Last updated on 2025-12-07 09:50:08 CET.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| csmpv | 5 | 3 | 5 | |
| NMRphasing | 1 | 12 |
Current CRAN status: ERROR: 5, NOTE: 3, OK: 5
Version: 1.0.3
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Aixiang Jiang <aijiang@bccrc.ca>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Aixiang",
family = "Jiang",
role = c("aut", "cre", "cph"),
email = "aijiang@bccrc.ca",
comment = c(ORCID = "0000-0002-6153-7595"))
as necessary.
The Description field contains
<arXiv:1603.02754>, - Aoki et al. (2023) <doi:10.1200/JCO.23.01115>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: package dependencies
Result: ERROR
Packages required but not available: 'Hmisc', 'rms', 'survminer'
Packages suggested but not available for checking:
'knitr', 'rmarkdown', 'devtools'
VignetteBuilder package required for checking but not installed: ‘knitr’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘csmpv-Ex.R’ failed
The error most likely occurred in:
> ### Name: LASSO2_XGBtraining
> ### Title: Variable Selection with LASSO2 and Modeling with XGBoost
> ### Aliases: LASSO2_XGBtraining
>
> ### ** Examples
>
> # Load in data sets:
> data("datlist", package = "csmpv")
> tdat = datlist$training
>
> # The function saves files locally. You can define your own temporary directory.
> # If not, tempdir() can be used to get the system's temporary directory.
> temp_dir = tempdir()
> # As an example, let's define Xvars, which will be used later:
> Xvars = c("highIPI", "B.Symptoms", "MYC.IHC", "BCL2.IHC", "CD10.IHC", "BCL6.IHC")
> # The function can work with three different outcome types.
> # Here, we use binary as an example:
> blxfit = LASSO2_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig",
+ outfile = paste0(temp_dir, "/binary_LASSO2_XGBoost"))
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :
Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'gamma' has been renamed to 'min_split_loss'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version.
Error in xgboost::xgboost(objective = "binary:logistic", data = Dtrain, :
argument "y" is missing, with no default
Calls: LASSO2_XGBtraining ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘csmpv_vignette.rmd’ using rmarkdown
Quitting from csmpv_vignette.rmd:421-425 [unnamed-chunk-34]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgboost::xgboost()`:
! argument "y" is missing, with no default
---
Backtrace:
▆
1. └─csmpv::XGBtraining(...)
2. └─xgboost::xgboost(...)
3. └─xgboost:::process.y.margin.and.objective(...)
4. └─base::NROW(y)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'csmpv_vignette.rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building ‘csmpv_vignette.rmd’
SUMMARY: processing the following file failed:
‘csmpv_vignette.rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘csmpv-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LASSO2_XGBtraining
> ### Title: Variable Selection with LASSO2 and Modeling with XGBoost
> ### Aliases: LASSO2_XGBtraining
>
> ### ** Examples
>
> # Load in data sets:
> data("datlist", package = "csmpv")
> tdat = datlist$training
>
> # The function saves files locally. You can define your own temporary directory.
> # If not, tempdir() can be used to get the system's temporary directory.
> temp_dir = tempdir()
> # As an example, let's define Xvars, which will be used later:
> Xvars = c("highIPI", "B.Symptoms", "MYC.IHC", "BCL2.IHC", "CD10.IHC", "BCL6.IHC")
> # The function can work with three different outcome types.
> # Here, we use binary as an example:
> blxfit = LASSO2_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig",
+ outfile = paste0(temp_dir, "/binary_LASSO2_XGBoost"))
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :
Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'gamma' has been renamed to 'min_split_loss'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :
Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version.
Error in xgboost::xgboost(objective = "binary:logistic", data = Dtrain, :
argument "y" is missing, with no default
Calls: LASSO2_XGBtraining ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘csmpv_vignette.rmd’ using rmarkdown
Quitting from csmpv_vignette.rmd:421-425 [unnamed-chunk-34]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgboost::xgboost()`:
! argument "y" is missing, with no default
---
Backtrace:
▆
1. └─csmpv::XGBtraining(...)
2. └─xgboost::xgboost(...)
3. └─xgboost:::process.y.margin.and.objective(...)
4. └─base::NROW(y)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'csmpv_vignette.rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building ‘csmpv_vignette.rmd’
SUMMARY: processing the following file failed:
‘csmpv_vignette.rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.3
Check: installed package size
Result: NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
doc 7.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: WARN: 1, OK: 12
Version: 1.0.7
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking: 'knitr', 'rmarkdown'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.7
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc