packages (from sfaira==0.3.12) (1.20.2)
Collecting matplotlib
  Downloading matplotlib-3.5.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
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Collecting xlrd==1.*
  Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
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Collecting rich>=9.10.0
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Collecting torchmetrics
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Collecting requests
  Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB)
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Collecting scanpy>=1.7.0
  Downloading scanpy-1.9.1-py3-none-any.whl (2.0 MB)
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Collecting pyarrow
  Downloading pyarrow-8.0.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.4 MB)
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Requirement already satisfied: h5py in /home/pkgbuild/.cache/R/basilisk/1.8.0/SimBu/0.99.2/SimBu_env_0_99_2/lib/python3.9/site-packages (from sfaira==0.3.12) (3.2.1)
Collecting fuzzywuzzy
  Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB)
Collecting switchlang>=0.1.0
  Downloading switchlang-0.1.0-py3-none-any.whl (6.3 kB)
Collecting python-Levenshtein
  Downloading python-Levenshtein-0.12.2.tar.gz (50 kB)
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  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting sparse
  Downloading sparse-0.13.0-py2.py3-none-any.whl (77 kB)
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Collecting torch
  Downloading torch-1.11.0-cp39-cp39-manylinux1_x86_64.whl (750.6 MB)
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Collecting crossref-commons
  Downloading crossref_commons-0.0.7-py3-none-any.whl (14 kB)
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Building wheels for collected packages: loompy, owlready2, python-Levenshtein, ratelimit, termcolor, umap-learn, asciitree, session-info, pynndescent
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Successfully built loompy owlready2 python-Levenshtein ratelimit termcolor umap-learn asciitree session-info pynndescent
Installing collected packages: wcwidth, tf-estimator-nightly, text-unidecode, termcolor, tensorboard-plugin-wit, switchlang, stdlib_list, ratelimit, pyasn1, pure-eval, ptyprocess, pickleshare, numpy-groupies, libclang, keras, iniconfig, fuzzywuzzy, flatbuffers, executing, commonmark, certifi, boltons, backcall, asciitree, zipp, xlrd, wrapt, werkzeug, versioneer, urllib3, typing-extensions, traitlets, tqdm, toolz, tomli, threadpoolctl, tensorflow-io-gcs-filesystem, tensorboard-data-server, session-info, rsa, PyYAML, python-slugify, python-Levenshtein, pygments, pyDeprecate, pyasn1-modules, pyarrow, py, protobuf, prompt_toolkit, poyo, pluggy, pillow, pexpect, patsy, parso, packaging, owlready2, opt-einsum, oauthlib, numcodecs, networkx, MarkupSafe, locket, llvmlite, kiwisolver, keras-preprocessing, joblib, idna, grpcio, google-pasta, gast, fsspec, fonttools, flatten-dict, fasteners, et-xmlfile, docutils, decorator, cycler, cloudpickle, click, charset-normalizer, chardet, cachetools, attrs, astunparse, asttokens, absl-py, zarr, torch, stack-data, scikit-learn, rich, requests, questionary, pytest, partd, openpyxl, obonet, numexpr, numba, matplotlib-inline, matplotlib, Jinja2, jedi, importlib-metadata, google-auth, binaryornot, arrow, torchmetrics, tables, statsmodels, sparse, seaborn, requests-oauthlib, pynndescent, markdown, loompy, jinja2-time, IPython, dask, crossref-commons, umap-learn, google-auth-oauthlib, cookiecutter, tensorboard, scanpy, tensorflow, sfaira
  Attempting uninstall: packaging
    Found existing installation: packaging 20.9
    Uninstalling packaging-20.9:
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Successfully installed IPython-8.3.0 Jinja2-3.1.2 MarkupSafe-2.1.1 PyYAML-6.0 absl-py-1.0.0 arrow-1.2.2 asciitree-0.3.3 asttokens-2.0.5 astunparse-1.6.3 attrs-21.4.0 backcall-0.2.0 binaryornot-0.4.4 boltons-21.0.0 cachetools-5.0.0 certifi-2021.10.8 chardet-4.0.0 charset-normalizer-2.0.12 click-8.1.3 cloudpickle-2.0.0 commonmark-0.9.1 cookiecutter-1.7.3 crossref-commons-0.0.7 cycler-0.11.0 dask-2022.5.0 decorator-5.1.1 docutils-0.18.1 et-xmlfile-1.1.0 executing-0.8.3 fasteners-0.17.3 flatbuffers-2.0 flatten-dict-0.4.2 fonttools-4.33.3 fsspec-2022.3.0 fuzzywuzzy-0.18.0 gast-0.5.3 google-auth-2.6.6 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.46.0 idna-3.3 importlib-metadata-4.11.3 iniconfig-1.1.1 jedi-0.18.1 jinja2-time-0.2.0 joblib-1.1.0 keras-2.8.0 keras-preprocessing-1.1.2 kiwisolver-1.4.2 libclang-14.0.1 llvmlite-0.38.0 locket-1.0.0 loompy-3.0.7 markdown-3.3.7 matplotlib-3.5.2 matplotlib-inline-0.1.3 networkx-2.8 numba-0.55.1 numcodecs-0.9.1 numexpr-2.8.1 numpy-groupies-0.9.16 oauthlib-3.2.0 obonet-0.3.0 openpyxl-3.0.9 opt-einsum-3.3.0 owlready2-0.37 packaging-21.3 parso-0.8.3 partd-1.2.0 patsy-0.5.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.1.0 pluggy-1.0.0 poyo-0.5.0 prompt_toolkit-3.0.29 protobuf-3.20.1 ptyprocess-0.7.0 pure-eval-0.2.2 py-1.11.0 pyDeprecate-0.3.2 pyarrow-8.0.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pygments-2.12.0 pynndescent-0.5.6 pytest-7.1.2 python-Levenshtein-0.12.2 python-slugify-6.1.2 questionary-1.10.0 ratelimit-2.2.1 requests-2.27.1 requests-oauthlib-1.3.1 rich-12.4.1 rsa-4.8 scanpy-1.9.1 scikit-learn-1.0.2 seaborn-0.11.2 session-info-1.0.0 sfaira-0.3.12 sparse-0.13.0 stack-data-0.2.0 statsmodels-0.13.2 stdlib_list-0.8.0 switchlang-0.1.0 tables-3.7.0 tensorboard-2.8.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tensorflow-2.8.0 tensorflow-io-gcs-filesystem-0.25.0 termcolor-1.1.0 text-unidecode-1.3 tf-estimator-nightly-2.8.0.dev2021122109 threadpoolctl-3.1.0 tomli-2.0.1 toolz-0.11.2 torch-1.11.0 torchmetrics-0.8.2 tqdm-4.64.0 traitlets-5.1.1 typing-extensions-4.2.0 umap-learn-0.5.3 urllib3-1.26.9 versioneer-0.22 wcwidth-0.2.5 werkzeug-2.1.2 wrapt-1.14.1 xlrd-1.2.0 zarr-2.11.3 zipp-3.8.0
Error in SimBu::dataset_h5ad(h5ad_file_counts = h5, name = "h5ad_dataset",  : 
  Cannot find "ID" column in cell annotation of h5ad_file_counts.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [38s/38s]
 [39s/39s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2627/b79c1b2d8323feb77cb09a6d9803245a3e100113/SimBu.Rcheck/00check.log’
for details.





===============================

 BiocCheck('SimBu_0.99.2.tar.gz')

===============================

─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: SimBu
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/RtmpRYiiuU/filec2ad9360c1684/SimBu
─ installDir: /tmp/RtmpRYiiuU/filec2ad955b5358
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2627/b79c1b2d8323feb77cb09a6d9803245a3e100113/SimBu.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SimBu...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid '<<-' if possible (found 1 times)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
* Checking function lengths...
    * NOTE: Recommended function length <= 50 lines.There are 6
      functions > 50 lines.
* Checking man page documentation...
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * NOTE: Usage of dontrun{} / donttest{} found in man page
      examples.15% of man pages use one of these cases.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 668 lines (17%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1173 lines
      (30%) are not.
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    * ERROR: Maintainer must subscribe to the bioc-devel mailing list.
      Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
2 ERRORS | 1 WARNINGS | 13 NOTES

See the SimBu.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.