Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/ReUseData
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 22.04.1 LTS)/x86_64   OK     ERROR     skipped     OK  
merida1 macOS 10.14.6 Mojave/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo1 Summary

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Package: ReUseData
Version: 0.99.9
RVersion: 4.3
BiocVersion: 3.17
BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData
BuildTime: 0 minutes 49.62 seconds
CheckCommand: BiocCheckGitClone('ReUseData') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2868/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2868/ReUseData_20230103191509/ReUseData.install-out.txt ReUseData_0.99.9.tar.gz && BiocCheck('ReUseData_0.99.9.tar.gz', `new-package`=TRUE)
CheckTime: 2 minutes 18.12 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 580.96 KiB
BuildID:: ReUseData_20230103191509
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ReUseData. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* 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 ‘ReUseData_0.99.9.tar.gz’

nebbiolo1 CHECK output

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

 BiocCheckGitClone('ReUseData')

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

─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.9
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/ReUseData_20230103191509/ReUseData
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc 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/2868/ReUseData_20230103191509/ReUseData.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘0.99.9’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ReUseData’ can be installed ... OK
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Rcwl:::env_Rcwl’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [13s/13s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [35s/40s] OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
dataUpdate    8.292  0.312  10.453
getCloudData  6.226  0.243   7.662
dataHub-class 4.936  0.268   5.279
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [14s/15s]
 [14s/15s] 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 ... [4s/4s] OK
* DONE

Status: 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2868/ReUseData_20230103191509/ReUseData.Rcheck/00check.log’
for details.






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

 BiocCheck('ReUseData_0.99.9.tar.gz')

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

─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: ReUseData
─ PackageVersion: 0.99.9
─ sourceDir: /tmp/RtmpRq9jaV/file18f4a12b044e55/ReUseData
─ installDir: /tmp/RtmpRq9jaV/file18f4a17e1206aa
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2868/ReUseData_20230103191509/ReUseData.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      WorkflowManagement
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ReUseData...
* 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
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
    * ERROR: Avoid references to external hosting platforms
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 41 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 18% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* 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; 42 lines (2%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 117 lines
      (5%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.

─ BiocCheck results ──
2 ERRORS | 0 WARNINGS | 16 NOTES

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

nebbiolo1 BUILD BIN output

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merida1 Summary
 
                			
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Package: ReUseData
 
                					
Version: 0.99.9
 
                					
RVersion: 4.3
                
 
                					
BiocVersion: 3.17
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReUseData
 
                					
BuildTime: 8 minutes 53.62 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: ReUseData_20230103191509
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: ReUseData. Starting Build package. 
 
                					
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1. 
        				
                				
 
                			
 
                			
 
                			    
                				
merida1 BUILD SRC output
 
                    			
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===============================

 R CMD BUILD

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

* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* preparing ‘ReUseData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ReUseData_data.Rmd’ using rmarkdown
trying URL 'https://github.com/rworkflow/ReUseDataRecipe/archive/refs/heads/master.zip'
downloaded 17 KB

trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py38_4.12.0-MacOSX-x86_64.sh'
Content type 'application/x-sh' length 59150526 bytes (56.4 MB)
==================================================
downloaded 56.4 MB

PREFIX=/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/0
Unpacking payload ...

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Extracting : libcxx-12.0.0-h2f01273_0.conda:  31%|███▏      | 11/35 [00:02<00:07,  3.23it/s]
Extracting : libffi-3.3-hb1e8313_2.conda:  34%|███▍      | 12/35 [00:02<00:07,  3.23it/s]   
Extracting : ncurses-6.3-hca72f7f_2.conda:  37%|███▋      | 13/35 [00:02<00:06,  3.23it/s]
Extracting : openssl-1.1.1n-hca72f7f_0.conda:  40%|████      | 14/35 [00:02<00:06,  3.23it/s]
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Extracting : pysocks-1.7.1-py38_1.conda:  54%|█████▍    | 19/35 [00:02<00:04,  3.23it/s]         
Extracting : python-3.8.13-hdfd78df_0.conda:  57%|█████▋    | 20/35 [00:02<00:04,  3.23it/s]
Extracting : python.app-3-py38hca72f7f_0.conda:  60%|██████    | 21/35 [00:02<00:04,  3.23it/s]
Extracting : readline-8.1.2-hca72f7f_1.conda:  63%|██████▎   | 22/35 [00:02<00:04,  3.23it/s]  
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda:  66%|██████▌   | 23/35 [00:02<00:03,  3.23it/s]
Extracting : ruamel_yaml-0.15.100-py38h9ed2024_0.conda:  69%|██████▊   | 24/35 [00:02<00:03,  3.23it/s]
Extracting : setuptools-61.2.0-py38hecd8cb5_0.conda:  71%|███████▏  | 25/35 [00:02<00:03,  3.23it/s]   
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Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda:  83%|████████▎ | 29/35 [00:02<00:01,  3.23it/s]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda:  86%|████████▌ | 30/35 [00:02<00:01,  3.23it/s]
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Extracting : xz-5.2.5-h1de35cc_0.conda:  91%|█████████▏| 32/35 [00:02<00:00,  3.23it/s]      
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Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/0

