Last updated on 2026-03-30 09:52:07 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ProjectTemplate | 3 | 3 | 8 |
Current CRAN status: ERROR: 3, NOTE: 3, OK: 8
Version: 0.11.1
Check: Rd cross-references
Result: NOTE
Unknown package ‘qs’ in Rd xrefs
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.11.1
Check: tests
Result: ERROR
Running ‘run-all.R’ [25s/46s]
Running ‘testthat.R’ [24s/41s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
> library(testthat)
>
> test_check("ProjectTemplate")
Loading required package: ProjectTemplate
Loading required package: digest
Loading required package: tibble
Project name: test_project9529271e926e0
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project9529217f24732
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project95292205c4bbe
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project95292205c4bbe
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
dummy 999
Configuration for project: test_project95292205c4bbe
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
Additional custom config present for this project:
Objects to clear from memory: config helper.function project.info
Project name: test_project95292410852e1
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: foo.reader.R
Running helper script: helpers.R
Autoloading data
Loading data set: example
Creating cache entry from global environment: example
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: cache.RData
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Following objects not in memory:
Objects to clear from memory: xxxx
Project name: test_project952927f304acc
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: helper.function project.info
Clearing cache for project: test_project952927f304acc
Clearing cache for project: test_project9529276fd0809
Objects to clear from memory: xxx
Project name: test_project9529276fd0809
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from CODE: xxxx
Objects to clear from memory: config project.info
Objects to clear from memory: project.info
Objects to clear from memory: yyy
Following objects not in memory: xxx
Following objects not in memory: xxx
Variables not cleared: config
No objects to clear
Objects to clear from memory: .yyy helper.function project.info
Project name: test_project952922df10b09
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project952922df10b09
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project952925e2399f3
Project name: test_project952923eb2abc9
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project9529274427c5a
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
Current Directory: test_project95292976d4d6 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project95292976d4d6 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project29529262d5e7c1 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Objects to clear from memory: config helper.function project.info
No objects to clear
Objects to clear from memory: config file9529217aad0f0 helper.function project.info
Creating cache entry from CODE: test_data
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run load.project()
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run clear.cache() again.
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run cache() again.
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run reload.project() again.
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run test.project() again.
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run stub.tests() again.
Current Directory: test_project952924e1a6cba is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run project.config()
Project name: test_project95292586e1649
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: Thumbs
Loading required namespace: RSQLite
Creating cache entry from global environment: var_to_cache
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
version, data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
cache_loaded_data
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file contained unused entries which have been
removed. The unused entries are:
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] TRUE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Project name: test_project952926c692a06
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: .Random.seed config helper.function project.info
Project name: test_project9529250826002
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project9529250826002
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project95292347d9fd4
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project95292347d9fd4
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project952923a766bfc
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project952923a766bfc
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project952923dd521e8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project9529242eb372f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project9529242eb372f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project952924d31710d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project952924d31710d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project952925412f29c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project952925412f29c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project95292611f5ee
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project95292611f5ee
Loading project configuration
Objects to clear from memory: config helper.function project.info
Project name: test_project9529274b81a13
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project9529274b81a13
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Loading table: example_30a
Loading table: example_30b
Loading table: example_31a
Loading table: example_31b
Loading table: example_28
re-encoding from CP1252
re-encoding from CP1252
Objects to clear from memory: config helper.function project.info
Objects to clear from memory: config helper.function project.info
Items in cache will not be cleared
Use reload.project(reset=TRUE) to clear cache also
Objects to clear from memory: helper.function project.info z
Reloading Project ...
Project name: test_project952921ed2c18b
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading cached data set: z
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info x y z
Project name: test_project952926edbc4e9
Loading project configuration
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project9529219646229
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project9529278c51050
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: file_not_in_full_template
Translating data.frame to tibble: file_not_in_full_template
Creating cache entry from global environment: file_not_in_full_template
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
[1] FALSE
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-load.R:473:3'): pass munge files to run ────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─base::suppressMessages(load.project()) at test-load.R:473:3
2. │ └─base::withCallingHandlers(...)
3. └─ProjectTemplate::load.project()
4. └─ProjectTemplate:::.munge.data(config, my.project.info)
5. └─reticulate::source_python(file.path(dir_name, preprocessing.script))
6. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
7. └─reticulate:::ensure_python_initialized()
8. └─reticulate:::initialize_python()
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
Error:
! Test failures.
