* using log directory ‘/srv/hornik/tmp/CRAN/MantaID.Rcheck’
* using R Under development (unstable) (2024-07-14 r86899)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘MantaID/DESCRIPTION’ ... OK
* this is package ‘MantaID’ version ‘1.0.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/8s] NOTE
Maintainer: ‘Zhengpeng Zeng <molaison@foxmail.com>’

New maintainer:
  Zhengpeng Zeng <molaison@foxmail.com>
Old maintainer(s):
  Zeng Zhengpeng <molaison@foxmail.com>

Found the following (possibly) invalid URLs:
  URL: https://molaison.shinyapps.io/MantaID/
    From: README.md
    Status: 202
    Message: Accepted
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'biomaRt', 'xgboost', 'caret', 'data.table', 'dplyr', 'ggplot2',
  'keras', 'magrittr', 'mlr3tuning', 'mlr3', 'mlr3learners', 'purrr',
  'reshape2', 'scutr', 'stringr', 'tibble', 'tidyr', 'tidyselect',
  'paradox', 'RColorBrewer', 'ggcorrplot', 'ranger', 'rpart',
  'mlr3hyperband'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘MantaID’ can be installed ... [16s/17s] WARNING
Found the following significant warnings:
  Note: possible error in 'tune(method = tnr("hyperband", ': unused argument (method = tnr("hyperband", eta = 3)) 
See ‘/srv/hornik/tmp/CRAN/MantaID.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘mlr3hyperband’ ‘mlr3learners’ ‘ranger’ ‘rpart’ ‘xgboost’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [21s/21s] NOTE
mi_unify_mod : prd_new: warning in across(.col = everything(), .fns =
  as.numeric): partial argument match of '.col' to '.cols'
mi_filter_feat: no visible binding for global variable ‘Var1’
mi_filter_feat: no visible binding for global variable ‘Var2’
mi_filter_feat: no visible binding for global variable ‘value’
mi_filter_feat: no visible global function definition for ‘pmap’
mi_filter_feat: no visible global function definition for ‘add_column’
mi_filter_feat: no visible global function definition for ‘distinct’
mi_filter_feat: no visible binding for global variable ‘Key’
mi_filter_feat: no visible global function definition for ‘starts_with’
mi_filter_feat: no visible binding for global variable ‘var’
mi_get_ID : to_2col: no visible global function definition for
  ‘str_detect’
mi_get_ID : to_2col: no visible binding for global variable ‘ID’
mi_get_ID : to_2col: no visible global function definition for ‘tibble’
mi_get_ID: no visible global function definition for ‘drop_na’
mi_tune_xgb: possible error in tune(method = tnr("hyperband", eta = 3),
  task = task, learner = learner, resampling = resampling, measures =
  measure, search_space = search_space): unused argument (method =
  tnr("hyperband", eta = 3))
mi_unify_mod : prd_new: no visible binding for global variable ‘truth’
mi_unify_mod : prd_new: no visible binding for global variable
  ‘row_ids’
mi_unify_mod : major: no visible global function definition for
  ‘tibble’
mi_unify_mod : major: no visible binding for global variable ‘weight’
mi_unify_mod: no visible global function definition for ‘pmap’
Undefined global functions or variables:
  ID Key Var1 Var2 add_column distinct drop_na pmap row_ids starts_with
  str_detect tibble truth value var weight
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'mi_predict_new.Rd'
  ‘result’ ‘ifnet’
Documented arguments not in \usage in Rd file 'mi_predict_new.Rd':
  ‘learner’

Undocumented arguments in Rd file 'mi_train_BP.Rd'
  ‘verbose’

Undocumented arguments in Rd file 'mi_unify_mod.Rd'
  ‘result_rg’ ‘result_rp’ ‘result_xgb’ ‘result_BP’ ‘c_value’ ‘pad_len’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [7s/7s] ERROR
Running examples in ‘MantaID-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mi_get_padlen
> ### Title: Get max length of ID data.
> ### Aliases: mi_get_padlen
> 
> ### ** Examples
> 
> data(mi_data_rawID)
Warning in data(mi_data_rawID) : data set ‘mi_data_rawID’ not found
> mi_get_padlen(mi_data_rawID)
Error: object 'mi_data_rawID' not found
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: 1 ERROR, 2 WARNINGs, 4 NOTEs