Last updated on 2024-07-27 05:49:35 CEST.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 0.1.1 | 6.28 | 1050.91 | 1057.19 | ERROR | |
r-devel-linux-x86_64-debian-gcc | 0.1.1 | ERROR | ||||
r-devel-linux-x86_64-fedora-clang | 0.1.1 | 1113.18 | ERROR | |||
r-devel-linux-x86_64-fedora-gcc | 0.1.2 | 1182.00 | OK | |||
r-devel-windows-x86_64 | 0.1.2 | 8.00 | 647.00 | 655.00 | OK | |
r-patched-linux-x86_64 | 0.1.1 | ERROR | ||||
r-release-linux-x86_64 | 0.1.1 | 3.64 | 971.64 | 975.28 | ERROR | |
r-release-macos-arm64 | 0.1.2 | 195.00 | OK | |||
r-release-macos-x86_64 | 0.1.2 | 408.00 | OK | |||
r-release-windows-x86_64 | 0.1.1 | 7.00 | 683.00 | 690.00 | ERROR | |
r-oldrel-macos-arm64 | 0.1.1 | 357.00 | ERROR | |||
r-oldrel-macos-x86_64 | 0.1.2 | 13.00 | ERROR | |||
r-oldrel-windows-x86_64 | 0.1.1 | 7.00 | 928.00 | 935.00 | ERROR |
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14573 bytes
Input file size = 14663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
Output IDAT size = 12889 bytes (1684 bytes decrease)
Output file size = 12967 bytes (1696 bytes = 11.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6402 bytes
Input file size = 7248 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
Output IDAT size = 4816 bytes (1586 bytes decrease)
Output file size = 4894 bytes (2354 bytes = 32.48% decrease)
--- finished re-building ‘a01_Introduction.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘a02_Generate_a_sequence_cohort_set.Rmd’
‘a03_Summarise_sequence_ratios.Rmd’
‘a04_Visualise_sequence_ratios.Rmd’
‘a05_Summarise_temporal_symmetry.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14573 bytes
Input file size = 14663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
Output IDAT size = 12889 bytes (1684 bytes decrease)
Output file size = 12967 bytes (1696 bytes = 11.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6402 bytes
Input file size = 7248 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
Output IDAT size = 4816 bytes (1586 bytes decrease)
Output file size = 4894 bytes (2354 bytes = 32.48% decrease)
--- finished re-building ‘a01_Introduction.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘a02_Generate_a_sequence_cohort_set.Rmd’
‘a03_Summarise_sequence_ratios.Rmd’
‘a04_Visualise_sequence_ratios.Rmd’
‘a05_Summarise_temporal_symmetry.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14573 bytes
Input file size = 14663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
Output IDAT size = 12889 bytes (1684 bytes decrease)
Output file size = 12967 bytes (1696 bytes = 11.57% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6402 bytes
Input file size = 7248 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
Output IDAT size = 4816 bytes (1586 bytes decrease)
Output file size = 4894 bytes (2354 bytes = 32.48% decrease)
--- finished re-building ‘a01_Introduction.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘a02_Generate_a_sequence_cohort_set.Rmd’
‘a03_Summarise_sequence_ratios.Rmd’
‘a04_Visualise_sequence_ratios.Rmd’
‘a05_Summarise_temporal_symmetry.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14573 bytes
Input file size = 14663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
Output IDAT size = 12889 bytes (1684 bytes decrease)
Output file size = 12967 bytes (1696 bytes = 11.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6402 bytes
Input file size = 7248 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
Output IDAT size = 4816 bytes (1586 bytes decrease)
Output file size = 4894 bytes (2354 bytes = 32.48% decrease)
--- finished re-building ‘a01_Introduction.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘a02_Generate_a_sequence_cohort_set.Rmd’
‘a03_Summarise_sequence_ratios.Rmd’
‘a04_Visualise_sequence_ratios.Rmd’
‘a05_Summarise_temporal_symmetry.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14573 bytes
Input file size = 14663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
Output IDAT size = 12889 bytes (1684 bytes decrease)
Output file size = 12967 bytes (1696 bytes = 11.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6402 bytes
Input file size = 7248 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
Output IDAT size = 4816 bytes (1586 bytes decrease)
Output file size = 4894 bytes (2354 bytes = 32.48% decrease)
--- finished re-building ‘a01_Introduction.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘a02_Generate_a_sequence_cohort_set.Rmd’
‘a03_Summarise_sequence_ratios.Rmd’
‘a04_Visualise_sequence_ratios.Rmd’
‘a05_Summarise_temporal_symmetry.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a01_Introduction.Rmd' using rmarkdown
--- finished re-building 'a01_Introduction.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a02_Generate_a_sequence_cohort_set.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building 'a02_Generate_a_sequence_cohort_set.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a03_Summarise_sequence_ratios.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building 'a03_Summarise_sequence_ratios.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a04_Visualise_sequence_ratios.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building 'a04_Visualise_sequence_ratios.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a05_Summarise_temporal_symmetry.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building 'a05_Summarise_temporal_symmetry.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building 'a06_Visualise_temporal_symmetry.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building 'a06_Visualise_temporal_symmetry.Rmd'
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
'a02_Generate_a_sequence_cohort_set.Rmd'
'a03_Summarise_sequence_ratios.Rmd'
'a04_Visualise_sequence_ratios.Rmd'
'a05_Summarise_temporal_symmetry.Rmd'
'a06_Visualise_temporal_symmetry.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.1.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a01_Introduction.Rmd’
...
> library(here)
here() starts at /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmp5Qaben/filed8514dde3f85/vignettes
> knitr::include_graphics(here("vignettes/workflow.png"))
When sourcing ‘a01_Introduction.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmp5Qaben/filed8514dde3f85/vignettes/vignettes/workflow.png"
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘a02_Generate_a_sequence_cohort_set.Rmd’
...
> library(here)
here() starts at /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmpgjp3Qq/fileda3d2f6ad03b/vignettes
> knitr::include_graphics(here("vignettes/1-NoRestrictions.png"))
When sourcing ‘a02_Generate_a_sequence_cohort_set.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmpgjp3Qq/fileda3d2f6ad03b/vignettes/vignettes/1-NoRestrictions.png"
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘a01_Introduction.Rmd’ using ‘UTF-8’... failed
‘a02_Generate_a_sequence_cohort_set.Rmd’ using ‘UTF-8’... failed
‘a03_Summarise_sequence_ratios.Rmd’ using ‘UTF-8’... [12s/13s] OK
‘a04_Visualise_sequence_ratios.Rmd’ using ‘UTF-8’... [13s/14s] OK
‘a05_Summarise_temporal_symmetry.Rmd’ using ‘UTF-8’... [11s/11s] OK
‘a06_Visualise_temporal_symmetry.Rmd’ using ‘UTF-8’... [12s/14s] OK
Flavor: r-oldrel-macos-arm64
Version: 0.1.2
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘CodelistGenerator’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64