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ProjectTemplate)
Loading required package: digest
Loading required package: tibble
>
> test_check("ProjectTemplate")
Project name: test_project996e164e18895
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e1b021974
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e12994e309
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project996e12994e309
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
dummy 999
Configuration for project: test_project996e12994e309
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
Additional custom config present for this project:
Objects to clear from memory: config helper.function project.info
Project name: test_project996e115a3c2d4
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: foo.reader.R
Running helper script: helpers.R
Autoloading data
Loading data set: example
Creating cache entry from global environment: example
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: cache.RData
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Following objects not in memory:
Objects to clear from memory: xxxx
Project name: test_project996e14ee902b8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: helper.function project.info
Clearing cache for project: test_project996e14ee902b8
Clearing cache for project: test_project996e13e5ad75
Objects to clear from memory: xxx
Project name: test_project996e13e5ad75
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from CODE: xxxx
Objects to clear from memory: config project.info
Objects to clear from memory: project.info
Objects to clear from memory: yyy
Following objects not in memory: xxx
Following objects not in memory: xxx
Variables not cleared: config
No objects to clear
Objects to clear from memory: .yyy helper.function project.info
Project name: test_project996e13968aca8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e13968aca8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project996e179baba82
Project name: test_project996e14556e172
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e163ee2f98
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
Current Directory: test_project996e12d821dcf is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project996e12d821dcf is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project2996e11b3e86ab is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Objects to clear from memory: config helper.function project.info
No objects to clear
Objects to clear from memory: config file996e13bea615 helper.function project.info
Creating cache entry from CODE: test_data
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run load.project()
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run clear.cache() again.
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run cache() again.
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run reload.project() again.
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run test.project() again.
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run stub.tests() again.
Current Directory: test_project996e118ad4d1b is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run project.config()
Project name: test_project996e123b476d8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: Thumbs
Loading required namespace: RSQLite
Creating cache entry from global environment: var_to_cache
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
version, data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
cache_loaded_data
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file contained unused entries which have been
removed. The unused entries are:
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] TRUE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Project name: test_project996e124015c4
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: .Random.seed config helper.function project.info
Project name: test_project996e154634ac7
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e154634ac7
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e161fe5bc3
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e161fe5bc3
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e17640b88f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e17640b88f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e17f77d2b9
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e13554b8c8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e13554b8c8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project996e17b074ae3
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e17b074ae3
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project996e13e3648d5
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e13e3648d5
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project996e1313af652
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e1313af652
Loading project configuration
Objects to clear from memory: config helper.function project.info
Project name: test_project996e1504fe7fe
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e1504fe7fe
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Loading table: example_30a
Loading table: example_30b
Loading table: example_31a
Loading table: example_31b
Loading table: example_28
re-encoding from CP1252
re-encoding from CP1252
Objects to clear from memory: config helper.function project.info
Objects to clear from memory: config helper.function project.info
Items in cache will not be cleared
Use reload.project(reset=TRUE) to clear cache also
Objects to clear from memory: helper.function project.info z
Reloading Project ...
Project name: test_project996e14eeb8fbe
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading cached data set: z
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info x y z
Project name: test_project996e170abc2cc
Loading project configuration
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e1660e294d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project996e15fcb6407
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: file_not_in_full_template
Translating data.frame to tibble: file_not_in_full_template
Creating cache entry from global environment: file_not_in_full_template
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
[1] FALSE
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-load.R:473:3'): pass munge files to run ────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─base::suppressMessages(load.project()) at test-load.R:473:3
2. │ └─base::withCallingHandlers(...)
3. └─ProjectTemplate::load.project()
4. └─ProjectTemplate:::.munge.data(config, my.project.info)
5. └─reticulate::source_python(file.path(dir_name, preprocessing.script))
6. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
7. └─reticulate:::ensure_python_initialized()
8. └─reticulate:::initialize_python()
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.11.1
Check: tests
Result: ERROR
Running ‘run-all.R’ [15s/25s]
Running ‘testthat.R’ [16s/27s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
> library(testthat)
>
> test_check("ProjectTemplate")
Loading required package: ProjectTemplate
Loading required package: digest
Loading required package: tibble
Project name: test_project36c785eaa95a7
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c7825b5b6ee
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c783d7c6daf
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project36c783d7c6daf
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
dummy 999
Configuration for project: test_project36c783d7c6daf
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
Additional custom config present for this project:
Objects to clear from memory: config helper.function project.info
Project name: test_project36c784dcb7a2f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: foo.reader.R
Running helper script: helpers.R
Autoloading data
Loading data set: example
Creating cache entry from global environment: example
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: cache.RData
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Following objects not in memory:
Objects to clear from memory: xxxx
Project name: test_project36c78653aa3a1
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: helper.function project.info
Clearing cache for project: test_project36c78653aa3a1
Clearing cache for project: test_project36c787ffbbb75
Objects to clear from memory: xxx
Project name: test_project36c787ffbbb75
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from CODE: xxxx
Objects to clear from memory: config project.info
Objects to clear from memory: project.info
Objects to clear from memory: yyy
Following objects not in memory: xxx
Following objects not in memory: xxx
Variables not cleared: config
No objects to clear
Objects to clear from memory: .yyy helper.function project.info
Project name: test_project36c7846e0f083
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c7846e0f083
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project36c78bff5a21
Project name: test_project36c786d0d4f49
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c78278ba75a
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
Current Directory: test_project36c78287e7c70 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project36c78287e7c70 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project236c7819d3554b is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Objects to clear from memory: config helper.function project.info
No objects to clear
Objects to clear from memory: config file36c7863d95042 helper.function project.info
Creating cache entry from CODE: test_data
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run load.project()
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run clear.cache() again.
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run cache() again.
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run reload.project() again.
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run test.project() again.
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run stub.tests() again.
Current Directory: test_project36c7835deb06c is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run project.config()
Project name: test_project36c782502001c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: Thumbs
Loading required namespace: RSQLite
Creating cache entry from global environment: var_to_cache
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
version, data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
cache_loaded_data
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file contained unused entries which have been
removed. The unused entries are:
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] TRUE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Project name: test_project36c783f801b2e
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: .Random.seed config helper.function project.info
Project name: test_project36c783472b730
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c783472b730
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c78187f98d1
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c78187f98d1
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c782d60b5c0
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c782d60b5c0
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c781f6706fd
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c787e2c1301
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c787e2c1301
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project36c78ffee9cd
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c78ffee9cd
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project36c782577e020
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c782577e020
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project36c7863dabf25
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c7863dabf25
Loading project configuration
Objects to clear from memory: config helper.function project.info
Project name: test_project36c7878ca3899
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c7878ca3899
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Loading table: example_30a
Loading table: example_30b
Loading table: example_31a
Loading table: example_31b
Loading table: example_28
re-encoding from CP1252
re-encoding from CP1252
Objects to clear from memory: config helper.function project.info
Objects to clear from memory: config helper.function project.info
Items in cache will not be cleared
Use reload.project(reset=TRUE) to clear cache also
Objects to clear from memory: helper.function project.info z
Reloading Project ...
Project name: test_project36c786838ec03
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading cached data set: z
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info x y z
Project name: test_project36c786d8d79ca
Loading project configuration
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c78549f9df8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project36c78227b9e65
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: file_not_in_full_template
Translating data.frame to tibble: file_not_in_full_template
Creating cache entry from global environment: file_not_in_full_template
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
[1] FALSE
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-load.R:473:3'): pass munge files to run ────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─base::suppressMessages(load.project()) at test-load.R:473:3
2. │ └─base::withCallingHandlers(...)
3. └─ProjectTemplate::load.project()
4. └─ProjectTemplate:::.munge.data(config, my.project.info)
5. └─reticulate::source_python(file.path(dir_name, preprocessing.script))
6. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
7. └─reticulate:::ensure_python_initialized()
8. └─reticulate:::initialize_python()
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
Error:
! Test failures.
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ProjectTemplate)
Loading required package: digest
Loading required package: tibble
>
> test_check("ProjectTemplate")
Project name: test_project3f5163c06addb
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5165f3ee8d3
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5161f61ec1a
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project3f5161f61ec1a
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
dummy 999
Configuration for project: test_project3f5161f61ec1a
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
Additional custom config present for this project:
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5167a38f649
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: foo.reader.R
Running helper script: helpers.R
Autoloading data
Loading data set: example
Creating cache entry from global environment: example
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: cache.RData
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Following objects not in memory:
Objects to clear from memory: xxxx
Project name: test_project3f51622477038
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: helper.function project.info
Clearing cache for project: test_project3f51622477038
Clearing cache for project: test_project3f5166bc6e566
Objects to clear from memory: xxx
Project name: test_project3f5166bc6e566
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from CODE: xxxx
Objects to clear from memory: config project.info
Objects to clear from memory: project.info
Objects to clear from memory: yyy
Following objects not in memory: xxx
Following objects not in memory: xxx
Variables not cleared: config
No objects to clear
Objects to clear from memory: .yyy helper.function project.info
Project name: test_project3f51615e3681d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f51615e3681d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project3f5161567b1d8
Project name: test_project3f516431d2ba2
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f51672cab0d1
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
Current Directory: test_project3f516270d1cf6 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project3f516270d1cf6 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project23f5163984aa7b is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Objects to clear from memory: config helper.function project.info
No objects to clear
Objects to clear from memory: config file3f51682bdfa helper.function project.info
Creating cache entry from CODE: test_data
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run load.project()
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run clear.cache() again.
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run cache() again.
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run reload.project() again.
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run test.project() again.
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run stub.tests() again.
Current Directory: test_project3f5167c10a5b4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run project.config()
Project name: test_project3f5167c2bc40d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: Thumbs
Loading required namespace: RSQLite
Creating cache entry from global environment: var_to_cache
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
version, data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
cache_loaded_data
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file contained unused entries which have been
removed. The unused entries are:
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] TRUE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Project name: test_project3f5166bd0dc8c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: .Random.seed config helper.function project.info
Project name: test_project3f516687f697d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f516687f697d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f516133f1e99
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f516133f1e99
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5161a28402d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f5161a28402d
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f51611b686e7
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f51619b02797
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f51619b02797
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5163a85c00
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f5163a85c00
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5167480b017
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f5167480b017
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project3f5164e750b78
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f5164e750b78
Loading project configuration
Objects to clear from memory: config helper.function project.info
Project name: test_project3f51640b0ca7c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f51640b0ca7c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Loading table: example_30a
Loading table: example_30b
Loading table: example_31a
Loading table: example_31b
Loading table: example_28
re-encoding from CP1252
re-encoding from CP1252
Objects to clear from memory: config helper.function project.info
Objects to clear from memory: config helper.function project.info
Items in cache will not be cleared
Use reload.project(reset=TRUE) to clear cache also
Objects to clear from memory: helper.function project.info z
Reloading Project ...
Project name: test_project3f5161b4d8466
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading cached data set: z
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info x y z
Project name: test_project3f5161aeb67c
Loading project configuration
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f51616ba3ae
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project3f51652eee69
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: file_not_in_full_template
Translating data.frame to tibble: file_not_in_full_template
Creating cache entry from global environment: file_not_in_full_template
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
[1] FALSE
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-load.R:473:3'): pass munge files to run ────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─base::suppressMessages(load.project()) at test-load.R:473:3
2. │ └─base::withCallingHandlers(...)
3. └─ProjectTemplate::load.project()
4. └─ProjectTemplate:::.munge.data(config, my.project.info)
5. └─reticulate::source_python(file.path(dir_name, preprocessing.script))
6. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
7. └─reticulate:::ensure_python_initialized()
8. └─reticulate:::initialize_python()
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.11.1
Check: tests
Result: ERROR
Running ‘run-all.R’ [23s/44s]
Running ‘testthat.R’ [23s/44s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
> library(testthat)
>
> test_check("ProjectTemplate")
Loading required package: ProjectTemplate
Loading required package: digest
Loading required package: tibble
Project name: test_project117ec525f9ccc5
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec51104f391
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec51cf8ecbd
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project117ec51cf8ecbd
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
dummy 999
Configuration for project: test_project117ec51cf8ecbd
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
Additional custom config present for this project:
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec5386bdd74
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: foo.reader.R
Running helper script: helpers.R
Autoloading data
Loading data set: example
Creating cache entry from global environment: example
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: cache.RData
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Following objects not in memory:
Objects to clear from memory: xxxx
Project name: test_project117ec5ee14a27
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: helper.function project.info
Clearing cache for project: test_project117ec5ee14a27
Clearing cache for project: test_project117ec5eb91adc
Objects to clear from memory: xxx
Project name: test_project117ec5eb91adc
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from CODE: xxxx
Objects to clear from memory: config project.info
Objects to clear from memory: project.info
Objects to clear from memory: yyy
Following objects not in memory: xxx
Following objects not in memory: xxx
Variables not cleared: config
No objects to clear
Objects to clear from memory: .yyy helper.function project.info
Project name: test_project117ec55f58255a
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec55f58255a
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project117ec52751ff00
Project name: test_project117ec56012e333
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec514e28fde
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
Current Directory: test_project117ec52dd2fec7 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project117ec52dd2fec7 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project2117ec563b35e5d is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Objects to clear from memory: config helper.function project.info
No objects to clear
Objects to clear from memory: config file117ec52b16e99d helper.function project.info
Creating cache entry from CODE: test_data
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run load.project()
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run clear.cache() again.
