Last updated on 2026-05-12 13:52:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.20 | 12.63 | 236.63 | 249.26 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.20 | 8.51 | 183.30 | 191.81 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.20 | 22.00 | 380.63 | 402.63 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.20 | 20.00 | 396.15 | 416.15 | OK | |
| r-devel-windows-x86_64 | 0.1.20 | 18.00 | 369.00 | 387.00 | OK | |
| r-patched-linux-x86_64 | 0.1.20 | 13.55 | 226.72 | 240.27 | OK | |
| r-release-linux-x86_64 | 0.1.20 | 10.78 | 226.16 | 236.94 | OK | |
| r-release-macos-arm64 | 0.1.20 | 3.00 | 78.00 | 81.00 | OK | |
| r-release-macos-x86_64 | 0.1.20 | 9.00 | 309.00 | 318.00 | OK | |
| r-release-windows-x86_64 | 0.1.20 | 18.00 | 368.00 | 386.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.20 | 3.00 | 84.00 | 87.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.20 | 10.00 | 616.00 | 626.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.20 | 21.00 | 411.00 | 432.00 | OK |
Version: 0.1.20
Check: tests
Result: ERROR
Running ‘testthat.R’ [48s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(worcs)
Welcome to WORCS: Workflow for Open Reproducible Code in Science. Run `check_worcs_installation()` to make sure all dependencies are installed. For more information, see the package vignettes (<https://cjvanlissa.github.io/worcs/articles>) and accompanying paper: Van Lissa and colleagues (2020) (<https://doi.org/10.3233/DS-210031>)
>
> test_check("worcs")
v Creating manuscript files.
v Creating manuscript files.
v Creating manuscript files.
v Creating preregistration files.
v Creating preregistration files.
v Creating manuscript files.
v Creating manuscript files.
v Creating manuscript files.
v Creating manuscript files.
v Creating manuscript files.
[1] "_targets.Rmd" "references.bib"
Linking to libgit2 v1.9.2, ssh support: YES
Global config: /home/hornik/.gitconfig
Default user: yourname <yourname@email.com>
v Setting active project to "/tmp/RtmpNjksyc/aaa1473cf32bbe07e".
v Storing original data in 'dat.csv' and updating the checksum in '.worcs'.
v Updating '.gitignore'.
v Creating a codebook in 'codebook_dat.Rmd'.
processing file: manuscript.Rmd
output file: manuscript.knit.md
/usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md
/usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --syntax-highlighting pygments --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax
Preview created: manuscript.html
Output created: manuscript.md
v Setting active project to "<no active project>".
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
processing file: test.Rmd
output file: test.knit.md
Preview created: test.html
Output created: test.md
v Storing original data in 'iris.csv' and updating the checksum in '.worcs'.
v Updating '.gitignore'.
v Creating a codebook in 'codebook_iris.Rmd'.
v Storing value labels in 'value_labels_iris.yml'.
v Loading original data from 'iris.csv'.
v Loading original data from 'iris.csv'.
v Loading original data from 'iris.csv'.
v Loading original data from 'iris.csv'.
x Checksum for file '/tmp/RtmpNjksyc/saveload/iris.csv' did not match the
checksum on record (in '.worcs'). This means that the file has changed since
the checksum was stored.
v Loading original data from 'iris.csv'.
v Storing original data in 'iris.csv' and updating the checksum in '.worcs'.
v Generating synthetic data for public use. Ensure that no identifying
information is included.
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
v Storing value labels in 'value_labels_iris.yml'.
v Loading original data from 'iris.csv'.
v Loading synthetic data from 'synthetic_iris.csv'.
v Storing original data in 'iris.csv' and updating the checksum in '.worcs'.
v Updating '.gitignore'.
v Storing value labels in 'value_labels_iris.yml'.
v Storing original data in 'iris.csv' and updating the checksum in '.worcs'.
v Updating '.gitignore'.
v Creating a codebook in 'codebook_iris.Rmd'.
v Storing value labels in 'value_labels_iris.yml'.
v Storing original data in 'cars.csv' and updating the checksum in '.worcs'.
v Generating synthetic data for public use. Ensure that no identifying
information is included.
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
v Creating a codebook in 'codebook_cars.Rmd'.
v Loading original data from 'iris.csv'.
v Loading synthetic data from 'synthetic_cars.csv'.
v Loading original data from 'iris.csv'.
v Loading synthetic data from 'synthetic_cars.csv'.
v Storing original data in 'df.csv' and updating the checksum in '.worcs'.
v Generating synthetic data for public use. Ensure that no identifying
information is included.
