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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hipathia.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings hipathia_3.6.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'hipathia/DESCRIPTION' ... OK
* this is package 'hipathia' version '3.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'hipathia' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      4.1Mb
    extdata   4.4Mb
* checking package directory ... OK
* checking 'build' directory ... 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 ... 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DAreport: no visible binding for global variable 'ID'
DAreport: no visible binding for global variable 'FDRp.value'
DAtop : <anonymous>: no visible binding for global variable
  'FDRp.value'
DAtop : <anonymous>: no visible binding for global variable 'statistic'
DAtop : <anonymous>: no visible binding for global variable 'p.value'
DAtop : <anonymous>: no visible binding for global variable 'name'
DAtop : <anonymous>: no visible binding for global variable 'logPV'
DAtop : <anonymous>: no visible binding for global variable 'feature'
DAtop: no visible binding for global variable 'name'
DAtop: no visible binding for global variable 'logPV'
DAtop: no visible binding for global variable 'direction'
get_edges_df: no visible binding for global variable 'from'
get_edges_df: no visible binding for global variable 'to'
nsig_plot: no visible binding for global variable 'total'
nsig_plot: no visible binding for global variable 'UPs'
nsig_plot: no visible binding for global variable 'DOWNs'
nsig_plot: no visible binding for global variable 'feature'
nsig_plot: no visible binding for global variable 'UP'
nsig_plot: no visible binding for global variable 'DOWN'
nsig_plot: no visible binding for global variable 'Not'
nsig_plot: no visible binding for global variable 'value'
nsig_plot: no visible binding for global variable 'variable'
prepare_DAedges: no visible binding for global variable 'to'
prepare_DAedges: no visible binding for global variable 'functional'
prepare_DAedges: no visible binding for global variable 'status'
prepare_DAedges: no visible binding for global variable 'type'
prepare_DAnodes : <anonymous>: no visible binding for global variable
  'ID'
prepare_DAnodes : <anonymous>: no visible binding for global variable
  'FDRp.value'
prepare_DAnodes : <anonymous>: no visible binding for global variable
  'statistic'
prepare_DAnodes : <anonymous>: no visible binding for global variable
  'p.value'
prepare_edges: no visible binding for global variable 'to'
prepare_edges: no visible binding for global variable 'functional'
summary_plot: no visible binding for global variable 'total'
summary_plot: no visible binding for global variable 'UPs'
summary_plot: no visible binding for global variable 'DOWNs'
summary_plot: no visible binding for global variable 'name'
summary_plot: no visible binding for global variable 'UP'
summary_plot: no visible binding for global variable 'DOWN'
summary_plot: no visible binding for global variable 'Not'
summary_plot: no visible binding for global variable 'value'
summary_plot: no visible binding for global variable 'variable'
summary_plot: no visible binding for global variable 'UP.nodes'
summary_plot: no visible binding for global variable 'DOWN.nodes'
summary_plot: no visible binding for global variable 'nodes'
summary_plot: no visible binding for global variable 'ratio.sigs'
summary_plot: no visible binding for global variable 'ratio.UPs'
summary_plot: no visible binding for global variable 'ratio.DOWNs'
Undefined global functions or variables:
  DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction
  feature from functional logPV name nodes p.value ratio.DOWNs
  ratio.UPs ratio.sigs statistic status to total type value variable
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
quantify_terms           29.58   3.18   34.44
get_pathways_annotations 23.94   1.74   26.13
create_report            22.69   1.14   25.38
normalize_data           21.99   1.11   23.53
visualize_report         20.44   1.04   21.66
translate_data           20.26   0.96   21.49
node_color_per_de        19.76   0.89   20.96
node_color               19.69   0.94   20.81
save_results             19.16   1.00   20.31
get_path_names           19.27   0.87   20.27
normalize_paths          19.14   0.94   20.23
load_pathways            18.91   0.84   20.64
get_node_names           18.66   0.87   19.64
get_pathways_list        18.58   0.91   19.56
pathway_comparison_plot  18.17   1.06   19.50
hipathia                 17.50   0.91   18.64
get_pathways_summary     15.89   0.76   16.80
DAreport                  2.31   0.53   10.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck/00check.log'
for details.