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run cache() again.
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run reload.project() again.
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run test.project() again.
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run stub.tests() again.
Current Directory: test_project117ec51308edf4 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run project.config()
Project name: test_project117ec52229d6b6
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: Thumbs
Loading required namespace: RSQLite
Creating cache entry from global environment: var_to_cache
Loading required package: data.table
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
version, data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
cache_loaded_data
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file contained unused entries which have been
removed. The unused entries are:
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] TRUE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Project name: test_project117ec564406be8
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: .Random.seed config helper.function project.info
Project name: test_project117ec53ce9bd2f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec53ce9bd2f
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec550d012fe
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec550d012fe
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec566780e57
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec566780e57
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec51fdf6630
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec565e7c4f6
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec565e7c4f6
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec5766d04
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec5766d04
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec54d279229
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec54d279229
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec54e710a6a
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec54e710a6a
Loading project configuration
Objects to clear from memory: config helper.function project.info
Project name: test_project117ec57e616172
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec57e616172
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Loading table: example_30a
Loading table: example_30b
Loading table: example_31a
Loading table: example_31b
Loading table: example_28
re-encoding from CP1252
re-encoding from CP1252
Objects to clear from memory: config helper.function project.info
Objects to clear from memory: config helper.function project.info
Items in cache will not be cleared
Use reload.project(reset=TRUE) to clear cache also
Objects to clear from memory: helper.function project.info z
Reloading Project ...
Project name: test_project117ec572654979
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading cached data set: z
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info x y z
Project name: test_project117ec57d82fc57
Loading project configuration
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec5683dcd6e
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project117ec55740bf74
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: file_not_in_full_template
Translating data.frame to tibble: file_not_in_full_template
Creating cache entry from global environment: file_not_in_full_template
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
[1] FALSE
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-load.R:473:3'): pass munge files to run ────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─base::suppressMessages(load.project()) at test-load.R:473:3
2. │ └─base::withCallingHandlers(...)
3. └─ProjectTemplate::load.project()
4. └─ProjectTemplate:::.munge.data(config, my.project.info)
5. └─reticulate::source_python(file.path(dir_name, preprocessing.script))
6. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
7. └─reticulate:::ensure_python_initialized()
8. └─reticulate:::initialize_python()
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
Error:
! Test failures.
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ProjectTemplate)
Loading required package: digest
Loading required package: tibble
>
> test_check("ProjectTemplate")
Project name: test_project11c6b023595004
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b01e7320bc
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b045cf750
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project11c6b045cf750
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
dummy 999
Configuration for project: test_project11c6b045cf750
version 0.11.1
data_loading TRUE
data_loading_header TRUE
data_ignore
cache_loading TRUE
recursive_loading FALSE
munging TRUE
logging FALSE
logging_level INFO
load_libraries FALSE
libraries reshape2, plyr, tidyverse, stringr, lubridate
as_factors FALSE
tables_type tibble
attach_internal_libraries FALSE
cache_loaded_data TRUE
sticky_variables NONE
underscore_variables TRUE
cache_file_format RData
Additional custom config present for this project:
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b04aa6f333
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: foo.reader.R
Running helper script: helpers.R
Autoloading data
Loading data set: example
Creating cache entry from global environment: example
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: xxxx
Creating cache entry from global environment: cache.RData
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Following objects not in memory:
Objects to clear from memory: xxxx
Project name: test_project11c6b041c97f65
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: helper.function project.info
Clearing cache for project: test_project11c6b041c97f65
Clearing cache for project: test_project11c6b045d98475
Objects to clear from memory: xxx
Project name: test_project11c6b045d98475
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Creating cache entry from CODE: xxxx
Objects to clear from memory: config project.info
Objects to clear from memory: project.info
Objects to clear from memory: yyy
Following objects not in memory: xxx
Following objects not in memory: xxx
Variables not cleared: config
No objects to clear
Objects to clear from memory: .yyy helper.function project.info
Project name: test_project11c6b06f9fdb64
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b06f9fdb64
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Configuration for project: test_project11c6b07ce37c7d
Project name: test_project11c6b02d35b6a7
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b067904824
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
== Testing 1.R =================================================================
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] Done!
Current Directory: test_project11c6b05d3eb4b6 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project11c6b05d3eb4b6 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Directory: test_project211c6b07dacfe34 is a ProjectTemplate directory
Cannot create a new project inside an existing one
Please change to another directory and re-run create.project()
Objects to clear from memory: config helper.function project.info
No objects to clear
Objects to clear from memory: config file11c6b0a30c892 helper.function project.info
Creating cache entry from CODE: test_data
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run load.project()
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run clear.cache() again.
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run cache() again.
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run reload.project() again.
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run test.project() again.
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Change to a valid ProjectTemplate directory and run stub.tests() again.
Current Directory: test_project11c6b0dcad850 is not a valid ProjectTemplate directory because one or more mandatory directories are missing. If you believe you are in a ProjectTemplate directory and seeing this message in error, try running migrate.project(). migrate.project() will ensure the ProjectTemplate structure is consistent with your version of ProjectTemplate.
Please change to correct directory and re-run project.config()
Project name: test_project11c6b02c417450
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: Thumbs
Loading required namespace: RSQLite
Creating cache entry from global environment: var_to_cache
Loading required package: data.table
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
version, data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
data_loading_header, data_ignore, logging_level, tables_type, attach_internal_libraries, cache_loaded_data, sticky_variables, underscore_variables, cache_file_format
There is a new config item called cache_loaded_data which auto-caches data
after it has been loaded from the data directory. This has been switched
off for this project in case it breaks your scripts. However you can switch
it on manually by editing global.dcf
data_tables has been renamed tables_type. It can take the value 'tibble',
'data_table', or 'data_frame. If data_tables is TRUE, tables_type will be
set to 'data_table', otherwise the default 'data_frame' will be used. if you
wish a different default set it manually by editing global.dcf. Future new
projects will use 'tibble' by default.
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
cache_loaded_data
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file contained unused entries which have been
removed. The unused entries are:
Migrating project configuration
[1] FALSE
Migrating project configuration
[1] TRUE
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Migrating project configuration
[1] FALSE
Your existing project configuration in globals.dcf does not contain up to
date configuration settings in this version 0.11.1 of ProjectTemplate. They will
be added automatically during migration, but you should review afterward.
Your config.dcf file was missing entries and defaults
have been used. The missing entries are:
tables_type
Project name: test_project11c6b0aaca123
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: .Random.seed config helper.function project.info
Project name: test_project11c6b025454908
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b025454908
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b01d5d2432
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b01d5d2432
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b06b542290
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b06b542290
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b0317db1b2
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b027dd9362
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b027dd9362
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b01b06b312
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b01b06b312
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b033016506
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b033016506
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b02be9884c
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b02be9884c
Loading project configuration
Objects to clear from memory: config helper.function project.info
Project name: test_project11c6b0adbb60b
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b0adbb60b
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info
Loading table: example_30a
Loading table: example_30b
Loading table: example_31a
Loading table: example_31b
Loading table: example_28
re-encoding from CP1252
re-encoding from CP1252
Objects to clear from memory: config helper.function project.info
Objects to clear from memory: config helper.function project.info
Items in cache will not be cleared
Use reload.project(reset=TRUE) to clear cache also
Objects to clear from memory: helper.function project.info z
Reloading Project ...
Project name: test_project11c6b075417fd9
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading cached data set: z
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Objects to clear from memory: config helper.function project.info x y z
Project name: test_project11c6b01456f8b4
Loading project configuration
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b05061a840
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
Project name: test_project11c6b02f669f82
Loading project configuration
Autoloading helper functions
Running helper script: globals.R
Running helper script: helpers.R
Autoloading data
Loading data set: file_not_in_full_template
Translating data.frame to tibble: file_not_in_full_template
Creating cache entry from global environment: file_not_in_full_template
Munging data
Running preprocessing script: 01-A.R
Sourcing R script: 01-A.R
[1] FALSE
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-load.R:473:3'): pass munge files to run ────────────────────────
<Rcpp::exception/C++Error/error/condition>
Error: /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─base::suppressMessages(load.project()) at test-load.R:473:3
2. │ └─base::withCallingHandlers(...)
3. └─ProjectTemplate::load.project()
4. └─ProjectTemplate:::.munge.data(config, my.project.info)
5. └─reticulate::source_python(file.path(dir_name, preprocessing.script))
6. └─reticulate::py_run_file(file, local = FALSE, convert = convert)
7. └─reticulate:::ensure_python_initialized()
8. └─reticulate:::initialize_python()
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
[ FAIL 1 | WARN 214 | SKIP 0 | PASS 870 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64