  added / updated specs:
    - brotlipy==0.7.0=py38h9ed2024_1003
    - ca-certificates==2022.3.29=hecd8cb5_1
    - certifi==2021.10.8=py38hecd8cb5_2
    - cffi==1.15.0=py38hc55c11b_1
    - charset-normalizer==2.0.4=pyhd3eb1b0_0
    - colorama==0.4.4=pyhd3eb1b0_0
    - conda-content-trust==0.1.1=pyhd3eb1b0_0
    - conda-package-handling==1.8.1=py38hca72f7f_0
    - conda==4.12.0=py38hecd8cb5_0
    - cryptography==36.0.0=py38hf6deb26_0
    - idna==3.3=pyhd3eb1b0_0
    - libcxx==12.0.0=h2f01273_0
    - libffi==3.3=hb1e8313_2
    - ncurses==6.3=hca72f7f_2
    - openssl==1.1.1n=hca72f7f_0
    - pip==21.2.4=py38hecd8cb5_0
    - pycosat==0.6.3=py38h1de35cc_1
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py38_1
    - python.app==3=py38hca72f7f_0
    - python==3.8.13=hdfd78df_0
    - readline==8.1.2=hca72f7f_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py38h9ed2024_0
    - setuptools==61.2.0=py38hecd8cb5_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=h707629a_0
    - tk==8.6.11=h7bc2e8c_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h1de35cc_0
    - yaml==0.2.5=haf1e3a3_0
    - zlib==1.2.12=h4dc903c_1


The following NEW packages will be INSTALLED:

  brotlipy           pkgs/main/osx-64::brotlipy-0.7.0-py38h9ed2024_1003
  ca-certificates    pkgs/main/osx-64::ca-certificates-2022.3.29-hecd8cb5_1
  certifi            pkgs/main/osx-64::certifi-2021.10.8-py38hecd8cb5_2
  cffi               pkgs/main/osx-64::cffi-1.15.0-py38hc55c11b_1
  charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
  colorama           pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
  conda              pkgs/main/osx-64::conda-4.12.0-py38hecd8cb5_0
  conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
  conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.8.1-py38hca72f7f_0
  cryptography       pkgs/main/osx-64::cryptography-36.0.0-py38hf6deb26_0
  idna               pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
  libcxx             pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
  libffi             pkgs/main/osx-64::libffi-3.3-hb1e8313_2
  ncurses            pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
  openssl            pkgs/main/osx-64::openssl-1.1.1n-hca72f7f_0
  pip                pkgs/main/osx-64::pip-21.2.4-py38hecd8cb5_0
  pycosat            pkgs/main/osx-64::pycosat-0.6.3-py38h1de35cc_1
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
  pyopenssl          pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
  pysocks            pkgs/main/osx-64::pysocks-1.7.1-py38_1
  python             pkgs/main/osx-64::python-3.8.13-hdfd78df_0
  python.app         pkgs/main/osx-64::python.app-3-py38hca72f7f_0
  readline           pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/osx-64::ruamel_yaml-0.15.100-py38h9ed2024_0
  setuptools         pkgs/main/osx-64::setuptools-61.2.0-py38hecd8cb5_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/osx-64::sqlite-3.38.2-h707629a_0
  tk                 pkgs/main/osx-64::tk-8.6.11-h7bc2e8c_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  yaml               pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0
  zlib               pkgs/main/osx-64::zlib-1.2.12-h4dc903c_1


