Fix CRAN check warnings on r-devel for cross-references in R docs #7982

exalate-issue-sync · 2023-05-11T18:34:44Z

Here's the report from CRAN auto-check service. Cross references are bad on r-devel (debian linux) for the following functions. Info about this issue here: [https://stackoverflow.com/questions/62420464/non-file-package-anchored-links-in-documentation-object|https://stackoverflow.com/questions/62420464/non-file-package-anchored-links-in-documentation-object]

This warning came back at the same time as an unrelated error [https://0xdata.atlassian.net/browse/PUBDEV-7642|https://0xdata.atlassian.net/browse/PUBDEV-7642|smart-link] (which has now been fixed), so our last CRAN submission failed. So this documentation warning is a blocker which needs to be fixed before we can update h2o on CRAN. My plan is to get this fix merged into rel-z, but then also to patch the h2o_3.30.0.6.tar.gz file with the fix so we can submit to 3.30.0.6 to CRAN (and don’t have to wait until 3.30.1.1).

{noformat}Flavor: r-devel-linux-x86_64-debian-gcc
Check: Rd cross-references, Result: WARNING
Non-file package-anchored link(s) in documentation object 'h2o.abs.Rd':
'[base]{abs}'

Non-file package-anchored link(s) in documentation object 'h2o.acos.Rd':
'[base]{acos}'

Non-file package-anchored link(s) in documentation object 'h2o.asfactor.Rd':
'[base]{as.numeric}'

Non-file package-anchored link(s) in documentation object 'h2o.asnumeric.Rd':
'[base]{as.factor}'

Non-file package-anchored link(s) in documentation object 'h2o.ceiling.Rd':
'[base]{ceiling}'

Non-file package-anchored link(s) in documentation object 'h2o.cos.Rd':
'[base]{cos}'

Non-file package-anchored link(s) in documentation object 'h2o.cosh.Rd':
'[base]{cosh}'

Non-file package-anchored link(s) in documentation object 'h2o.cummax.Rd':
'[base]{cummax}'

Non-file package-anchored link(s) in documentation object 'h2o.cummin.Rd':
'[base]{cummin}'

Non-file package-anchored link(s) in documentation object 'h2o.cumprod.Rd':
'[base]{cumprod}'

Non-file package-anchored link(s) in documentation object 'h2o.exp.Rd':
'[base]{exp}'

Non-file package-anchored link(s) in documentation object 'h2o.floor.Rd':
'[base]{floor}'

Non-file package-anchored link(s) in documentation object 'h2o.ischaracter.Rd':
'[base]{is.character}'

Non-file package-anchored link(s) in documentation object 'h2o.isfactor.Rd':
'[base]{is.factor}'

Non-file package-anchored link(s) in documentation object 'h2o.isnumeric.Rd':
'[base]{is.numeric}'

Non-file package-anchored link(s) in documentation object 'h2o.log.Rd':
'[base]{log}'

Non-file package-anchored link(s) in documentation object 'h2o.log10.Rd':
'[base]{log10}'

Non-file package-anchored link(s) in documentation object 'h2o.log1p.Rd':
'[base]{log1p}'

Non-file package-anchored link(s) in documentation object 'h2o.log2.Rd':
'[base]{log2}'

Non-file package-anchored link(s) in documentation object 'h2o.max.Rd':
'[base]{max}'

Non-file package-anchored link(s) in documentation object 'h2o.mean.Rd':
'[base]{rowMeans}' '[base]{colMeans}'

Non-file package-anchored link(s) in documentation object 'h2o.min.Rd':
'[base]{min}'

Non-file package-anchored link(s) in documentation object 'h2o.ncol.Rd':
'[base]{ncol}'

Non-file package-anchored link(s) in documentation object 'h2o.rbind.Rd':
'[base]{rbind}'

Non-file package-anchored link(s) in documentation object 'h2o.round.Rd':
'[base]{round}'

Non-file package-anchored link(s) in documentation object 'h2o.signif.Rd':
'[base]{signif}'

Non-file package-anchored link(s) in documentation object 'h2o.sin.Rd':
'[base]{sin}'

Non-file package-anchored link(s) in documentation object 'h2o.sqrt.Rd':
'[base]{sqrt}'

Non-file package-anchored link(s) in documentation object 'h2o.tan.Rd':
'[base]{tan}'

Non-file package-anchored link(s) in documentation object 'h2o.tanh.Rd':
'[base]{tanh}'

Non-file package-anchored link(s) in documentation object 'h2o.trunc.Rd':
'[base]{trunc}'

