Adressing the r-opensci review #153

b-rodrigues · 2024-03-24T20:56:52Z

Let's push our commits to this branch

b-rodrigues · 2024-03-24T20:58:03Z

Still several things to deal with:

Several comments need answer not in code.

philipp-baumann · 2024-04-07T20:22:59Z

@b-rodrigues why is fusen putting arrow in imports? we have no code that states to do so, i'm confused.

philipp-baumann · 2024-04-07T20:23:51Z

also, we don't want dplyr.

b-rodrigues · 2024-04-08T07:10:07Z

@b-rodrigues why is fusen putting arrow in imports? we have no code that states to do so, i'm confused.

i’m not sure I follow what you mean, I’ve never seen arrow being added to the DESCRIPTION

philipp-baumann · 2024-04-12T13:10:20Z

@b-rodrigues I am using exactly the same version of {fusen}. Because of some hidden wizardry, it produces different DESCRIPTION.

> fusen::inflate_all_no_check()
✔ The flat file flat_available_R.Rmd is going to be inflated
✔ The flat file flat_cicd.Rmd is going to be inflated
✔ The flat file flat_cran_archive.Rmd is going to be inflated
✔ The flat file flat_data_doc.Rmd is going to be inflated
✔ The flat file flat_fetchers.Rmd is going to be inflated
✔ The flat file flat_find_rev.Rmd is going to be inflated
✔ The flat file flat_get_latest.Rmd is going to be inflated
✔ The flat file flat_get_os.Rmd is going to be inflated
✔ The flat file flat_get_sri_hash_deps.Rmd is going to be inflated
✔ The flat file flat_nix_build.Rmd is going to be inflated
✔ The flat file flat_rix_init.Rmd is going to be inflated
✔ The flat file flat_rix.Rmd is going to be inflated
✔ The flat file flat_with_nix.Rmd is going to be inflated
✔ The flat file flat_zzz.Rmd is going to be inflated
✔ The flat file a-getting_started.Rmd is going to be inflated
── config file for dev/b1-linux_win.Rmd ─────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/b2-macos.Rmd ─────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/c-building_envs_with_rix.Rmd ─────────────────────────────────────────────────────────────────────────────
── config file for dev/d1-install_r_pkgs.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/d2-install_sys_pkgs.Rmd ──────────────────────────────────────────────────────────────────────────────────
── config file for dev/e-interactive_use.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_available_R.Rmd ─────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_cicd.Rmd ────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_cran_archive.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_data_doc.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_fetchers.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_find_rev.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_get_latest.Rmd ──────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_get_os.Rmd ──────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_get_sri_hash_deps.Rmd ───────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_nix_build.Rmd ───────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_rix.Rmd ─────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_rix_init.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_with_nix.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_zzz.Rmd ─────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-inst_rix.Rmd ───────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-literate_programming.Rmd ───────────────────────────────────────────────────────────────────────────────
── config file for dev/z-pkgs_with_remotes.Rmd ──────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-raps_with_nix.Rmd ──────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-save_r_nix_revs.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-subshells.Rmd ──────────────────────────────────────────────────────────────────────────────────────────
── check not registered files ───────────────────────────────────────────────────────────────────────────────────────────────────
ℹ Some files in your package are not registered in the configuration file: dev/config_fusen.yaml
fusen uses a configuration file to store the structure of your package and help you clean it when needed.
You will find a list of unregistered files there: csv_file that you can open with `file.edit('dev/config_not_registered.csv')`
Delete unregistered files that you do not need anymore. Then run `fusen::register_all_to_config()`.
After that, this message should not appear in your next `fusen::inflate_all()` calls.
For more information, read `vignette('register-files-in-config (`vignette(fusen::register-files-in-config)`)', package = 'fusen')`
cli-62920-987
Documentation parameters were restored from attachment config file.
Updating rix documentation
Writing NAMESPACE
ℹ Loading rix
ℹ The package "arrow" is required.
✖ Would you like to install it?