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

## Package Plan ##

  environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.3/env_Rcwl

  added / updated specs:
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.12.7  |       h033912b_0         142 KB  conda-forge
    libcxx-14.0.6              |       hccf4f1f_0         1.3 MB  conda-forge
    libffi-3.3                 |       h046ec9c_2          45 KB  conda-forge
    libsqlite-3.40.0           |       ha978bb4_0         873 KB  conda-forge
    libzlib-1.2.13             |       hfd90126_4          64 KB  conda-forge
    ncurses-6.3                |       h96cf925_1         915 KB  conda-forge
    openssl-1.1.1s             |       hfd90126_1         1.6 MB  conda-forge
    pip-22.3.1                 |     pyhd8ed1ab_0         1.5 MB  conda-forge
    python-3.8.13              |       hdfd78df_1        10.8 MB
    readline-8.1.2             |       h3899abd_0         266 KB  conda-forge
    setuptools-65.6.3          |     pyhd8ed1ab_0         619 KB  conda-forge
    sqlite-3.40.0              |       h9ae0607_0         885 KB  conda-forge
    tk-8.6.12                  |       h5dbffcc_0         3.4 MB  conda-forge
    wheel-0.38.4               |     pyhd8ed1ab_0          32 KB  conda-forge
    xz-5.2.6                   |       h775f41a_0         233 KB  conda-forge
    zlib-1.2.13                |       hfd90126_4          93 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        22.7 MB

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2022.12.7-h033912b_0
  libcxx             conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
  libffi             conda-forge/osx-64::libffi-3.3-h046ec9c_2
  libsqlite          conda-forge/osx-64::libsqlite-3.40.0-ha978bb4_0
  libzlib            conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
  ncurses            conda-forge/osx-64::ncurses-6.3-h96cf925_1
  openssl            conda-forge/osx-64::openssl-1.1.1s-hfd90126_1
  pip                conda-forge/noarch::pip-22.3.1-pyhd8ed1ab_0
  python             pkgs/main/osx-64::python-3.8.13-hdfd78df_1
  readline           conda-forge/osx-64::readline-8.1.2-h3899abd_0
  setuptools         conda-forge/noarch::setuptools-65.6.3-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.40.0-h9ae0607_0
  tk                 conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
  wheel              conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0
  zlib               conda-forge/osx-64::zlib-1.2.13-hfd90126_4


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: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.3/env_Rcwl

  added / updated specs:
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.10.11 |       hecd8cb5_0         125 KB
    openssl-1.1.1s             |       hca72f7f_0         2.8 MB
    ------------------------------------------------------------
                                           Total:         2.9 MB

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

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2022.10.11-hecd8cb5_0
  openssl            conda-forge::openssl-1.1.1s-hfd90126_1 --> pkgs/main::openssl-1.1.1s-hca72f7f_0



Downloading and Extracting Packages

ca-certificates-2022 | 125 KB    |            |   0% 
ca-certificates-2022 | 125 KB    | ########## | 100% 

openssl-1.1.1s       | 2.8 MB    |            |   0% 
openssl-1.1.1s       | 2.8 MB    | ########## | 100% 
openssl-1.1.1s       | 2.8 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 22.11.1

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: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.3/env_Rcwl