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
v Storing value labels in 'value_labels_df.yml'.
v Setting active project to "/tmp/RtmpNjksyc/savedat21473cf615e768d".
v Creating manuscript files.
v Storing original data in 'df1.csv' and updating the checksum in '.worcs'.
v Generating synthetic data for public use. Ensure that no identifying
information is included.
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
v Creating a codebook in 'codebook_df1.Rmd'.
v Storing original data in 'df2.csv' and updating the checksum in '.worcs'.
v Generating synthetic data for public use. Ensure that no identifying
information is included.
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
v Creating a codebook in 'codebook_df2.Rmd'.
v Setting active project to "<no active project>".
v Setting active project to "/tmp/RtmpNjksyc/aaa1473cf1ddb55f8".
v Adding recipe to '.worcs'.
v Creating first commit (committing README.md).
v Setting active project to "/tmp/RtmpNjksyc/zip".
v Setting active project to "/tmp/RtmpNjksyc/aaa1473cf1ddb55f8".
v Setting active project to "<no active project>".
v Adding recipe to '.worcs'.
v Adding recipe to '.worcs'.
'Rscript' should not be used without a path -- see par. 1.6 of the manual
v Storing original data in 'dat.dat' and updating the checksum in '.worcs'.
v Updating '.gitignore'.
v Storing value labels in 'value_labels_dat.yml'.
v Loading original data from 'dat.dat'.
x No valid codebook found.
v Loading original data from 'dat.dat'.
x No valid codebook found.
v Loading original data from 'dat.dat'.
x No valid codebook found.
v Loading original data from 'dat.dat'.
x No valid codebook found.
x Checksum for file '/tmp/RtmpNjksyc/save_expression/dat.dat' did not match the
checksum on record (in '.worcs'). This means that the file has changed since
the checksum was stored.
v Loading original data from 'dat.dat'.
x No valid codebook found.
v Storing original data in 'dat.dat' and updating the checksum in '.worcs'.
v Generating synthetic data for public use. Ensure that no identifying
information is included.
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
i Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Storing synthetic data in "fn_write_synth_rel" and updating the checksum in...
v Updating '.gitignore'.
v Storing value labels in 'value_labels_dat.yml'.
v Loading original data from 'dat.dat'.
x No valid codebook found.
v Loading synthetic data from 'synthetic_dat.dat'.
x No valid codebook found.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
v Synthetic variable 'Seed' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
v Synthetic variable 'Assault' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'UrbanPop' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|====== | 8%
|
|============ | 17%
|
|================== | 25%
|
|======================= | 33%
|
|============================= | 42%
|
|=================================== | 50%
|
|========================================= | 58%
|
|=============================================== | 67%
|
|==================================================== | 75%
|
|========================================================== | 83%
|
|================================================================ | 92%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|========== | 14%
|
|==================== | 29%
|
|============================== | 43%
|
|======================================== | 57%
|
|================================================== | 71%
|
|============================================================ | 86%
|
|======================================================================| 100%
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
x Argument 'data' has missing values, but no 'missingness_expression' is
specified. Listwise deletion is used.
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
v Synthetic variable 'Solar.R' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'Temp' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'Month' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'Day' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|========= | 12%
|
|================== | 25%
|
|========================== | 38%
|
|=================================== | 50%
|
|============================================ | 62%
|
|==================================================== | 75%
|
|============================================================= | 88%
|
|======================================================================| 100%
x Argument 'data' has missing values, but no 'missingness_expression' is
specified. Listwise deletion is used.
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|========== | 14%
|
|==================== | 29%
|
|============================== | 43%
|
|======================================== | 57%
|
|================================================== | 71%
|
|============================================================ | 86%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
v Synthetic variable 'Freq' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
v Synthetic variable 'alcgp' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'tobgp' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|====== | 9%
|
|============= | 18%
|
|=================== | 27%
|
|========================= | 36%
|
|================================ | 45%
|
|====================================== | 55%
|
|============================================= | 64%
|
|=================================================== | 73%
|
|========================================================= | 82%
|
|================================================================ | 91%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
v Synthetic variable 'y' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
v Synthetic variable 'freeny.y' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|========= | 12%
|
|================== | 25%
|
|========================== | 38%
|
|=================================== | 50%
|
|============================================ | 62%
|
|==================================================== | 75%
|
|============================================================= | 88%
|
|======================================================================| 100%
v Synthetic variable 'stratum' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|========== | 14%
|
|==================== | 29%
|
|============================== | 43%
|
|======================================== | 57%
|
|================================================== | 71%
|
|============================================================ | 86%
|
|======================================================================| 100%
v Synthetic variable 'Year' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
v Synthetic variable 'Run' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'Speed' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|====== | 9%
|
|============= | 18%
|
|=================== | 27%
|
|========================= | 36%
|
|================================ | 45%
|
|====================================== | 55%
|
|============================================= | 64%
|
|=================================================== | 73%
|
|========================================================= | 82%
|
|================================================================ | 91%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
v Synthetic variable 'depth' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
v Synthetic variable 'stations' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|========= | 12%
|
|================== | 25%
|
|========================== | 38%
|
|=================================== | 50%
|
|============================================ | 62%
|
|==================================================== | 75%
|
|============================================================= | 88%
|
|======================================================================| 100%
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
v Synthetic variable 'Examination' did not have identical classes to its
original counterpart. Attempted to convert to its original type. Check the
input types of your variables, and check whether the data are synthesized
correctly.
v Synthetic variable 'Education' did not have identical classes to its original
counterpart. Attempted to convert to its original type. Check the input types
of your variables, and check whether the data are synthesized correctly.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|= | 2%
|
|== | 3%
|
|=== | 5%
|
|===== | 7%
|
|====== | 8%
|
|======= | 10%
|
|======== | 11%
|
|========= | 13%
|
|========== | 15%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 21%
|
|================ | 23%
|
|================= | 25%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 31%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 38%
|
|============================ | 39%
|
|============================= | 41%
|
|============================== | 43%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================= | 48%
|
|================================== | 49%
|
|==================================== | 51%
|
|===================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|======================================== | 57%
|
|========================================= | 59%
|
|========================================== | 61%
|
|============================================ | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 69%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|====================================================== | 77%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 85%
|
|============================================================= | 87%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|=================================================================== | 95%
|
|==================================================================== | 97%
|
|===================================================================== | 98%
|
|======================================================================| 100%
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
v Creating manuscript files.
v Adding recipe to '.worcs'.
v Wrote _targets.R
v Added targets to project.
v Setting recipe to targets::tar_make().
v Adding rmarkdown manuscript to targets pipeline.
v Adding targets to rmarkdown manuscript.
v Creating directory './R/' for targets scripts.
v Initializing 'targets' for a Make-like pipeline.
+ data dispatched
✔ data completed [12ms, 1.74 kB]
+ model dispatched
✔ model completed [3ms, 107 B]
+ manuscript dispatched
Quitting from manuscript.Rmd:9-24 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/tar_condition_validate>
Error:
! targets data store ../_targets not found. Utility functions like tar_read() and tar_load() require a pre-existing targets data store (default: _targets/) created by tar_make(), tar_make_clustermq(), or tar_make_future(). Details: https://books.ropensci.org/targets/data.html
---
Backtrace:
▆
1. └─targets::tar_load(model)
2. └─targets::tar_assert_store(store = store)
3. └─targets::tar_assert_path(...)
4. └─targets::tar_throw_validate(...)
5. └─targets::tar_error(...)
6. └─rlang::abort(message = message, class = class, call = tar_envir_base)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
✖ manuscript errored
✖ errored pipeline [2.7s, 2 completed, 0 skipped]
processing file: manuscript.Rmd
output file: manuscript.knit.md
/usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md --citeproc
/usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --syntax-highlighting pygments --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax
Preview created: manuscript.html
Output created: manuscript.md
# Created by use_targets(). # Follow the comments below to fill in this target script. # Then follow the manual to check and run the pipeline: # https://books.ropensci.org/targets/walkthrough.html#inspect-the-pipeline # Load packages required to define the pipeline: library(targets) # library(tarchetypes) # Load other packages as needed. # Set target options: tar_option_set( packages = c("tibble") # Packages that your targets need for their tasks. # format = "qs", # Optionally set the default storage format. qs is fast. # # Pipelines that take a long time to run may benefit from # optional distributed computing. To use this capability # in tar_make(), supply a {crew} controller # as discussed at https://books.ropensci.org/targets/crew.html. # Choose a controller that suits your needs. For example, the following # sets a controller that scales up to a maximum of two workers # which run as local R processes. Each worker launches when there is work # to do and exits if 60 seconds pass with no tasks to run. # # controller = crew::crew_controller_local(workers = 2, seconds_idle = 60) # # Alternatively, if you want workers to run on a high-performance computing # cluster, select a controller from the {crew.cluster} package. # For the cloud, see plugin packages like {crew.aws.batch}. # The following example is a controller for Sun Grid Engine (SGE). # # controller = crew.cluster::crew_controller_sge( # # Number of workers that the pipeline can scale