CRAN submission

[bvreede]

Checklist (source):

Edit (by @PabRod): the checklist is outdated, no need to use it now.

[PabRod]

Relevant check results

Warnings

• Checking for unstated dependencies in examples

❯ checking for unstated dependencies in examples ... OK
   WARNING
  ‘qpdf’ is needed for checks on size reduction of PDFs

--as-cran only

• Checking PDF version of manual

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File `inconsolata.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
       
l.326 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!

Notes

• Checking R code for possible problems

❯ checking R code for possible problems ... NOTE
 add_lines: no visible global function definition for ‘end’
 add_lines: no visible binding for global variable ‘begin’
 add_lines: no visible binding for global variable ‘line’
 add_lines: no visible binding for global variable ‘end’
 convplot: no visible binding for global variable ‘begin’
 convplot: no visible binding for global variable ‘uid’
 convplot: no visible binding for global variable ‘scope’
 convplot: no visible binding for global variable ‘participant’
 convplot: no visible binding for global variable ‘end’
 convplot: no visible binding for global variable ‘participation’
 convplot: no visible global function definition for ‘case_when’
 convplot: no visible binding for global variable ‘striplength’
 convplot: no visible binding for global variable ‘utterance’
 convplot: no visible binding for global variable ‘participant_int’
 convplot: no visible global function definition for ‘theme_tufte’
 convplot: no visible binding for global variable ‘begin0’
 convplot: no visible binding for global variable ‘end0’
 convplot: no visible global function definition for ‘filter’
 convplot: no visible binding for global variable ‘focus’
 convplot: no visible binding for global variable ‘uttshort’
 generate_plots: no visible binding for global variable ‘lang’
 get_uid_metadata: no visible binding for global variable ‘begin’
 get_uid_metadata: no visible binding for global variable ‘distance’
 get_uids: no visible binding for global variable ‘language’
 plot_FTO: no visible binding for global variable ‘FTO’
 plot_FTO: no visible binding for global variable ‘duration’
 plot_conversation: no visible binding for global variable ‘striplength’
 plot_conversation: no visible binding for global variable ‘utterance’
 plot_conversation: no visible binding for global variable
   ‘participant_int’
 plot_conversation: no visible binding for global variable ‘begin0’
 plot_conversation: no visible binding for global variable ‘end0’
 plot_conversation: no visible binding for global variable ‘uttshort’
 plot_token_rank: no visible binding for global variable ‘n’
 plot_token_rank: no visible binding for global variable ‘word’
 plot_top_turn_types: no visible binding for global variable ‘n’
 plot_top_turn_types: no visible binding for global variable
   ‘utterance_stripped’
 plot_transitions: no visible binding for global variable ‘FTO’
 plot_turn_duration: no visible binding for global variable ‘duration’
 prepare_convplot: no visible binding for global variable ‘language’
 process_for_plot: no visible binding for global variable ‘n’
 Undefined global functions or variables:
   FTO begin begin0 case_when distance duration end end0 filter focus
   lang language line n participant participant_int participation scope
   striplength theme_tufte uid utterance utterance_stripped uttshort
   word
 Consider adding
   importFrom("stats", "end", "filter", "line")
 to your NAMESPACE file.

--as-cran only

• Checking HTML version of manual

❯ checking HTML version of manual ... NOTE
Skipping checking HTML validation: no command 'tidy' found

• Checking for non-standard things in the check directory

❯ checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
‘talkr-manual.tex’

[mdingemanse]

I'm getting this from CRAN:

Dear maintainer,

package talkr_0.1.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:

Windows

https://win-builder.r-project.org/incoming_pretest/talkr_0.1.0_20240822_140518/Windows/00check.log

* using log directory 'd:/RCompile/CRANincoming/R-devel/talkr.Rcheck'
* using R Under development (unstable) (2024-08-21 r87038 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'talkr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'talkr' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Mark Dingemanse <[email protected]>'

New submission

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Remotes'