  added / updated specs:
    - cwl-utils=0.19
    - cwltool=3.1
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    argcomplete-1.12.3         |     pyhd8ed1ab_0          34 KB  conda-forge
    bagit-1.8.1                |     pyhd8ed1ab_0          25 KB  conda-forge
    black-22.10.0              |   py38h50d1736_2         231 KB  conda-forge
    brotlipy-0.7.0             |py38hef030d1_1005         367 KB  conda-forge
    cachecontrol-0.12.11       |     pyhd8ed1ab_0          24 KB  conda-forge
    certifi-2022.12.7          |     pyhd8ed1ab_0         147 KB  conda-forge
    cffi-1.14.6                |   py38h9688ba1_0         219 KB  conda-forge
    charset-normalizer-2.1.1   |     pyhd8ed1ab_0          36 KB  conda-forge
    click-8.1.3                |unix_pyhd8ed1ab_2          74 KB  conda-forge
    coloredlogs-15.0.1         |     pyhd8ed1ab_3          40 KB  conda-forge
    cryptography-39.0.0        |   py38ha6c3189_0         1.0 MB  conda-forge
    cwl-upgrader-1.2.3         |     pyhd8ed1ab_0          24 KB  conda-forge
    cwl-utils-0.19             |     pyhd8ed1ab_0         136 KB  conda-forge
    cwlformat-2022.02.18       |     pyhd8ed1ab_0          14 KB  conda-forge
    cwltool-3.1.20221201130942 |   py38h776f746_1         1.6 MB  conda-forge
    freetype-2.12.1            |       h3f81eb7_1         586 KB  conda-forge
    graphviz-2.42.3            |       h98dfb87_0         7.1 MB  conda-forge
    html5lib-1.1               |     pyh9f0ad1d_0          89 KB  conda-forge
    humanfriendly-10.0         |   py38h50d1736_4         119 KB  conda-forge
    icu-70.1                   |       h96cf925_0        13.1 MB  conda-forge
    idna-3.4                   |     pyhd8ed1ab_0          55 KB  conda-forge
    importlib-metadata-6.0.0   |     pyha770c72_0          24 KB  conda-forge
    isodate-0.6.1              |     pyhd8ed1ab_0          28 KB  conda-forge
    jpeg-9e                    |       hac89ed1_2         260 KB  conda-forge
    lerc-4.0.0                 |       hb486fe8_0         284 KB  conda-forge
    libdeflate-1.14            |       hb7f2c08_0          85 KB  conda-forge
    libiconv-1.17              |       hac89ed1_0         1.3 MB  conda-forge
    libpng-1.6.39              |       ha978bb4_0         265 KB  conda-forge
    libtiff-4.4.0              |       h6268bbc_5         443 KB  conda-forge
    libwebp-base-1.2.4         |       h775f41a_0         385 KB  conda-forge
    libxml2-2.10.3             |       hb9e07b5_0         672 KB  conda-forge
    libxslt-1.1.37             |       h5d22bc9_0         236 KB  conda-forge
    lockfile-0.12.2            |             py_1          11 KB  conda-forge
    lxml-4.9.2                 |   py38h64add32_0         1.2 MB  conda-forge
    mistune-2.0.4              |     pyhd8ed1ab_0          67 KB  conda-forge
    msgpack-python-1.0.4       |   py38h98b9b1b_1          82 KB  conda-forge
    mypy_extensions-0.4.3      |   py38h50d1736_6          11 KB  conda-forge
    networkx-2.8.8             |     pyhd8ed1ab_0         1.6 MB  conda-forge
    packaging-22.0             |     pyhd8ed1ab_0          40 KB  conda-forge
    pathspec-0.10.3            |     pyhd8ed1ab_0          37 KB  conda-forge
    platformdirs-2.6.2         |     pyhd8ed1ab_0          17 KB  conda-forge
    prov-1.5.1                 |             py_1         152 KB  conda-forge
    psutil-5.9.4               |   py38hef030d1_0         358 KB  conda-forge
    pycparser-2.21             |     pyhd8ed1ab_0         100 KB  conda-forge
    pydot-1.4.2                |   py38h50d1736_3          44 KB  conda-forge
    pydotplus-2.0.2            |     pyh243d235_4          24 KB  conda-forge
    pyopenssl-23.0.0           |     pyhd8ed1ab_0         124 KB  conda-forge
    pyparsing-3.0.9            |     pyhd8ed1ab_0          79 KB  conda-forge
    pysocks-1.7.1              |     pyha2e5f31_6          19 KB  conda-forge
    python-dateutil-2.8.2      |     pyhd8ed1ab_0         240 KB  conda-forge
    python_abi-3.8             |           2_cp38           4 KB  conda-forge
    rdflib-6.2.0               |     pyhd8ed1ab_0         3.1 MB  conda-forge
    requests-2.28.1            |     pyhd8ed1ab_1          53 KB  conda-forge
    ruamel.yaml-0.17.21        |   py38hef030d1_2         173 KB  conda-forge
    ruamel.yaml.clib-0.2.7     |   py38hef030d1_1         115 KB  conda-forge
    schema-salad-8.3.20221209165047|   py38hef030d1_0         847 KB  conda-forge
    shellescape-3.4.1          |             py_0           7 KB  conda-forge
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge
    tomli-2.0.1                |     pyhd8ed1ab_0          16 KB  conda-forge
    typing-extensions-4.4.0    |       hd8ed1ab_0           8 KB  conda-forge
    typing_extensions-4.4.0    |     pyha770c72_0          29 KB  conda-forge
    urllib3-1.26.13            |     pyhd8ed1ab_0         108 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    zipp-3.11.0                |     pyhd8ed1ab_0          15 KB  conda-forge
    zstd-1.5.2                 |       hfa58983_4         470 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        38.0 MB

