* using log directory 'd:/RCompile/CRANincoming/R-devel/MantaID.Rcheck'
* using R Under development (unstable) (2024-07-15 r86902 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 'MantaID/DESCRIPTION' ... OK
* this is package 'MantaID' version '1.0.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Zhengpeng Zeng <molaison@foxmail.com>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  APIs (12:769)

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

Reading CITATION file fails with
  A bibentry of bibtype 'Article' has to specify the fields: author, title, year
when package is not installed.

Size of tarball: 20710014 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MantaID' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'mi_get_importance(train, ': unused argument ("class") 
See 'd:/RCompile/CRANincoming/R-devel/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 installed package size ... 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' 'bacteria' 'final_result.rds' 'logo.svg'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in 'inst/CITATION':
  Error in .bibentry_check_bibentry1(rval): A bibentry of bibtype 'Article' has to specify the fields: author, title, year
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [10s] 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 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 ... [44s] NOTE
mi_unify_mod : prd_new: warning in across(.col = everything(), .fns =
  as.numeric): partial argument match of '.col' to '.cols'
mi: possible error in mi_get_importance(train, "class"): unused
  argument ("class")
mi: no visible binding for global variable 'cor_plor'
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_get_importance: no visible global function definition for 'tibble'
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 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 cor_plor distinct drop_na feature
  geom_bar importance pmap row_ids scale_y_discrete starts_with
  str_detect tibble truth value var weight
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'Example'
Undocumented data sets:
  'Example'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'mi.Rd':
  'mi_data_allID'

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 contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
  'data_blcd.RDS' 'result_BP.rds' 'result_net'
Please use e.g. 'inst/extdata' for non-R data files

* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [15s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 5 WARNINGs, 5 NOTEs