Non-file package-anchored link(s) in documentation object 'h2o.var.Rd':
'[stats]{var}'

Non-file package-anchored link(s) in documentation object 'h2o.which_max.Rd':
'[base]{which.max}'{noformat}

exalate-issue-sync · 2023-05-11T18:34:46Z

Erin LeDell commented: Rhub Output on 3.30.1.1:

{noformat}> devtools::check_rhub(pkg = "/Users/me/Downloads/h2o_3.30.1.1")
✓ checking for file ‘/Users/me/Downloads/h2o_3.30.1.1/DESCRIPTION’ ...
─ preparing ‘h2o’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts (546ms)
─ checking for empty or unneeded directories
Removed empty directory ‘h2o/inst/java’
─ building ‘h2o_3.30.1.1.tar.gz’

‘erin@h2o.ai’ is not validated, or does not match the package maintainer's email. To
validate it now, please enter the email address below. Note that R-hub will send a token to
this address. If the address does not belong to you, quit now by pressing ENTER .

Email address: erin@h2o.ai

Please check your emails for the R-hub access token.
Token: 8c8ed233770940b4b9c74e9d58615c98
Token added for ‘erin@h2o.ai’

─ Uploading package
─ Preparing build, see status at
https://builder.r-hub.io/status/h2o_3.30.1.1.tar.gz-605def10931143a882e456e44884803a
https://builder.r-hub.io/status/h2o_3.30.1.1.tar.gz-179debfea4de476ca4c9589a1b82d523
https://builder.r-hub.io/status/h2o_3.30.1.1.tar.gz-f927f2e543dd4ffaa08bd170d9c34079
─ Build started
─ Creating new user
─ Downloading and unpacking package file
─ Querying package dependencies
─ Installing package dependencies
─ Running R CMD check
setting R_CHECK_FORCE_SUGGESTS to false
setting R_COMPILE_AND_INSTALL_PACKAGES to never
setting R_CHECK_THINGS_IN_CHECK_DIR to false
setting R_REMOTES_STANDALONE to true
setting R_REMOTES_NO_ERRORS_FROM_WARNINGS to true
setting R_CHECK_FORCE_SUGGESTS to true
setting R_CHECK_CRAN_INCOMING_USE_ASPELL to true
─ using log directory 'C:/Users/USERtYUqIwHbxL/h2o.Rcheck' (1.1s)
─ using R Under development (unstable) (2020-07-05 r78784)
─ using platform: x86_64-w64-mingw32 (64-bit)
─ using session charset: ISO8859-1
─ using option '--as-cran' (1s)
✓ checking for file 'h2o/DESCRIPTION'
─ checking extension type ... Package
─ this is package 'h2o' version '3.30.1.1'
─ checking CRAN incoming feasibility ... Note_to_CRAN_maintainers (1.1s)
Maintainer: 'Erin LeDell erin@h2o.ai'
✓ checking package namespace information
✓ checking package dependencies
✓ checking if this is a source package (1.3s)
✓ checking if there is a namespace
✓ checking for executable files
✓ checking for hidden files and directories
✓ checking for portable file names (1.3s)
✓ checking serialization versions
✓ checking whether package 'h2o' can be installed
N checking installed package size
installed size is 134.3Mb
R 1.1Mb
sub-directories of 1Mb or more:
java 132.0Mb
✓ checking package directory (1.1s)
✓ checking for future file timestamps
✓ checking DESCRIPTION meta-information
✓ checking top-level files
✓ checking for left-over files (1.1s)
✓ checking index information
✓ checking package subdirectories
✓ checking R files for non-ASCII characters
✓ checking R files for syntax errors (1.5s)
✓ checking whether the package can be loaded
✓ checking whether the package can be loaded with stated dependencies
✓ checking whether the package can be unloaded cleanly
✓ checking whether the namespace can be loaded with stated dependencies (1.1s)
✓ checking whether the namespace can be unloaded cleanly
✓ checking loading without being on the library search path
✓ checking use of S3 registration
✓ checking dependencies in R code
✓ checking S3 generic/method consistency
✓ checking replacement functions
✓ checking foreign function calls
✓ checking R code for possible problems (1.3s)
✓ checking Rd files
✓ checking Rd metadata
✓ checking Rd line widths
W checking Rd cross-references (1.1s)
Package unavailable to check Rd xrefs: 'plyr'
Non-file package-anchored link(s) in documentation object 'h2o.abs.Rd':
'[base]{abs}'