The following NEW packages will be INSTALLED:

  argcomplete        conda-forge/noarch::argcomplete-1.12.3-pyhd8ed1ab_0
  bagit              conda-forge/noarch::bagit-1.8.1-pyhd8ed1ab_0
  black              conda-forge/osx-64::black-22.10.0-py38h50d1736_2
  brotlipy           conda-forge/osx-64::brotlipy-0.7.0-py38hef030d1_1005
  cachecontrol       conda-forge/noarch::cachecontrol-0.12.11-pyhd8ed1ab_0
  certifi            conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0
  cffi               conda-forge/osx-64::cffi-1.14.6-py38h9688ba1_0
  charset-normalizer conda-forge/noarch::charset-normalizer-2.1.1-pyhd8ed1ab_0
  click              conda-forge/noarch::click-8.1.3-unix_pyhd8ed1ab_2
  coloredlogs        conda-forge/noarch::coloredlogs-15.0.1-pyhd8ed1ab_3
  cryptography       conda-forge/osx-64::cryptography-39.0.0-py38ha6c3189_0
  cwl-upgrader       conda-forge/noarch::cwl-upgrader-1.2.3-pyhd8ed1ab_0
  cwl-utils          conda-forge/noarch::cwl-utils-0.19-pyhd8ed1ab_0
  cwlformat          conda-forge/noarch::cwlformat-2022.02.18-pyhd8ed1ab_0
  cwltool            conda-forge/osx-64::cwltool-3.1.20221201130942-py38h776f746_1
  freetype           conda-forge/osx-64::freetype-2.12.1-h3f81eb7_1
  graphviz           conda-forge/osx-64::graphviz-2.42.3-h98dfb87_0
  html5lib           conda-forge/noarch::html5lib-1.1-pyh9f0ad1d_0
  humanfriendly      conda-forge/osx-64::humanfriendly-10.0-py38h50d1736_4
  icu                conda-forge/osx-64::icu-70.1-h96cf925_0
  idna               conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
  importlib-metadata conda-forge/noarch::importlib-metadata-6.0.0-pyha770c72_0
  isodate            conda-forge/noarch::isodate-0.6.1-pyhd8ed1ab_0
  jpeg               conda-forge/osx-64::jpeg-9e-hac89ed1_2
  lerc               conda-forge/osx-64::lerc-4.0.0-hb486fe8_0
  libdeflate         conda-forge/osx-64::libdeflate-1.14-hb7f2c08_0
  libiconv           conda-forge/osx-64::libiconv-1.17-hac89ed1_0
  libpng             conda-forge/osx-64::libpng-1.6.39-ha978bb4_0
  libtiff            conda-forge/osx-64::libtiff-4.4.0-h6268bbc_5
  libwebp-base       conda-forge/osx-64::libwebp-base-1.2.4-h775f41a_0
  libxml2            conda-forge/osx-64::libxml2-2.10.3-hb9e07b5_0
  libxslt            conda-forge/osx-64::libxslt-1.1.37-h5d22bc9_0
  lockfile           conda-forge/noarch::lockfile-0.12.2-py_1
  lxml               conda-forge/osx-64::lxml-4.9.2-py38h64add32_0
  mistune            conda-forge/noarch::mistune-2.0.4-pyhd8ed1ab_0
  msgpack-python     conda-forge/osx-64::msgpack-python-1.0.4-py38h98b9b1b_1
  mypy_extensions    conda-forge/osx-64::mypy_extensions-0.4.3-py38h50d1736_6
  networkx           conda-forge/noarch::networkx-2.8.8-pyhd8ed1ab_0
  packaging          conda-forge/noarch::packaging-22.0-pyhd8ed1ab_0
  pathspec           conda-forge/noarch::pathspec-0.10.3-pyhd8ed1ab_0
  platformdirs       conda-forge/noarch::platformdirs-2.6.2-pyhd8ed1ab_0
  prov               conda-forge/noarch::prov-1.5.1-py_1
  psutil             conda-forge/osx-64::psutil-5.9.4-py38hef030d1_0
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
  pydot              conda-forge/osx-64::pydot-1.4.2-py38h50d1736_3
  pydotplus          conda-forge/noarch::pydotplus-2.0.2-pyh243d235_4
  pyopenssl          conda-forge/noarch::pyopenssl-23.0.0-pyhd8ed1ab_0
  pyparsing          conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab_0
  pysocks            conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/osx-64::python_abi-3.8-2_cp38
  rdflib             conda-forge/noarch::rdflib-6.2.0-pyhd8ed1ab_0
  requests           conda-forge/noarch::requests-2.28.1-pyhd8ed1ab_1
  ruamel.yaml        conda-forge/osx-64::ruamel.yaml-0.17.21-py38hef030d1_2
  ruamel.yaml.clib   conda-forge/osx-64::ruamel.yaml.clib-0.2.7-py38hef030d1_1
  schema-salad       conda-forge/osx-64::schema-salad-8.3.20221209165047-py38hef030d1_0
  shellescape        conda-forge/noarch::shellescape-3.4.1-py_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  tomli              conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0
  typing-extensions  conda-forge/noarch::typing-extensions-4.4.0-hd8ed1ab_0
  typing_extensions  conda-forge/noarch::typing_extensions-4.4.0-pyha770c72_0
  urllib3            conda-forge/noarch::urllib3-1.26.13-pyhd8ed1ab_0
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  zipp               conda-forge/noarch::zipp-3.11.0-pyhd8ed1ab_0
  zstd               conda-forge/osx-64::zstd-1.5.2-hfa58983_4

