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D4TAlink.light

GDP - Workflow Management

v2.1.21 · Sep 10, 2025 · GPL-3
CRAN GitHub Mirror

Description

Tools, methods and processes for the management of analysis workflows. These lightweight solutions facilitate structuring R&D activities. These solutions were developed to comply with Good Documentation Practice (GDP), with ALCOA+ principles as proposed by the U.S. FDA, and with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.

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r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc OK
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r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 ERROR
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 ERROR
r-oldrel-macos-x86_64 ERROR
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
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r-release-windows-x86_64 OK
Check details (14 non-OK)
OK r-devel-linux-x86_64-debian-clang

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                OK
                r-devel-linux-x86_64-debian-gcc
              

              
*

              

            

            

              

                OK
                r-devel-linux-x86_64-fedora-clang
              

              
*

              

            

            

              

                OK
                r-devel-linux-x86_64-fedora-gcc
              

              
*

              

            

            

              

                ERROR
                r-devel-macos-arm64
              

              
tests

              
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260213_myTask.Rmd
  output file: 20260213_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260213_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/Rtmp06XCdC/filec70c2c3fbc3/MySponsor/myProject/myPackage/docs/20260213_myTask.docx --lua-filter /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/officedown/examples/bookdown/template.docx 
  
  Output created: /Volumes/Temp/tmp/Rtmp06XCdC/filec70c2c3fbc3/MySponsor/myProject/myPackage/docs/20260213_myTask.docx
  
  
  processing file: 20260213_myTask.Rmd
  output file: 20260213_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260213_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/Rtmp06XCdC/filec70c2c3fbc3/MySponsor/myProject/myPackage/docs/20260213_myTask.docx --lua-filter /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/sonoma-arm64/results/4.6/D4TAlink.light.Rcheck/D4TAlink.light/template/SQU4REtemplate.docx 
  
  Output created: /Volumes/Temp/tmp/Rtmp06XCdC/filec70c2c3fbc3/MySponsor/myProject/myPackage/docs/20260213_myTask.docx
  updating: word/footer1.xml
  	zip warning: Local Entry CRC does not match CD: word/footer1.xml
   (deflated 75%)
  updating: word/header1.xml (deflated 88%)
  Saving _problems/test01-68.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.R:68:3'): (code run outside of `test_that()`) ────────────────
  Error in `find_quarto()`: Quarto command-line tools path not found!
  Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable.
  Backtrace:
      ▆
   1. └─D4TAlink.light::renderTaskQmd(task) at test01.R:68:3
   2.   └─quarto::quarto_render(...)
   3.     └─quarto:::find_quarto()
   4.       └─cli::cli_abort(quarto_not_found_msg)
   5.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted

            

            

              

                OK
                r-devel-windows-x86_64
              

              
*

              

            

            

              

                ERROR
                r-oldrel-macos-arm64
              

              
tests

              
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260310_myTask.Rmd
  2026-03-10 03:21:41.608 R[75888:419463] XType: Using static font registry.
  output file: 20260310_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260310_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpmFtNuX/file1287025eef95/MySponsor/myProject/myPackage/docs/20260310_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/officedown/examples/bookdown/template.docx 
  
  Output created: /Volumes/Temp/tmp/RtmpmFtNuX/file1287025eef95/MySponsor/myProject/myPackage/docs/20260310_myTask.docx
  
  
  processing file: 20260310_myTask.Rmd
  output file: 20260310_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260310_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpmFtNuX/file1287025eef95/MySponsor/myProject/myPackage/docs/20260310_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-arm64/results/4.4/D4TAlink.light.Rcheck/D4TAlink.light/template/SQU4REtemplate.docx 
  
  Output created: /Volumes/Temp/tmp/RtmpmFtNuX/file1287025eef95/MySponsor/myProject/myPackage/docs/20260310_myTask.docx
  updating: word/footer1.xml
  	zip warning: Local Entry CRC does not match CD: word/footer1.xml
   (deflated 75%)
  updating: word/header1.xml (deflated 88%)
  Saving _problems/test01-68.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.R:68:3'): (code run outside of `test_that()`) ────────────────
  Error in `find_quarto()`: Quarto command-line tools path not found!
  Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable.
  Backtrace:
      ▆
   1. └─D4TAlink.light::renderTaskQmd(task) at test01.R:68:3
   2.   └─quarto::quarto_render(...)
   3.     └─quarto:::find_quarto()
   4.       └─cli::cli_abort(quarto_not_found_msg)
   5.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted

            

            

              

                ERROR
                r-oldrel-macos-x86_64
              

              
tests

              
  Running ‘testthat.R’ [16s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260305_myTask.Rmd
  output file: 20260305_myTask.knit.md
  
  /opt/R/x86_64/bin/pandoc +RTS -K512m -RTS 20260305_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpAl7Cuw/filebc775e89de71/MySponsor/myProject/myPackage/docs/20260305_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/officedown/examples/bookdown/template.docx 
  
  Output created: /Volumes/Temp/tmp/RtmpAl7Cuw/filebc775e89de71/MySponsor/myProject/myPackage/docs/20260305_myTask.docx
  
  
  processing file: 20260305_myTask.Rmd
  output file: 20260305_myTask.knit.md
  
  /opt/R/x86_64/bin/pandoc +RTS -K512m -RTS 20260305_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpAl7Cuw/filebc775e89de71/MySponsor/myProject/myPackage/docs/20260305_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.4/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-x86_64/results/4.4/D4TAlink.light.Rcheck/D4TAlink.light/template/SQU4REtemplate.docx 
  
  Output created: /Volumes/Temp/tmp/RtmpAl7Cuw/filebc775e89de71/MySponsor/myProject/myPackage/docs/20260305_myTask.docx
  updating: word/footer1.xml
  	zip warning: Local Entry CRC does not match CD: word/footer1.xml
   (deflated 75%)
  updating: word/header1.xml (deflated 88%)
  Saving _problems/test01-68.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.R:68:3'): (code run outside of `test_that()`) ────────────────
  Error in `find_quarto()`: Quarto command-line tools path not found!
  Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable.
  Backtrace:
      ▆
   1. └─D4TAlink.light::renderTaskQmd(task) at test01.R:68:3
   2.   └─quarto::quarto_render(...)
   3.     └─quarto:::find_quarto()
   4.       └─cli::cli_abort(quarto_not_found_msg)
   5.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted

            

            

              

                OK
                r-oldrel-windows-x86_64
              

              
*

              

            

            

              

                OK
                r-patched-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-linux-x86_64
              

              
*

              

            

            

              

                ERROR
                r-release-macos-arm64
              

              
tests

              
  Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260310_myTask.Rmd
  2026-03-10 03:32:43.955 R[54400:848092] XType: Using static font registry.
  output file: 20260310_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260310_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/Rtmpcgc7Bb/filed48063944119/MySponsor/myProject/myPackage/docs/20260310_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/officedown/examples/bookdown/template.docx 
  
  Output created: /Volumes/Temp/tmp/Rtmpcgc7Bb/filed48063944119/MySponsor/myProject/myPackage/docs/20260310_myTask.docx
  
  
  processing file: 20260310_myTask.Rmd
  output file: 20260310_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260310_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/Rtmpcgc7Bb/filed48063944119/MySponsor/myProject/myPackage/docs/20260310_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-arm64/results/4.5/D4TAlink.light.Rcheck/D4TAlink.light/template/SQU4REtemplate.docx 
  
  Output created: /Volumes/Temp/tmp/Rtmpcgc7Bb/filed48063944119/MySponsor/myProject/myPackage/docs/20260310_myTask.docx
  updating: word/footer1.xml
  	zip warning: Local Entry CRC does not match CD: word/footer1.xml
   (deflated 75%)
  updating: word/header1.xml (deflated 88%)
  Saving _problems/test01-68.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.R:68:3'): (code run outside of `test_that()`) ────────────────
  Error in `find_quarto()`: Quarto command-line tools path not found!
  Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable.
  Backtrace:
      ▆
   1. └─D4TAlink.light::renderTaskQmd(task) at test01.R:68:3
   2.   └─quarto::quarto_render(...)
   3.     └─quarto:::find_quarto()
   4.       └─cli::cli_abort(quarto_not_found_msg)
   5.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted

            

            

              

                ERROR
                r-release-macos-x86_64
              

              
tests

              
  Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260305_myTask.Rmd
  output file: 20260305_myTask.knit.md
  
  /opt/R/x86_64/bin/pandoc +RTS -K512m -RTS 20260305_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpQmflZp/filebdeb438b9ce9/MySponsor/myProject/myPackage/docs/20260305_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/officedown/examples/bookdown/template.docx 
  
  Output created: /Volumes/Temp/tmp/RtmpQmflZp/filebdeb438b9ce9/MySponsor/myProject/myPackage/docs/20260305_myTask.docx
  
  
  processing file: 20260305_myTask.Rmd
  output file: 20260305_myTask.knit.md
  
  /opt/R/x86_64/bin/pandoc +RTS -K512m -RTS 20260305_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpQmflZp/filebdeb438b9ce9/MySponsor/myProject/myPackage/docs/20260305_myTask.docx --lua-filter /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/rmarkdown/rmarkdown/lua/pagebreak.lua --table-of-contents --toc-depth 3 --highlight-style tango --reference-doc /Volumes/Builds/packages/big-sur-x86_64/results/4.5/D4TAlink.light.Rcheck/D4TAlink.light/template/SQU4REtemplate.docx 
  
  Output created: /Volumes/Temp/tmp/RtmpQmflZp/filebdeb438b9ce9/MySponsor/myProject/myPackage/docs/20260305_myTask.docx
  updating: word/footer1.xml
  	zip warning: Local Entry CRC does not match CD: word/footer1.xml
   (deflated 75%)
  updating: word/header1.xml (deflated 88%)
  Saving _problems/test01-68.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.R:68:3'): (code run outside of `test_that()`) ────────────────
  Error in `find_quarto()`: Quarto command-line tools path not found!
  Please make sure you have installed and added Quarto to your PATH or set the QUARTO_PATH environment variable.
  Backtrace:
      ▆
   1. └─D4TAlink.light::renderTaskQmd(task) at test01.R:68:3
   2.   └─quarto::quarto_render(...)
   3.     └─quarto:::find_quarto()
   4.       └─cli::cli_abort(quarto_not_found_msg)
   5.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error:
  ! Test failures.
  Execution halted

            

            

              

                OK
                r-release-windows-x86_64
              

              
*

              

            

          

        

      



      

      
      

        
Check History

        

          

            
              ERROR
              
                9 OK ·                 0 NOTE ·                 0 WARNING ·                 5 ERROR ·                 0 FAILURE              
              Mar 9, 2026
            
            

              

                

                  ERROR
                  r-devel-macos-arm64
                

                
tests

                
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260213_myTask.Rmd
  output file: 20260213_myTask.

              

              

                

                  ERROR
                  r-release-macos-arm64
                

                
tests

                
  Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260310_myTask.Rmd
  2026-03-10 03:32:43.955 R[544

              

              

                

                  ERROR
                  r-release-macos-x86_64
                

                
tests

                
  Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260305_myTask.Rmd
  output file: 20260305_myTas

              

              

                

                  ERROR
                  r-oldrel-macos-arm64
                

                
tests

                
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260310_myTask.Rmd
  2026-03-10 03:21:41.608 R[758

              

              

                

                  ERROR
                  r-oldrel-macos-x86_64
                

                
tests

                
  Running ‘testthat.R’ [16s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # See https://github.com/tidyverse/dplyr/blob/main/tests/
  > library(testthat)
  > library(D4TAlink.light)
  Loading required package: rjson
  Loading required package: DBI
  Loading required package: RSQLite
  Loading required package: openssl
  Linking to: OpenSSL 3.5.4 30 Sep 2025
  > 
  > test_check("D4TAlink.light")
  
  
  processing file: 20260305_myTask.Rmd
  output file: 20260305_myTas

              

            

          

        

      


      

      
      

        
Dependency Network

        

          
            

            
            
            Dependencies
            
            Reverse dependencies

            
            
            
            
            
            
            
            
            
            
            
            
            

            

            
            
              
              rjson
            
            
              
              DBI
            
            
              
              RSQLite
            
            
              
              openssl
            
            
              
              officedown
            
            
              
              rmarkdown
            
            
              
              quarto
            
            
              
              Biobase
            
            
              
              openxlsx
            
            
              
              reticulate
            
            
              
              feather
            
            
              
              getPass
            

            

            
            
            D4TAlink.light
          
        

      


      
      

        
Version History

        

          

            new
            2.1.21
            Mar 9, 2026