* using log directory ‘/srv/hornik/tmp/CRAN/MantaID.Rcheck’
* using R Under development (unstable) (2024-07-20 r86909)
* 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 ... [3s/4s] NOTE
Maintainer: ‘Zhengpeng Zeng <molaison@foxmail.com>’

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-07-16 as issues were not corrected
    in time.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Size of tarball: 33316206 bytes
* 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/16s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘Graph’ ‘MantaID_tutorial.html’ ‘bacteria’ ‘logo.svg’
* 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_clean_data: no visible global function definition for ‘all_of’
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 binding for global variable ‘ID’
mi_get_importance: no visible global function definition for
  ‘scale_y_discrete’
mi_get_importance: no visible global function definition for ‘geom_bar’
mi_get_importance: no visible binding for global variable ‘importance’
mi_get_importance: no visible binding for global variable ‘feature’
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 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 all_of distinct feature geom_bar
  importance pmap row_ids scale_y_discrete starts_with 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [9s/9s] OK
* 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: 5 NOTEs