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2022.10.11~ --> conda-forge::ca-certificates-2022.12.7-h033912b_0
  openssl              pkgs/main::openssl-1.1.1s-hca72f7f_0 --> conda-forge::openssl-1.1.1s-hfd90126_1



Downloading and Extracting Packages

rdflib-6.2.0         | 3.1 MB    |            |   0% 
rdflib-6.2.0         | 3.1 MB    | 6          |   7% 
rdflib-6.2.0         | 3.1 MB    | ########## | 100% 
rdflib-6.2.0         | 3.1 MB    | ########## | 100% 

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

cwl-upgrader-1.2.3   | 24 KB     |            |   0% 
cwl-upgrader-1.2.3   | 24 KB     | ########## | 100% 

shellescape-3.4.1    | 7 KB      |            |   0% 
shellescape-3.4.1    | 7 KB      | ########## | 100% 

ruamel.yaml.clib-0.2 | 115 KB    |            |   0% 
ruamel.yaml.clib-0.2 | 115 KB    | ########## | 100% 
ruamel.yaml.clib-0.2 | 115 KB    | ########## | 100% 

freetype-2.12.1      | 586 KB    |            |   0% 
freetype-2.12.1      | 586 KB    | ########## | 100% 
freetype-2.12.1      | 586 KB    | ########## | 100% 

libtiff-4.4.0        | 443 KB    |            |   0% 
libtiff-4.4.0        | 443 KB    | ########## | 100% 
libtiff-4.4.0        | 443 KB    | ########## | 100% 

pyparsing-3.0.9      | 79 KB     |            |   0% 
pyparsing-3.0.9      | 79 KB     | ########## | 100% 

requests-2.28.1      | 53 KB     |            |   0% 
requests-2.28.1      | 53 KB     | ########## | 100% 

libxslt-1.1.37       | 236 KB    |            |   0% 
libxslt-1.1.37       | 236 KB    | ########## | 100% 
libxslt-1.1.37       | 236 KB    | ########## | 100% 

mistune-2.0.4        | 67 KB     |            |   0% 
mistune-2.0.4        | 67 KB     | ########## | 100% 

msgpack-python-1.0.4 | 82 KB     |            |   0% 
msgpack-python-1.0.4 | 82 KB     | ########## | 100% 

mypy_extensions-0.4. | 11 KB     |            |   0% 
mypy_extensions-0.4. | 11 KB     | ########## | 100% 

pydotplus-2.0.2      | 24 KB     |            |   0% 
pydotplus-2.0.2      | 24 KB     | ######6    |  67% 
pydotplus-2.0.2      | 24 KB     | ########## | 100% 

typing-extensions-4. | 8 KB      |            |   0% 
typing-extensions-4. | 8 KB      | ########## | 100% 

zipp-3.11.0          | 15 KB     |            |   0% 
zipp-3.11.0          | 15 KB     | ########## | 100% 
zipp-3.11.0          | 15 KB     | ########## | 100% 

pysocks-1.7.1        | 19 KB     |            |   0% 
pysocks-1.7.1        | 19 KB     | ########## | 100% 

platformdirs-2.6.2   | 17 KB     |            |   0% 
platformdirs-2.6.2   | 17 KB     | ########## | 100% 

cryptography-39.0.0  | 1.0 MB    |            |   0% 
cryptography-39.0.0  | 1.0 MB    | ########## | 100% 
cryptography-39.0.0  | 1.0 MB    | ########## | 100% 

libdeflate-1.14      | 85 KB     |            |   0% 
libdeflate-1.14      | 85 KB     | ########## | 100% 

pathspec-0.10.3      | 37 KB     |            |   0% 
pathspec-0.10.3      | 37 KB     | ########## | 100% 

schema-salad-8.3.202 | 847 KB    |            |   0% 
schema-salad-8.3.202 | 847 KB    | 1          |   2% 
schema-salad-8.3.202 | 847 KB    | ########## | 100% 
schema-salad-8.3.202 | 847 KB    | ########## | 100% 

pyopenssl-23.0.0     | 124 KB    |            |   0% 
pyopenssl-23.0.0     | 124 KB    | ########## | 100% 

cwl-utils-0.19       | 136 KB    |            |   0% 
cwl-utils-0.19       | 136 KB    | #1         |  12% 
cwl-utils-0.19       | 136 KB    | ########## | 100% 

bagit-1.8.1          | 25 KB     |            |   0% 
bagit-1.8.1          | 25 KB     | ########## | 100% 

jpeg-9e              | 260 KB    |            |   0% 
jpeg-9e              | 260 KB    | ########## | 100% 

typing_extensions-4. | 29 KB     |            |   0% 
typing_extensions-4. | 29 KB     | ########## | 100% 

libxml2-2.10.3       | 672 KB    |            |   0% 
libxml2-2.10.3       | 672 KB    | ########## | 100% 
libxml2-2.10.3       | 672 KB    | ########## | 100% 

charset-normalizer-2 | 36 KB     |            |   0% 
charset-normalizer-2 | 36 KB     | ########## | 100% 

psutil-5.9.4         | 358 KB    |            |   0% 
psutil-5.9.4         | 358 KB    | ########## | 100% 
psutil-5.9.4         | 358 KB    | ########## | 100% 

webencodings-0.5.1   | 12 KB     |            |   0% 
webencodings-0.5.1   | 12 KB     | ########## | 100% 

icu-70.1             | 13.1 MB   |            |   0% 
icu-70.1             | 13.1 MB   | #####6     |  56% 
icu-70.1             | 13.1 MB   | ########## | 100% 

libwebp-base-1.2.4   | 385 KB    |            |   0% 
libwebp-base-1.2.4   | 385 KB    | ########## | 100% 

lockfile-0.12.2      | 11 KB     |            |   0% 
lockfile-0.12.2      | 11 KB     | ########## | 100% 

cffi-1.14.6          | 219 KB    |            |   0% 
cffi-1.14.6          | 219 KB    | 7          |   7% 
cffi-1.14.6          | 219 KB    | ########## | 100% 

brotlipy-0.7.0       | 367 KB    |            |   0% 
brotlipy-0.7.0       | 367 KB    | ########## | 100% 

libpng-1.6.39        | 265 KB    |            |   0% 
libpng-1.6.39        | 265 KB    | ########## | 100% 
libpng-1.6.39        | 265 KB    | ########## | 100% 

certifi-2022.12.7    | 147 KB    |            |   0% 
certifi-2022.12.7    | 147 KB    | ########## | 100% 
certifi-2022.12.7    | 147 KB    | ########## | 100% 

lxml-4.9.2           | 1.2 MB    |            |   0% 
lxml-4.9.2           | 1.2 MB    | ########## | 100% 
lxml-4.9.2           | 1.2 MB    | ########## | 100% 

idna-3.4             | 55 KB     |            |   0% 
idna-3.4             | 55 KB     | ########## | 100% 

ruamel.yaml-0.17.21  | 173 KB    |            |   0% 
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pycparser-2.21       | 100 KB    |            |   0% 
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urllib3-1.26.13      | 108 KB    |            |   0% 
urllib3-1.26.13      | 108 KB    | ########## | 100% 
urllib3-1.26.13      | 108 KB    | ########## | 100% 

cachecontrol-0.12.11 | 24 KB     |            |   0% 
cachecontrol-0.12.11 | 24 KB     | ########## | 100% 

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

lerc-4.0.0           | 284 KB    |            |   0% 
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click-8.1.3          | 74 KB     |            |   0% 
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html5lib-1.1         | 89 KB     |            |   0% 
html5lib-1.1         | 89 KB     | ########## | 100% 

importlib-metadata-6 | 24 KB     |            |   0% 
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python_abi-3.8       | 4 KB      |            |   0% 
python_abi-3.8       | 4 KB      | ########## | 100% 

tomli-2.0.1          | 16 KB     |            |   0% 
tomli-2.0.1          | 16 KB     | ########## | 100% 

coloredlogs-15.0.1   | 40 KB     |            |   0% 
coloredlogs-15.0.1   | 40 KB     | ####       |  40% 
coloredlogs-15.0.1   | 40 KB     | ########## | 100% 

libiconv-1.17        | 1.3 MB    |            |   0% 
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libiconv-1.17        | 1.3 MB    | ########## | 100% 

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cwltool-3.1.20221201 | 1.6 MB    |            |   0% 
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cwltool-3.1.20221201 | 1.6 MB    | ########## | 100% 
cwltool-3.1.20221201 | 1.6 MB    | ########## | 100% 

black-22.10.0        | 231 KB    |            |   0% 
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argcomplete-1.12.3   | 34 KB     |            |   0% 
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prov-1.5.1           | 152 KB    |            |   0% 
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prov-1.5.1           | 152 KB    | ########## | 100% 

cwlformat-2022.02.18 | 14 KB     |            |   0% 
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humanfriendly-10.0   | 119 KB    |            |   0% 
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pydot-1.4.2          | 44 KB     |            |   0% 
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networkx-2.8.8       | 1.6 MB    |            |   0% 
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packaging-22.0       | 40 KB     |            |   0% 
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graphviz-2.42.3      | 7.1 MB    |            |   0% 
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graphviz-2.42.3      | 7.1 MB    | ###        |  31% 
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Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 22.11.1

Please update conda by running

    $ conda update -n base -c defaults conda


INFO /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.3/env_Rcwl/bin/cwltool 3.1.20221201130942
INFO Resolved '/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpTP75Uw/SharedData/ensembl_liftover_human_GRCh37_GRCh38.cwl' to 'file:///var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpTP75Uw/SharedData/ensembl_liftover_human_GRCh37_GRCh38.cwl'
INFO [job ensembl_liftover_human_GRCh37_GRCh38.cwl] /private/tmp/docker_tmpctwk2ez5$ bash \
    script.sh \
    human \
    GRCh37 \
    GRCh38
script.sh: line 12: wget: command not found
gzip: can't stat: GRCh37_to_GRCh38.chain.gz (GRCh37_to_GRCh38.chain.gz.gz): No such file or directory
WARNING [job ensembl_liftover_human_GRCh37_GRCh38.cwl] exited with status: 1
WARNING [job ensembl_liftover_human_GRCh37_GRCh38.cwl] completed permanentFail
WARNING Final process status is permanentFail
Quitting from lines 87-95 (ReUseData_data.Rmd) 
Error: processing vignette 'ReUseData_data.Rmd' failed with diagnostics:
HINT: The output file was not successfully generated. Please check the recipe (output globbing pattern, input parameters, parameter types, etc.)

--- failed re-building ‘ReUseData_data.Rmd’

--- re-building ‘ReUseData_recipe.Rmd’ using rmarkdown
INFO /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/Rcwl/1.15.3/env_Rcwl/bin/cwltool 3.1.20221201130942
INFO Resolved '/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpTP75Uw/SharedData/rcp_Hello_World!_outfile.cwl' to 'file:///var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/RtmpTP75Uw/SharedData/rcp_Hello_World%21_outfile.cwl'
INFO [job rcp_Hello_World%21_outfile.cwl] /private/tmp/docker_tmpzf_d4vfg$ bash \
    script.sh \
    'Hello World!' \
    outfile
INFO [job rcp_Hello_World%21_outfile.cwl] completed success
INFO Final process status is success
trying URL 'https://github.com/rworkflow/ReUseDataRecipe/archive/refs/heads/master.zip'
downloaded 17 KB

trying URL 'https://github.com/rworkflow/ReUseDataRecipe/archive/refs/heads/master.zip'
Content type 'application/zip' length 17833 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://github.com/rworkflow/ReUseDataRecipe/archive/refs/heads/master.zip'
Content type 'application/zip' length 17833 bytes (17 KB)
==================================================
downloaded 17 KB

Quitting from lines 266-267 (ReUseData_recipe.Rmd) 
Error: processing vignette 'ReUseData_recipe.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘ReUseData_recipe.Rmd’

SUMMARY: processing the following files failed:
  ‘ReUseData_data.Rmd’ ‘ReUseData_recipe.Rmd’

Error: Vignette re-building failed.
Execution halted


                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
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merida1 BUILD BIN output
 
                    			
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