Suggests or Enhances not in mainstream repositories:
  ifadv

Found the following (possibly) invalid URLs:
  URL: [email protected]:elpaco-escience/talkr
    From: README.md
    Message: Invalid URI scheme
  URL: https://codecov.io/github/elpaco-escience/talkr (moved to https://app.codecov.io/github/elpaco-escience/talkr)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://fon.hum.uva.nl/IFA-SpokenLanguageCorpora/IFADVcorpus/
    From: inst/doc/workflows.html
    Status: Error
    Message: schannel: SNI or certificate check failed: SEC_E_WRONG_PRINCIPAL (0x80090322) - Der Zielprinzipalname ist falsch.
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'ifadv'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'talkr' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_lines: no visible binding for global variable '.data'
add_lines: no visible global function definition for ':='
plot_density: no visible binding for global variable '.data'
plot_scatter: no visible binding for global variable '.data'
report: no visible binding for global variable '.data'
report_combined: no visible binding for global variable '.data'
theme_turnPlot: no visible global function definition for '%+replace%'
theme_turnPlot: no visible global function definition for 'theme'
theme_turnPlot: no visible global function definition for
  'element_text'
theme_turnPlot: no visible global function definition for 'margin'
theme_turnPlot: no visible global function definition for
  'element_blank'
tokenize: no visible binding for global variable '.data'
Undefined global functions or variables:
  %+replace% .data := element_blank element_text margin theme
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(talkr)
  > 
  > test_check("talkr")
  [ FAIL 2 | WARN 1 | SKIP 1 | PASS 71 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-calculate_timing.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plots.R:15:1'): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ifadv'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-plots.R:15:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-report.R:2:1'): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ifadv'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-report.R:2:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 1 | SKIP 1 | PASS 71 ]
  Deleting unused snapshots:
  • plots/plot_quality.png
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building 'workflows.Rmd' using rmarkdown

Quitting from lines 35-38 [unnamed-chunk-2] (workflows.Rmd)
Error: processing vignette 'workflows.Rmd' failed with diagnostics:
there is no package called 'ifadv'
--- failed re-building 'workflows.Rmd'

SUMMARY: processing the following file failed:
  'workflows.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs

Debian

https://win-builder.r-project.org/incoming_pretest/talkr_0.1.0_20240822_140518/Debian/00check.log

* using log directory ‘/srv/hornik/tmp/CRAN/talkr.Rcheck’
* using R Under development (unstable) (2024-08-21 r87038)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘talkr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘talkr’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Mark Dingemanse <[email protected]>’

New submission

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘Remotes’

Suggests or Enhances not in mainstream repositories:
  ifadv

Found the following (possibly) invalid URLs:
  URL: [email protected]:elpaco-escience/talkr
    From: README.md
    Message: Invalid URI scheme
  URL: https://codecov.io/github/elpaco-escience/talkr (moved to https://app.codecov.io/github/elpaco-escience/talkr)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://fon.hum.uva.nl/IFA-SpokenLanguageCorpora/IFADVcorpus/
    From: inst/doc/workflows.html
    Status: Error
    Message: SSL: certificate subject name (www.fon.hum.uva.nl) does not match target hostname 'fon.hum.uva.nl'
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ifadv’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘talkr’ can be installed ... [2s/2s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] NOTE
add_lines: no visible binding for global variable ‘.data’
add_lines: no visible global function definition for ‘:=’
plot_density: no visible binding for global variable ‘.data’
plot_scatter: no visible binding for global variable ‘.data’
report: no visible binding for global variable ‘.data’
report_combined: no visible binding for global variable ‘.data’
theme_turnPlot: no visible global function definition for ‘%+replace%’
theme_turnPlot: no visible global function definition for ‘theme’
theme_turnPlot: no visible global function definition for
  ‘element_text’
theme_turnPlot: no visible global function definition for ‘margin’
theme_turnPlot: no visible global function definition for
  ‘element_blank’
tokenize: no visible binding for global variable ‘.data’
Undefined global functions or variables:
  %+replace% .data := element_blank element_text margin theme
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] ERROR
  Running ‘testthat.R’ [2s/2s]
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/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(talkr)
  > 
  > test_check("talkr")
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 71 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-calculate_timing.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plots.R:15:1'): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ifadv'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-plots.R:15:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-report.R:2:1'): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ifadv'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-report.R:2:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 71 ]
  Deleting unused snapshots:
  • plots/plot_quality.png
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘workflows.Rmd’ using rmarkdown

Quitting from lines 35-38 [unnamed-chunk-2] (workflows.Rmd)
Error: processing vignette 'workflows.Rmd' failed with diagnostics:
there is no package called 'ifadv'
--- failed re-building ‘workflows.Rmd’

SUMMARY: processing the following file failed:
  ‘workflows.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs

[bvreede]

Tagging @pablo! Are you able to tackle these? Most of it, as far as I can see, hinges on ifadv installation (btw: does this need to be called twice in the description file? Once via Remotes, once separately?). Not sure what the fix is, so I hope Pablo has an idea? Thanks!!