1: Yes
2: No

Selection: 2
Warning message:
In readLines(path) :
  incomplete final line found on '/Users/philipp/git/philipp-baumann-shared/rix/R/_test.R'
> fusen::inflate_all_no_check()
✔ The flat file flat_available_R.Rmd is going to be inflated
✔ The flat file flat_cicd.Rmd is going to be inflated
✔ The flat file flat_cran_archive.Rmd is going to be inflated
✔ The flat file flat_data_doc.Rmd is going to be inflated
✔ The flat file flat_fetchers.Rmd is going to be inflated
✔ The flat file flat_find_rev.Rmd is going to be inflated
✔ The flat file flat_get_latest.Rmd is going to be inflated
✔ The flat file flat_get_os.Rmd is going to be inflated
✔ The flat file flat_get_sri_hash_deps.Rmd is going to be inflated
✔ The flat file flat_nix_build.Rmd is going to be inflated
✔ The flat file flat_rix_init.Rmd is going to be inflated
✔ The flat file flat_rix.Rmd is going to be inflated
✔ The flat file flat_with_nix.Rmd is going to be inflated
✔ The flat file flat_zzz.Rmd is going to be inflated
✔ The flat file a-getting_started.Rmd is going to be inflated
✔ The flat file b1-linux_win.Rmd is going to be inflated
✔ The flat file b2-macos.Rmd is going to be inflated
✔ The flat file c-building_envs_with_rix.Rmd is going to be inflated
✔ The flat file d1-install_r_pkgs.Rmd is going to be inflated
✔ The flat file d2-install_sys_pkgs.Rmd is going to be inflated
✔ The flat file e-interactive_use.Rmd is going to be inflated
✔ The flat file z-inst_rix.Rmd is going to be inflated
✔ The flat file z-literate_programming.Rmd is going to be inflated
✔ The flat file z-pkgs_with_remotes.Rmd is going to be inflated
✔ The flat file z-raps_with_nix.Rmd is going to be inflated
✔ The flat file z-save_r_nix_revs.Rmd is going to be inflated
✔ The flat file z-subshells.Rmd is going to be inflated
── config file for dev/a-getting_started.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/b1-linux_win.Rmd ─────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/b2-macos.Rmd ─────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/c-building_envs_with_rix.Rmd ─────────────────────────────────────────────────────────────────────────────
── config file for dev/d1-install_r_pkgs.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/d2-install_sys_pkgs.Rmd ──────────────────────────────────────────────────────────────────────────────────
── config file for dev/e-interactive_use.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_available_R.Rmd ─────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_cicd.Rmd ────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_cran_archive.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_data_doc.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_fetchers.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_find_rev.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_get_latest.Rmd ──────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_get_os.Rmd ──────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_get_sri_hash_deps.Rmd ───────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_nix_build.Rmd ───────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_rix.Rmd ─────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_rix_init.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_with_nix.Rmd ────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/flat_zzz.Rmd ─────────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-inst_rix.Rmd ───────────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-literate_programming.Rmd ───────────────────────────────────────────────────────────────────────────────
── config file for dev/z-pkgs_with_remotes.Rmd ──────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-raps_with_nix.Rmd ──────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-save_r_nix_revs.Rmd ────────────────────────────────────────────────────────────────────────────────────
── config file for dev/z-subshells.Rmd ──────────────────────────────────────────────────────────────────────────────────────────
── check not registered files ───────────────────────────────────────────────────────────────────────────────────────────────────
ℹ Some files in your package are not registered in the configuration file: dev/config_fusen.yaml
fusen uses a configuration file to store the structure of your package and help you clean it when needed.
You will find a list of unregistered files there: csv_file that you can open with `file.edit('dev/config_not_registered.csv')`
Delete unregistered files that you do not need anymore. Then run `fusen::register_all_to_config()`.
After that, this message should not appear in your next `fusen::inflate_all()` calls.
For more information, read `vignette('register-files-in-config (`vignette(fusen::register-files-in-config)`)', package = 'fusen')`
cli-62920-1238
Documentation parameters were restored from attachment config file.
Updating rix documentation
Writing NAMESPACE
ℹ Loading rix
✖ nix_build.R:130: @details requires a value.
Writing NAMESPACE
ℹ Loading rix
Error in att_to_desc_from_is(path.d, imports, suggests, normalize, must.exist,  : 
  The package arrow is missing or misspelled.
Please correct your typo or install it.
In addition: Warning message:
In readLines(path) :
  incomplete final line found on '/Users/philipp/git/philipp-baumann-shared/rix/R/_test.R'
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin22.6.0 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /nix/store/csam52q8ksy40sa4q7z5ijx7jixivrby-blas-3/lib/libblas.dylib 
LAPACK: /nix/store/i2ddi7h4bn0qr1bms5bilccp0rd9fnm5-openblas-0.3.26/lib/libopenblasp-r0.3.26.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rix_0.6.0

loaded via a namespace (and not attached):
 [1] xfun_0.43         htmlwidgets_1.6.4 devtools_2.4.5    remotes_2.5.0    
 [5] tzdb_0.4.0        vctrs_0.6.5       tools_4.3.3       generics_0.1.3   
 [9] curl_5.2.1        tibble_3.2.1      fansi_1.0.6       pkgconfig_2.0.3  
[13] checkmate_2.3.1   desc_1.4.3        lifecycle_1.0.4   compiler_4.3.3   
[17] stringr_1.5.1     brio_1.1.4        codetools_0.2-20  httpuv_1.6.15    
[21] htmltools_0.5.8.1 sys_3.4.2         usethis_2.2.3     yaml_2.3.8       
[25] later_1.3.2       pillar_1.9.0      crayon_1.5.2      urlchecker_1.0.1 
[29] tidyr_1.3.1       ellipsis_0.3.2    cachem_1.0.8      sessioninfo_1.2.2
[33] mime_0.12         commonmark_1.9.1  tidyselect_1.2.1  digest_0.6.35    
[37] stringi_1.8.3     dplyr_1.1.4       purrr_1.0.2       rprojroot_2.0.4  
[41] fastmap_1.1.1     cli_3.6.2         magrittr_2.0.3    pkgbuild_1.4.4   
[45] attachment_0.4.1  utf8_1.2.4        readr_2.1.5       withr_3.0.0      
[49] promises_1.3.0    backports_1.4.1   rmarkdown_2.26    roxygen2_7.3.1   
[53] httr_1.4.7        hms_1.1.3         parsermd_0.1.3    evaluate_0.23    
[57] memoise_2.0.1     shiny_1.8.1.1     knitr_1.46        testthat_3.2.1   
[61] miniUI_0.1.1.1    profvis_0.3.8     rlang_1.1.3       Rcpp_1.0.12      
[65] xtable_1.8-4      glue_1.7.0        xml2_1.3.6        pkgload_1.3.4    
[69] rstudioapi_0.16.0 jsonlite_1.8.8    R6_2.5.1          fusen_0.5.2      
[73] fs_1.6.3

b-rodrigues · 2024-04-12T13:15:17Z

Are you inflating from this branch? Just inflated again, it's actually even automatically removing arrow and dplyr for me:

✔ There are no unregistered files.
Documentation parameters were restored from attachment config file.
Updating rix documentation
Writing NAMESPACE
ℹ Loading rix
Writing NAMESPACE
ℹ Loading rix
[-] 2 package(s) removed: arrow, dplyr.
── Launching check() ────────────────────

But no matter, one issue at a time. Let's try to see what's going on once we merge this to master.

b-rodrigues · 2024-04-12T13:18:24Z

Also, you have a lot more packages loaded for some reason:

> devtools::load_all()
ℹ Loading rix
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed

Matrix products: default
BLAS/LAPACK: /nix/store/0wbgymcg4aj6n9dpsl5645j3zj1rcl64-blas-3/lib/libblas.so.3;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Luxembourg
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rix_0.6.0      testthat_3.2.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8    miniUI_0.1.1.1    compiler_4.3.3    brio_1.1.4       
 [5] promises_1.3.0    Rcpp_1.0.12       stringr_1.5.1     later_1.3.2      
 [9] fastmap_1.1.1     mime_0.12         R6_2.5.1          curl_5.2.1       
[13] htmlwidgets_1.6.4 desc_1.4.3        profvis_0.3.8     rprojroot_2.0.4  
[17] shiny_1.8.1.1     rlang_1.1.3       cachem_1.0.8      stringi_1.8.3    
[21] httpuv_1.6.15     sys_3.4.2         fs_1.6.3          pkgload_1.3.4    
[25] memoise_2.0.1     cli_3.6.2         withr_3.0.0       magrittr_2.0.3   
[29] digest_0.6.35     rstudioapi_0.16.0 xtable_1.8-4      remotes_2.5.0    
[33] devtools_2.4.5    lifecycle_1.0.4   vctrs_0.6.5       glue_1.7.0       
[37] urlchecker_1.0.1  codetools_0.2-20  sessioninfo_1.2.2 pkgbuild_1.4.4   
[41] httr_1.4.7        purrr_1.0.2       tools_4.3.3       usethis_2.2.3    
[45] ellipsis_0.3.2    htmltools_0.5.8.1

b-rodrigues · 2024-05-10T19:10:03Z

Merging this to avoid future conflicts, and then continue on another PR

b-rodrigues requested a review from philipp-baumann March 24, 2024 20:57

b-rodrigues mentioned this pull request Mar 28, 2024

rix: Reproducible Environments with Nix ropensci/software-review#625

Open

29 tasks

b-rodrigues force-pushed the address_review branch from 347223e to d73597a Compare April 5, 2024 12:24

Bruno Rodrigues and others added 20 commits May 10, 2024 21:03

changed = to <-

7ddc189

R expression -> Nix expression

30b846b

Update a-getting_started.Rmd

5f6c546

added test to flat_get_latest.Rmd

f5e78ce

archive to archive_pkgs to avoid partial matching in flat_rix.Rmd

60bbc0e

combined two error messages into one flat_with_nix.Rmd

dd88d8a

Update CONTRIBUTING.md

6359257

more paragraphs a-getting_started.Rmd

c51339b

test get latest not passing

08eeb71

test for get_latest()

b82ca33

with_mock -> with_mocked_bindings()

ceba4ea

fixed merge conflicts

5238cde

resolve conflicts

bf49791

now?

b85e5de

checkout-v3 -> checkout-v4

da34357

checkout v3 -> v4

25f90a6

checkout v3 -> v4

2b5b3c6

checkout and upload-artifact v3-> v4

f85d49e

checkout and upload-artifact v3 -> v4

6f39e42

Update flat_rix.Rmd: refactor rix()

65a4a19

Bruno Rodrigues and others added 5 commits May 10, 2024 21:07

inflated

6baf3cc

we don't need to import arrow

bda260e

satisfy vignette; override strange behavior of fusen

5c81dfb

no dplyr again

cf2274f

updated description

8a7dc6a

b-rodrigues force-pushed the address_review branch from db031e3 to 8a7dc6a Compare May 10, 2024 19:09

b-rodrigues merged commit 9979382 into master May 10, 2024
12 checks passed

b-rodrigues deleted the address_review branch May 10, 2024 19:10

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Adressing the r-opensci review #153

Adressing the r-opensci review #153

b-rodrigues commented Mar 24, 2024 •

edited

b-rodrigues commented Mar 24, 2024

philipp-baumann commented Apr 7, 2024 •

edited

philipp-baumann commented Apr 7, 2024

b-rodrigues commented Apr 8, 2024

philipp-baumann commented Apr 12, 2024 •

edited

b-rodrigues commented Apr 12, 2024

b-rodrigues commented Apr 12, 2024

b-rodrigues commented May 10, 2024

Adressing the r-opensci review #153

Adressing the r-opensci review #153

Conversation

b-rodrigues commented Mar 24, 2024 • edited

b-rodrigues commented Mar 24, 2024

philipp-baumann commented Apr 7, 2024 • edited

philipp-baumann commented Apr 7, 2024

b-rodrigues commented Apr 8, 2024

philipp-baumann commented Apr 12, 2024 • edited

b-rodrigues commented Apr 12, 2024

b-rodrigues commented Apr 12, 2024

b-rodrigues commented May 10, 2024

b-rodrigues commented Mar 24, 2024 •

edited

philipp-baumann commented Apr 7, 2024 •

edited

philipp-baumann commented Apr 12, 2024 •

edited