D4TAlink.light

GDP - Workflow Management

v2.1.21 · Sep 10, 2025 · GPL-3

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>.

Downloads

537

Last 30 days

7499th

1.4K

Last 90 days

4.6K

Last year

Trend: +6.6% (30d vs prior 30d)

CRAN Check Status

5 ERROR

9 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	180.3s
r-devel-linux-x86_64-debian-gcc	OK	127.9s
r-devel-linux-x86_64-fedora-clang	OK	275.9s
r-devel-linux-x86_64-fedora-gcc	OK	334.5s
r-devel-macos-arm64	ERROR	47s
r-devel-windows-x86_64	OK	197s
r-oldrel-macos-arm64	ERROR	51s
r-oldrel-macos-x86_64	ERROR	162s
r-oldrel-windows-x86_64	OK	239s
r-patched-linux-x86_64	OK	170.3s
r-release-linux-x86_64	OK	160.8s
r-release-macos-arm64	ERROR	53s
r-release-macos-x86_64	ERROR	162s
r-release-windows-x86_64	OK	191s

Check details (5 non-OK)

ERROR r-devel-macos-arm64

tests

Running ‘testthat.R’ [6s/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: 20260328_myTask.Rmd
  output file: 20260328_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260328_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/Rtmp9fvfb1/file1250613f2131d/MySponsor/myProject/myPackage/docs/20260328_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/bo
...[truncated]...
/tmp/Rtmp9fvfb1/file1250613f2131d/MySponsor/myProject/myPackage/docs/20260328_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-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: 20260323_myTask.Rmd
  2026-03-23 08:16:05.423 R[47853:364382] XType: Using static font registry.
  output file: 20260323_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260323_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpSUklxH/filebaed3f273578/MySponsor/myProject/myPackage/docs/20260323_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 --refere
...[truncated]...
p/tmp/RtmpSUklxH/filebaed3f273578/MySponsor/myProject/myPackage/docs/20260323_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/24s]
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: 20260401_myTask.Rmd
  output file: 20260401_myTask.knit.md
  
  /opt/R/x86_64/bin/pandoc +RTS -K512m -RTS 20260401_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmphYeNXi/file2be0b91a6d2/MySponsor/myProject/myPackage/docs/20260401_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/exampl
...[truncated]...
mp/tmp/RtmphYeNXi/file2be0b91a6d2/MySponsor/myProject/myPackage/docs/20260401_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-arm64

tests

Running ‘testthat.R’ [6s/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: 20260406_myTask.Rmd
  2026-04-06 10:56:44.486 R[53355:365411] XType: Using static font registry.
  output file: 20260406_myTask.knit.md
  
  /opt/R/arm64/bin/pandoc +RTS -K512m -RTS 20260406_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpLjuYjn/filed06b432fcbce/MySponsor/myProject/myPackage/docs/20260406_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 --refere
...[truncated]...
p/tmp/RtmpLjuYjn/filed06b432fcbce/MySponsor/myProject/myPackage/docs/20260406_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’ [17s/19s]
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: 20260401_myTask.Rmd
  output file: 20260401_myTask.knit.md
  
  /opt/R/x86_64/bin/pandoc +RTS -K512m -RTS 20260401_myTask.knit.md --to docx --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Volumes/Temp/tmp/RtmpgyU25t/file186084ba7deb7/MySponsor/myProject/myPackage/docs/20260401_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/exam
...[truncated]...
/tmp/RtmpgyU25t/file186084ba7deb7/MySponsor/myProject/myPackage/docs/20260401_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

Check History

ERROR 9 OK · 0 NOTE · 0 WARNING · 5 ERROR · 0 FAILURE Mar 10, 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 
...[truncated]...
8:3
   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-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 
...[truncated]...
8:3
   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
  Loadin
...[truncated]...
8:3
   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-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 
...[truncated]...
8:3
   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
  Loadin
...[truncated]...
8:3
   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

Dependency Network

Version History

new 2.1.21 Mar 10, 2026

updated 2.1.21 ← 2.1.18 diff Sep 10, 2025

updated 2.1.18 ← 2.1.17 diff Apr 1, 2025

updated 2.1.17 ← 2.1.14 diff Dec 1, 2024

updated 2.1.14 ← 2.1.11 diff Oct 3, 2023

updated 2.1.11 ← 2.1.9 diff Oct 21, 2022

updated 2.1.9 ← 2.1.8 diff Sep 15, 2022

updated 2.1.8 ← 2.1.7 diff Sep 14, 2022

updated 2.1.7 ← 2.1.5 diff Sep 4, 2022

new 2.1.5 Aug 25, 2022

Maintainer

Gregoire Thomas

Dependencies

Depends

R (>= 4.1.0) rjson DBI RSQLite openssl

Imports

officedown utils rmarkdown quarto Biobase openxlsx reticulate feather getPass

Suggests

knitr roxygen2 (>= 3.1.0) WriteXLS XLConnect xlsx testthat

Compilation

No compilation needed

First Published

Aug 25, 2022

RSS Feed

CRAN Checks

View on CRAN →