up to: # workers = 10, # # It is recommended to set an idle time so workers can shut themselves # # down if they are not running tasks. # seconds_idle = 120, # # Many clusters install R as an environment module, and you can load it # # with the script_lines argument. To select a specific verison of R, # # you may need to include a version string, e.g. "module load R/4.3.2". # # Check with your system administrator if you are unsure. # script_lines = "module load R" # ) # # Set other options as needed. ) # Run the R scripts in the R/ folder with your custom functions: tar_source() # tar_source("other_functions.R") # Source other scripts as needed. # Replace the target list below with your own: list( tar_target( name = data, command = tibble(x = rnorm(100), y = rnorm(100)) # format = "qs" # Efficient storage for general data objects. ), tar_target( name = model, command = coefficients(lm(y ~ x, data = data)) ), tarchetypes::tar_render(manuscript, "manuscript/manuscript.Rmd", cue = tar_cue(mode = 'always')) )[1] "_targets.yaml" "manuscript.Rmd" "manuscript.md" "manuscript_files"
[5] "references.bib"
+ data dispatched
✔ data completed [11ms, 1.74 kB]
+ model dispatched
✔ model completed [3ms, 107 B]
+ manuscript dispatched
✔ manuscript completed [2.8s, 11.31 kB]
✔ ended pipeline [3s, 3 completed, 0 skipped]
v Creating manuscript files.
v Adding recipe to '.worcs'.
v Added targets to project.
v Setting recipe to targets::tar_make().
v Creating directory './R/' for targets scripts.
v Initializing 'targets' for a Make-like pipeline.
processing file: _targets.Rmd
output file: _targets.knit.md
/usr/bin/pandoc +RTS -K512m -RTS _targets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output _targets.html --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmd/h/default.html --syntax-highlighting none --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpNjksyc/rmarkdown-str1473cf6dd933cb.html --citeproc
Output created: _targets.html
Missing value imputation by random forests
Variables to impute: Sepal.Length, Petal.Length, Species, Petal.Width, Sepal.Width
Variables used to impute: Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species
iter 1
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
iter 2
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
iter 3
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
v Adding recipe to '.worcs'.
v Setting active project to "/tmp/RtmpNjksyc/file1473cf5c6a562e".
v Creating 'tests/testthat/'.
v Writing 'tests/testthat.R'.
[ ] Call `usethis::use_test()` to initialize a basic test file and open it for
editing.
i Updating 'tests/testthat.R'
v Updating 'tests/testthat.R' ... done
i You can run `add_endpoint('testthat')` to add the test suite as an endpoint,
and `github_action_testthat()` to add a GitHub action that evaluates the
integration tests, or `github_action_reproduce()` to reproduce the project
and then run the tests.
v Setting active project to "<no active project>".
processing file: manuscript.Rmd
output file: manuscript.knit.md
/usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.md --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/default.md --citeproc
/usr/bin/pandoc +RTS -K512m -RTS manuscript.md --to html4 --from gfm-tex_math_gfm --output manuscript.html --embed-resources --standalone --syntax-highlighting pygments --template /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax
Preview created: manuscript.html
Output created: manuscript.md
v Setting active project to "/tmp/RtmpNjksyc/file1473cf5c6a562e".
i Loading 'tests/testthat.R'
v Loading 'tests/testthat.R' ... done
v | F W S OK | Context
/ | 0 | mytest
v | 1 | mytest
== Results =====================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
v Setting active project to "<no active project>".
v Setting active project to "/tmp/RtmpNjksyc/file1473cf5c6a562e".
i Loading 'tests/testthat.R'
v Loading 'tests/testthat.R' ... done
v | F W S OK | Context
/ | 0 | mytest
v | 1 | mytest
== Results =====================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
v Setting active project to "<no active project>".
v Setting active project to "/tmp/RtmpNjksyc/aaa1473cf15b239ab".
v Creating manuscript files.
v Adding recipe to '.worcs'.
v Creating preregistration files.
v Creating first commit (committing README.md).
v Setting active project to "<no active project>".
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 191 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-boilerplate_in_manuscript.R:34:1',
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-can_clone.R:10:3'): gert can clone repos ───────────────────────
<GIT_ERROR/libgit2_error/error/condition>
Error in `libgit2::git_clone`: SSL error: syscall failure: Connection reset by peer
Backtrace:
▆
1. ├─gert::git_clone(...) at test-can_clone.R:10:3
2. └─gert:::raise_libgit2_error(...)
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 191 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc