Here are the results ofrom devtools::check_win_devel() in preparaion for a potential CRAN release. I will create separate sub-issues for each of the five NOTES and one ERROR. If you assign yourself to one of the sub-issues, please edit the bullet list below to indicate what you have done.
[ ] Possibly mis-spelled words
[x] URLs permanently moved [@Puzzled-Face #848]
[x] Non-portable file paths [@puzzled-Face #849]
[ ] Documentation issues
[ ] example.Rmd fails to knit on CRAN
[ ] knit_print.qmd fails to render on CRAN
* using log directory 'd:/RCompile/CRANguest/R-devel/crmPack.Rcheck'
* using R Under development (unstable) (2024-06-26 r86840 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 'crmPack/DESCRIPTION' ... OK
* this is package 'crmPack' version '2.0.0.9155'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [16s] NOTE
Maintainer: 'Daniel Sabanes Bove <john.kirkpatrick@roche.com>'
Version contains large components (2.0.0.9155)
Days since last update: 1
New maintainer:
Daniel Sabanes Bove <john.kirkpatrick@roche.com>
Old maintainer(s):
Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Possibly misspelled words in DESCRIPTION:
Bove (34:26)
Sabanes (34:18)
al (34:34)
et (34:31)
Found the following (possibly) invalid URLs:
URL: http://CRAN.R-project.org/package=crmPack
From: inst/doc/crmPack-jss-paper.html
CRAN URL not in canonical form
URL: http://ggplot2.org
From: inst/doc/crmPack-jss-paper.html
Status: Error
Message: Could not resolve host: ggplot2.org
URL: http://mcmc-jags.sourceforge.net (moved to https://mcmc-jags.sourceforge.io/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: http://onlinelibrary.wiley.com/doi/10.1002/sim.3230 (moved to https://onlinelibrary.wiley.com/doi/10.1002/sim.3230)
From: inst/doc/example.html
Status: 301
Message: Moved Permanently
URL: http://www.berryconsultants.com/software (moved to https://www.berryconsultants.com/software/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: http://www.cytel.com/software/east/ (moved to https://cytel.com/east-horizon/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: http://www.iconplc.com/innovation/addplan/ (moved to https://www.iconplc.com/innovation/addplan/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: http://www.sas.com/ (moved to https://www.sas.com/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: http://www.stata.com/ (moved to https://www.stata.com/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: https://cran.r-project.org/web/packages/knitr/vignettes/knit_print.html
From: inst/doc/knit_print.html
Status: 200
Message: OK
CRAN URL not in canonical form
URL: https://www.ncbi.nlm.nih.gov/pubmed/21318084 (moved to https://pubmed.ncbi.nlm.nih.gov/21318084/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: https://www.ncbi.nlm.nih.gov/pubmed/2790129 (moved to https://pubmed.ncbi.nlm.nih.gov/2790129/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
URL: https://yihui.name/knitr/ (moved to https://yihui.org/knitr/)
From: inst/doc/crmPack-jss-paper.html
Status: 301
Message: Moved Permanently
The canonical URL of the CRAN page for a package is
https://CRAN.R-project.org/package=pkgname
Canonical CRAN.R-project.org URLs use https.
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 ... OK
* 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 ... NOTE
Found the following non-portable file paths:
crmPack/vignettes/crmPack-jss-paper_cache/html/OneParExp-model-example_339dc3c612da97ca32ef5a87efc0f63a.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/OneParExp-model-example_339dc3c612da97ca32ef5a87efc0f63a.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/OneParExp-model-example_339dc3c612da97ca32ef5a87efc0f63a.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/classOneParExp-dose_prob_12659bc78c487089dbfdbfe1e7ff85dd.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/classOneParExp-dose_prob_12659bc78c487089dbfdbfe1e7ff85dd.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/classOneParExp-dose_prob_12659bc78c487089dbfdbfe1e7ff85dd.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/classOneParExp-init_527bdf64d783a418c1cb035e1dc9a679.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/classOneParExp-init_527bdf64d783a418c1cb035e1dc9a679.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/classOneParExp-init_527bdf64d783a418c1cb035e1dc9a679.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/doseRecommendation_4730acae2bb8e7aa1d0ed71e8e1bd1dd.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/doseRecommendation_4730acae2bb8e7aa1d0ed71e8e1bd1dd.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/doseRecommendation_4730acae2bb8e7aa1d0ed71e8e1bd1dd.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/newNextBest-def_06e74ef99a533205dd5edf08c3ab58b4.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/newNextBest-method_e2ea244dbbdea34fd8a954385fcd2c47.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/newNextBest-method_e2ea244dbbdea34fd8a954385fcd2c47.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/newNextBest-method_e2ea244dbbdea34fd8a954385fcd2c47.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/newNextBest-try_6fd048b969d641555cb8f29b552400cd.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/newdualstopping-rule_10b3946482c88235fe2bb5ce71d7dabf.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/newdualstopping-rule_10b3946482c88235fe2bb5ce71d7dabf.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/newdualstopping-rule_10b3946482c88235fe2bb5ce71d7dabf.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/nextBest-ncrm-def_c389c78fb3cda4189a0c99e37489d158.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/nextBest-ncrm-def_c389c78fb3cda4189a0c99e37489d158.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/nextBest-ncrm-def_c389c78fb3cda4189a0c99e37489d158.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/nextBest-ncrm-eval_4e72125736095de4fe2d1f6615384cb5.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/nextBest-ncrm-eval_4e72125736095de4fe2d1f6615384cb5.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/nextBest-ncrm-eval_4e72125736095de4fe2d1f6615384cb5.rdx
crmPack/vignettes/crmPack-jss-paper_cache/html/sim-summary-plot_3aff30c0eb825ce978dad370e904167c.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/stop-rules-eval_758cbaf55dfd673e52ebbb07833804cc.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/true-def-alternative_8c63f0de4ed8c6150472573d761959c8.RData
crmPack/vignettes/crmPack-jss-paper_cache/html/true-def-alternative_8c63f0de4ed8c6150472573d761959c8.rdb
crmPack/vignettes/crmPack-jss-paper_cache/html/true-def-alternative_8c63f0de4ed8c6150472573d761959c8.rdx
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'crmPack' 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 whether startup messages can be suppressed ... 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 ... [25s] OK
* checking Rd files ... NOTE
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:45: Lost braces
45 | \item{trueNu}{(not with code{\linkS4class{EffFlexi}}) the precision, the inverse of the
| ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:48: Lost braces
48 | \item{trueSigma2}{(only with code{\linkS4class{EffFlexi}}) the true variance of the efficacy
| ^
checkRd: (-1) simulate-DualResponsesSamplesDesign-method.Rd:51: Lost braces
51 | \item{trueSigma2betaW}{(only with code{\linkS4class{EffFlexi}}) the true variance for the
| ^
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'crmPack-package.Rd':
'-package'
* 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 ... [95s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [162s] OK
Running 'test-package-load.R'
Running 'testthat.R' [161s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [422s] ERROR
Error(s) in re-building vignettes:
--- re-building 'crmPack-jss-paper.Rmd' using rmarkdown
Warning: The label(s) fig:doseRecommendation not found
--- finished re-building 'crmPack-jss-paper.Rmd'
--- re-building 'example.Rmd' using rmarkdown
Quitting from lines 67-76 [unnamed-chunk-1] (example.Rmd)
Error: processing vignette 'example.Rmd' failed with diagnostics:
Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
--- failed re-building 'example.Rmd'
--- re-building 'migration_from_the_old_crmPack.Rmd' using rmarkdown
--- finished re-building 'migration_from_the_old_crmPack.Rmd'
--- re-building 'ordinal-crm.Rmd' using rmarkdown
--- finished re-building 'ordinal-crm.Rmd'
--- re-building 'parallel_computing_with_extensions.Rmd' using rmarkdown
--- finished re-building 'parallel_computing_with_extensions.Rmd'
--- re-building 'rolling-crm.Rmd' using rmarkdown
--- finished re-building 'rolling-crm.Rmd'
--- re-building 'simulations.Rmd' using rmarkdown
--- finished re-building 'simulations.Rmd'
--- re-building 'tidy_method.Rmd' using rmarkdown
--- finished re-building 'tidy_method.Rmd'
--- re-building 'trial_analysis.Rmd' using rmarkdown
--- finished re-building 'trial_analysis.Rmd'
--- re-building 'trial_definition.Rmd' using rmarkdown
--- finished re-building 'trial_definition.Rmd'
--- re-building 'trial_sanity_checks.Rmd' using rmarkdown
--- finished re-building 'trial_sanity_checks.Rmd'
--- re-building 'trial_simulation.Rmd' using rmarkdown
--- finished re-building 'trial_simulation.Rmd'
--- re-building 'knit_print.qmd' using html
processing file: knit_print.qmd
Error in `getClasses()`:
! could not find function "getClasses"
Quitting from lines 323-363 [coverage-1] (knit_print.qmd)
Execution halted
Error: processing vignette 'knit_print.qmd' failed with diagnostics:
✖ Error running quarto cli.
Caused by error:
! System command 'quarto.exe' failed
--- failed re-building 'knit_print.qmd'
SUMMARY: processing the following files failed:
'example.Rmd' 'knit_print.qmd'
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [25s] OK
* checking HTML version of manual ... [47s] NOTE
Found the following HTML validation problems:
plot-PseudoDualFlexiSimulations-missing-method.html:19:1 (plot-PseudoDualFlexiSimulations-missing-method.Rd:5): Warning: missing </h2> before <dl>
plot-PseudoDualFlexiSimulations-missing-method.html:32:28 (plot-PseudoDualFlexiSimulations-missing-method.Rd:12): Warning: discarding unexpected </h2>
* DONE
Status: 1 ERROR, 5 NOTEs
Here are the results ofrom
devtools::check_win_devel()in preparaion for a potential CRAN release. I will create separate sub-issues for each of the five NOTES and one ERROR. If you assign yourself to one of the sub-issues, please edit the bullet list below to indicate what you have done.example.Rmdfails to knit on CRANknit_print.qmdfails to render on CRAN