…

On Fri, 23 Aug 2024 at 10:55, mdingemanse ***@***.***> wrote: I'm getting this from CRAN: Dear maintainer, package talkr_0.1.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows https://win-builder.r-project.org/incoming_pretest/talkr_0.1.0_20240822_140518/Windows/00check.log * using log directory 'd:/RCompile/CRANincoming/R-devel/talkr.Rcheck' * using R Under development (unstable) (2024-08-21 r87038 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'talkr/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'talkr' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Mark Dingemanse ***@***.***>' New submission Unknown, possibly misspelled, fields in DESCRIPTION: 'Remotes' Suggests or Enhances not in mainstream repositories: ifadv Found the following (possibly) invalid URLs: URL: ***@***.***:elpaco-escience/talkr From: README.md Message: Invalid URI scheme URL: https://codecov.io/github/elpaco-escience/talkr (moved to https://app.codecov.io/github/elpaco-escience/talkr) From: README.md Status: 301 Message: Moved Permanently URL: https://fon.hum.uva.nl/IFA-SpokenLanguageCorpora/IFADVcorpus/ From: inst/doc/workflows.html Status: Error Message: schannel: SNI or certificate check failed: SEC_E_WRONG_PRINCIPAL (0x80090322) - Der Zielprinzipalname ist falsch. For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: 'ifadv' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'talkr' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE add_lines: no visible binding for global variable '.data' add_lines: no visible global function definition for ':=' plot_density: no visible binding for global variable '.data' plot_scatter: no visible binding for global variable '.data' report: no visible binding for global variable '.data' report_combined: no visible binding for global variable '.data' theme_turnPlot: no visible global function definition for '%+replace%' theme_turnPlot: no visible global function definition for 'theme' theme_turnPlot: no visible global function definition for 'element_text' theme_turnPlot: no visible global function definition for 'margin' theme_turnPlot: no visible global function definition for 'element_blank' tokenize: no visible binding for global variable '.data' Undefined global functions or variables: %+replace% .data := element_blank element_text margin theme * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... NONE * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(talkr) > > test_check("talkr") [ FAIL 2 | WARN 1 | SKIP 1 | PASS 71 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-calculate_timing.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plots.R:15:1'): (code run outside of `test_that()`) ──────────── <packageNotFoundError/error/condition> Error in `loadNamespace(x)`: there is no package called 'ifadv' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-plots.R:15:1 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-report.R:2:1'): (code run outside of `test_that()`) ──────────── <packageNotFoundError/error/condition> Error in `loadNamespace(x)`: there is no package called 'ifadv' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-report.R:2:1 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) [ FAIL 2 | WARN 1 | SKIP 1 | PASS 71 ] Deleting unused snapshots: • plots/plot_quality.png Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'workflows.Rmd' using rmarkdown Quitting from lines 35-38 [unnamed-chunk-2] (workflows.Rmd) Error: processing vignette 'workflows.Rmd' failed with diagnostics: there is no package called 'ifadv' --- failed re-building 'workflows.Rmd' SUMMARY: processing the following file failed: 'workflows.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs Debian https://win-builder.r-project.org/incoming_pretest/talkr_0.1.0_20240822_140518/Debian/00check.log * using log directory ‘/srv/hornik/tmp/CRAN/talkr.Rcheck’ * using R Under development (unstable) (2024-08-21 r87038) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘talkr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘talkr’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Mark Dingemanse ***@***.***>’ New submission Unknown, possibly misspelled, fields in DESCRIPTION: ‘Remotes’ Suggests or Enhances not in mainstream repositories: ifadv Found the following (possibly) invalid URLs: URL: ***@***.***:elpaco-escience/talkr From: README.md Message: Invalid URI scheme URL: https://codecov.io/github/elpaco-escience/talkr (moved to https://app.codecov.io/github/elpaco-escience/talkr) From: README.md Status: 301 Message: Moved Permanently URL: https://fon.hum.uva.nl/IFA-SpokenLanguageCorpora/IFADVcorpus/ From: inst/doc/workflows.html Status: Error Message: SSL: certificate subject name (www.fon.hum.uva.nl) does not match target hostname 'fon.hum.uva.nl' For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘ifadv’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘talkr’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] NOTE add_lines: no visible binding for global variable ‘.data’ add_lines: no visible global function definition for ‘:=’ plot_density: no visible binding for global variable ‘.data’ plot_scatter: no visible binding for global variable ‘.data’ report: no visible binding for global variable ‘.data’ report_combined: no visible binding for global variable ‘.data’ theme_turnPlot: no visible global function definition for ‘%+replace%’ theme_turnPlot: no visible global function definition for ‘theme’ theme_turnPlot: no visible global function definition for ‘element_text’ theme_turnPlot: no visible global function definition for ‘margin’ theme_turnPlot: no visible global function definition for ‘element_blank’ tokenize: no visible binding for global variable ‘.data’ Undefined global functions or variables: %+replace% .data := element_blank element_text margin theme * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [2s/2s] ERROR Running ‘testthat.R’ [2s/2s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(talkr) > > test_check("talkr") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 71 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-calculate_timing.R:5:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plots.R:15:1'): (code run outside of `test_that()`) ──────────── <packageNotFoundError/error/condition> Error in `loadNamespace(x)`: there is no package called 'ifadv' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-plots.R:15:1 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-report.R:2:1'): (code run outside of `test_that()`) ──────────── <packageNotFoundError/error/condition> Error in `loadNamespace(x)`: there is no package called 'ifadv' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-report.R:2:1 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) [ FAIL 2 | WARN 0 | SKIP 1 | PASS 71 ] Deleting unused snapshots: • plots/plot_quality.png Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘workflows.Rmd’ using rmarkdown Quitting from lines 35-38 [unnamed-chunk-2] (workflows.Rmd) Error: processing vignette 'workflows.Rmd' failed with diagnostics: there is no package called 'ifadv' --- failed re-building ‘workflows.Rmd’ SUMMARY: processing the following file failed: ‘workflows.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 3 NOTEs — Reply to this email directly, view it on GitHub <#61 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABL3FTKGFUDV7EMRKWJ32ILZS32IHAVCNFSM6AAAAABMXIX5MSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBWGYZDGNZXGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[PabRod]

The ifadv package seems to be the main offender, indeed. One question for @mdingemanse: do they give you the option to answer these emails?

[PabRod]

Splitted into issue #117

[PabRod]

does this need to be called twice in the description file? Once via Remotes, once separately?)

To the best of my knowledge, yes.

[mdingemanse]

The ifadv package seems to be the main offender, indeed. One question for @mdingemanse: do they give you the option to answer these emails?

I've forwarded the email to you. Looks like they want to see a new submission that fixes the problem.

[mdingemanse]

Is there a way for us to check whether with the recent changes it is now passing the test? Would love to get some human eyes to look at it for CRAN!

[PabRod]

I'd say we are ready for a new submission. Do you want me to do it, or prefer to try it yourself? It is quite straightforward and takes no more than 10 minutes.

[mdingemanse]

I'd be happy if you can do this round @PabRod but once we're in the same place perhaps you can show me how it works.

[PabRod]

Dear @mdingemanse, you'd like to know that I just resubmitted.

Just so you know, the steps are:

0. Go to RStudio's Build menu
1. Make sure Check passes
2. Build the package, it will generate a *.<version>.tar.gz file
3. Go to CRAN's submission page and fill in the blanks. And rejoice that most of them are auto-filled from DESCRIPTION

[mdingemanse]

Okay. The confirmation link asks me to confirm that I've run winbuilder so I'm trying to do that using this form.

However before I do so, the Check on my system runs into the issue I reported before, of one of the test plots not wanting to be removed.

✔  checking for unstated dependencies in 'tests' ... 
─  checking tests ...
─  Running 'testthat.R' (7.1s)
E  Some test files failed
   Running the tests in 'tests/testthat.R' failed.
   Last 13 lines of output:
     cannot remove file 'plot_quality.png', reason 'Permission denied'
     Backtrace:
         ▆
      1. └─base::file.remove(path)
      

So @PabRod if you have / can build the tarball and confirm that it survives the Winbuilder check I can confirm the submission. And we can try to fix that issue on my system later.

[PabRod]

Dear @mdingemanse,

I just uploaded the tarball Winbuilder check. You are listed as the only maintainer so the results will be mailed to you later today.

Regarding your tests, let's take a look at that in person.

[mdingemanse]

Excellent. No errors, just two notes. These are the relevant log lines:

Found the following (possibly) invalid URLs:
  URL: [email protected]:elpaco-escience/talkr
    From: README.md
    Message: Invalid URI scheme
  URL: https://codecov.io/github/elpaco-escience/talkr (moved to https://app.codecov.io/github/elpaco-escience/talkr)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://fon.hum.uva.nl/IFA-SpokenLanguageCorpora/IFADVcorpus/
    From: inst/doc/workflows.html
    Status: Error
    Message: schannel: SNI or certificate check failed: SEC_E_WRONG_PRINCIPAL (0x80090322) - Der Zielprinzipalname ist falsch.
  For content that is 'Moved Permanently', please change http to https,
  add trailing slashes, or replace the old by the new URL.
* checking R code for possible problems ... NOTE
add_lines: no visible binding for global variable '.data'
add_lines: no visible global function definition for ':='
plot_density: no visible binding for global variable '.data'
plot_scatter: no visible binding for global variable '.data'
report: no visible binding for global variable '.data'
report_combined: no visible binding for global variable '.data'
tokenize: no visible binding for global variable '.data'
Undefined global functions or variables:
  .data :=
...
* DONE
Status: 2 NOTEs

[mdingemanse]

Re the URLs, I don't think we can fix the IFADV one (their certificate is not valid anymore).
Should we fix the Codecov one?

Re the "no visible binding for global variable", I am not sure how to interpret it but since it is a note and not an error I guess it is low priority.

/edit actually I am getting an autoreject by email again (forwarded to you @PabRod ) with the request to "Fix these errors". Although they do provide an out:

If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

[mdingemanse]

I see that the fon.uva.nl site does have a valid certificate, it's just that they have tied it to the www subdomain. So this URL is valid, and we should use it: https://www.fon.hum.uva.nl/IFA-SpokenLanguageCorpora/IFADVcorpus/

[mdingemanse]

So, PR for that URL #122

[mdingemanse]

I lost track of this — did we resubmit? Should we be expecting a response?

[PabRod]

We did resubmit, indeed. As the main author, all the communications should arrive in your inbox (not very practical, I know).

[PabRod]

Just submitted v0.1.2.

@mdingemanse, as the maintainer, you should have received a confirmation email that requires your acceptance. Please share any updates! :)

[PabRod]

Editor Benjamin Altmann requested us the following changes:

• Please do not start the description with "This package", "Functions to", package name, title or similar.

Details:
The Description field is intended to be a (one paragraph) description of what the package does and why it may be useful. Please add more details about the package functionality and implemented methods in your Description text.

• Add references to DESCRIPTION

Details:
If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form authors (year) doi:... authors (year, ISBN:...) or if those are not available: <[https:...]https:...> with no space after 'doi:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")

• Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation.

Note from @PabRod: .Rd files are not supposed to be edited directly. \value field maps @return in the .R source file.

Details:
Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar).
Missing Rd-tags:
geom_token.Rd: \value
geom_turn.Rd: \value
report_stats.Rd: \value
theme_turnPlot.Rd: \value

• Please add small executable examples in your Rd-files to illustrate the use of the exported function but also enable automatic testing.

[PabRod]

Dear @mdingemanse, can you please provide me one or two key references for addressing the second point¹?

Footnotes

1. "Add references to DESCRIPTION" ↩

[PabRod]

From text to talk looks like the key reference. Am I right, @mdingemanse?

[mdingemanse]

Just to record here, too, that the package has cleared all hurdles and is on its way to CRAN now! Finally time to celebrate @bvreede and @PabRod !

One thing that I don't think we know yet is how this may or may not affect regular work. It is probably useful to have a development branch on github in which we can keep iterating.

• What do we need to know about releases, versions, etc.?
• What is the minimum kind of change that justifies a version bump and a resubmission to CRAN?
• Would CRAN be pulling directly from a git branch or do we have to go through the manual submission route anytime we want to release a new version?

[PabRod]

Yay! Let's find a date, place and time 😁

Regarding your practical questions, the answer for the first and second is the same: we just need to use common sense.

Regarding the third, the answer is no. CRAN will never automatically pull from our repository. Whenever we judge a future version as relevant enough to merit a new version number and to be pushed to CRAN, we'll have to do it manually.

Summarizing, this will affect our regular work very, very little. Being in CRAN is 100% good news 😊