10-list-adams #28

laxamanaj · 2025-10-14T00:01:54Z

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…ADSL variables - Added extract_common_adsl_variables() main function with full documentation - Added extract_variable_info_from_define() helper function for XML parsing - Added custom print.common_adsl_vars() method for formatted output - Added %||% null coalescing utility function - Created comprehensive testthat test suite covering all functions - Added tests for edge cases, error handling, and input validation - Updated DESCRIPTION with testthat and xml2 dependencies - All functions include proper roxygen2 documentation with examples

…ectories; add vignette for extracting common ADSL variables

…irectory or one file.

Merge branch '6-core-variables' into 10---ADaM-progress # Conflicts: # .Rbuildignore # .gitignore

laxamanaj · 2025-10-14T21:31:22Z

Hi, @Lovemore-Gakava .

These steps in the PR are great. I like that it's a checklist. At this time, I'm trying to run the devtools::document step, but I run into the error of not being able to install jsonlite. Do you know the fix by chance? I tried google with no resolution.

> renv::install("devtools")
# Downloading packages -------------------------------------------------------
- Downloading devtools from CRAN ...            OK [file is up to date]
- Downloading miniUI from CRAN ...              OK [file is up to date]
- Downloading shiny from CRAN ...               OK [file is up to date]
- Downloading jsonlite from CRAN ...            OK [file is up to date]
- Downloading xtable from CRAN ...              OK [file is up to date]
- Downloading fontawesome from CRAN ...         OK [file is up to date]
- Downloading sourcetools from CRAN ...         OK [file is up to date]
- Downloading bslib from CRAN ...               OK [file is up to date]
- Downloading sass from CRAN ...                OK [file is up to date]
- Downloading rappdirs from CRAN ...            OK [file is up to date]
- Downloading jquerylib from CRAN ...           OK [file is up to date]
- Downloading pkgbuild from CRAN ...            OK [file is up to date]
- Downloading callr from CRAN ...               OK [file is up to date]
- Downloading processx from CRAN ...            OK [file is up to date]
- Downloading ps from CRAN ...                  OK [file is up to date]
- Downloading pkgdown from CRAN ...             OK [file is up to date]
- Downloading downlit from CRAN ...             OK [file is up to date]
- Downloading brio from CRAN ...                OK [file is up to date]
- Downloading httr from CRAN ...                OK [file is up to date]
- Downloading curl from CRAN ...                OK [file is up to date]
- Downloading openssl from CRAN ...             OK [file is up to date]
- Downloading ragg from CRAN ...                OK [file is up to date]
- Downloading systemfonts from CRAN ...         OK [file is up to date]
- Downloading textshaping from CRAN ...         OK [file is up to date]
- Downloading rmarkdown from CRAN ...           OK [file is up to date]
- Downloading knitr from CRAN ...               OK [file is up to date]
- Downloading tinytex from CRAN ...             OK [file is up to date]
- Downloading whisker from CRAN ...             OK [file is up to date]
- Downloading pkgload from CRAN ...             OK [file is up to date]
- Downloading profvis from CRAN ...             OK [file is up to date]
- Downloading htmlwidgets from CRAN ...         OK [file is up to date]
- Downloading rcmdcheck from CRAN ...           OK [file is up to date]
- Downloading sessioninfo from CRAN ...         OK [file is up to date]
- Downloading xopen from CRAN ...               OK [file is up to date]
- Downloading remotes from CRAN ...             OK [file is up to date]
- Downloading roxygen2 from CRAN ...            OK [file is up to date]
- Downloading brew from CRAN ...                OK [file is up to date]
- Downloading rversions from CRAN ...           OK [file is up to date]
- Downloading testthat from CRAN ...            OK [file is up to date]
- Downloading praise from CRAN ...              OK [file is up to date]
- Downloading waldo from CRAN ...               OK [file is up to date]
- Downloading diffobj from CRAN ...             OK [file is up to date]
- Downloading rematch2 from CRAN ...            OK [file is up to date]
- Downloading urlchecker from CRAN ...          OK [file is up to date]
- Downloading usethis from CRAN ...             OK [file is up to date]
- Downloading gert from CRAN ...                OK [file is up to date]
- Downloading credentials from CRAN ...         OK [file is up to date]
- Downloading rstudioapi from CRAN ...          OK [file is up to date]
- Downloading zip from CRAN ...                 OK [file is up to date]
- Downloading gh from CRAN ...                  OK [file is up to date]
- Downloading gitcreds from CRAN ...            OK [file is up to date]
- Downloading httr2 from CRAN ...               OK [file is up to date]
- Downloading ini from CRAN ...                 OK [file is up to date]
Successfully downloaded 53 packages in 11 seconds.

The following package(s) will be installed:
- askpass     [1.1]
- brew        [1.0-8]
- brio        [1.1.3]
- bslib       [0.4.2]
- callr       [3.7.3]
- clipr       [0.8.0]
- crayon      [1.5.2]
- credentials [1.3.2]
- curl        [5.0.0]
- desc        [1.4.2]
- devtools    [2.4.5]
- diffobj     [0.3.5]
- downlit     [0.4.2]
- fontawesome [0.5.0]
- fs          [1.6.1]
- gert        [1.9.2]
- gh          [1.4.0]
- gitcreds    [0.1.2]
- htmlwidgets [1.6.1]
- httpuv      [1.6.9]
- httr        [1.4.5]
- httr2       [0.2.2]
- ini         [0.3.1]
- jquerylib   [0.1.4]
- jsonlite    [1.8.4]
- knitr       [1.42]
- later       [1.3.0]
- mime        [0.12]
- miniUI      [0.1.1.1]
- openssl     [2.0.6]
- pkgbuild    [1.4.0]
- pkgdown     [2.0.7]
- pkgload     [1.3.2]
- praise      [1.0.0]
- prettyunits [1.1.1]
- processx    [3.8.0]
- profvis     [0.3.7]
- promises    [1.2.0.1]
- ps          [1.7.2]
- ragg        [1.2.5]
- rappdirs    [0.3.3]
- rcmdcheck   [1.4.0]
- Rcpp        [1.0.10]
- rematch2    [2.1.2]
- remotes     [2.4.2]
- rmarkdown   [2.20]
- roxygen2    [7.2.3]
- rprojroot   [2.0.3]
- rstudioapi  [0.14]
- rversions   [2.1.2]
- sass        [0.4.5]
- sessioninfo [1.2.2]
- shiny       [1.7.4]
- sourcetools [0.1.7-1]
- sys         [3.4.1]
- systemfonts [1.0.4]
- testthat    [3.1.7]
- textshaping [0.3.6]
- tinytex     [0.44]
- urlchecker  [1.0.1]
- usethis     [2.1.6]
- waldo       [0.4.0]
- whisker     [0.4.1]
- xopen       [1.0.0]
- xtable      [1.8-4]
- zip         [2.2.2]
These packages will be installed into "/cloud/home/r1749251/.cache/R/renv/library/project-4b716941/linux-ubuntu-focal/R-4.4/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: yu
- Unrecognized response: please enter 'y' or 'n', or type Ctrl + C to cancel.
Do you want to proceed? [Y/n]: y

The following required system packages are not installed:
- libcurl4-openssl-dev  [required by curl]
- pandoc                [required by knitr, rmarkdown, pkgdown]
The R packages depending on these system packages may fail to install.

An administrator can install these packages with:
- sudo apt install libcurl4-openssl-dev pandoc

Do you want to proceed? [Y/n]: y

# Installing packages --------------------------------------------------------
- Installing rprojroot ...                      OK [linked from cache]
- Installing desc ...                           OK [linked from cache]
- Installing fs ...                             OK [linked from cache]
- Installing Rcpp ...                           OK [linked from cache]
- Installing later ...                          OK [linked from cache]
- Installing promises ...                       OK [linked from cache]
- Installing httpuv ...                         OK [linked from cache]
- Installing mime ...                           OK [linked from cache]
- Installing jsonlite ...                       FAILED
Error: Error installing package 'jsonlite':
====================================

* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c base64.c -o base64.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_array.c -o collapse_array.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_object.c -o collapse_object.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c escape_chars.c -o escape_chars.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_datelist.c -o is_datelist.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_recordlist.c -o is_recordlist.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c null_to_na.c -o null_to_na.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c num_to_char.c -o num_to_char.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c parse.c -o parse.o
parse.c: In function ‘R_parse’:
parse.c:38:32: warning: format not a string literal and no format arguments [-Wformat-security]
   38 |       Rf_errorcall(R_NilValue, errbuf);
      |                                ^~~~~~
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c prettify.c -o prettify.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c push_parser.c -o push_parser.o
push_parser.c: In function ‘R_parse_connection’:
push_parser.c:71:14: warning: format not a string literal and no format arguments [-Wformat-security]
   71 |     Rf_error(errbuf);
      |              ^~~~~~
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c r-base64.c -o r-base64.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c register.c -o register.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c row_collapse.c -o row_collapse.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c transpose_list.c -o transpose_list.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c validate.c -o validate.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/opt/R/4.4.3/lib/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/opt/R/4.4.3/lib/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/opt/R/4.4.3/lib/R/lib -lR
installing to /cloud/project/renv/staging/1/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : 
  invalid non-character version specification 'x' (type: double)
Error: unable to load R code in package ‘jsonlite’
Execution halted
ERROR: lazy loading failed for package ‘jsonlite’
* removing ‘/cloud/project/renv/staging/1/jsonlite’
install of package 'jsonlite' failed [error code 1]

…ns in one cell as would be seen in the adrg.

…export and improve examples

- Setting R_INSTALL_STAGED: false, disabling this two-step process. Instead: The package installs directly to the final location No file locking is required Installation happens in one step instead of two

…elop. We lock the files when we have the stable draft of the package.

Lovemore-Gakava · 2025-10-15T13:37:25Z

@laxamanaj we agreed to use the latest packages during development. I have removed the renv files for now.

… manual

laxamanaj and others added 8 commits March 29, 2025 01:39

first commit for listing R packages function

8112657

added lock file

1db6b44

Update .Rbuildignore and .gitignore to include 'doc/' and 'Meta/' dir…

f7a3b1e

…ectories; add vignette for extracting common ADSL variables

first commit

8aaf940

updated to include help page and process either multiple files in a d…

305406d

…irectory or one file.

getting latest from branch 6

fd970d2

Merge branch '6-core-variables' into 10---ADaM-progress # Conflicts: # .Rbuildignore # .gitignore

updated

f7a7172

laxamanaj and others added 5 commits October 14, 2025 22:12

updated the output to list the adams in 5 rows and all of the functio…

ef09b48

…ns in one cell as would be seen in the adrg.

update documentation, NAMESPACE, and DESCRIPTION; add list_adam_pgms …

b738037

…export and improve examples

Update Description field ORCD.

917d790

- Setting R_INSTALL_STAGED: false, disabling this two-step process. Instead: The package installs directly to the final location No file locking is required Installation happens in one step instead of two

Add NCmiscto description file.

d9c2a28

Remove renv files as team agreed to use the latest packages as we dev…

2917ef1

…elop. We lock the files when we have the stable draft of the package.

lvgk_nngithub and others added 9 commits October 15, 2025 14:43

remove renv

18912e4

addresed R CMD check warnings

33fb3a4

Add documentation and export for list_r_packages function

98565d4

updated to include better user warnings and errors

fe39e31

removed unneeded comments

9362e04

updating roxygen block for list_adam_pgms.r and updating documentation

6ad2795

updated to include tidry and purrr

040df4f

updated to include further description on all_one_file description in…

7c9fc42

… manual

updated description for all_one_file

4a262c6

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10-list-adams #28

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laxamanaj commented Oct 14, 2025 •

edited

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laxamanaj commented Oct 14, 2025

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Lovemore-Gakava commented Oct 15, 2025

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laxamanaj commented Oct 14, 2025 •

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