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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hipathia.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings hipathia_2.99.3.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/hipathia.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'hipathia/DESCRIPTION' ... OK
* this is package 'hipathia' version '2.99.3'
* 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 R 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           19.45   1.61   21.61
create_report            15.65   0.68   84.92
get_pathways_annotations 15.33   0.94   16.45
hipathia                 15.08   0.54   15.68
normalize_paths          14.40   0.34   14.82
normalize_data           13.73   0.60   14.62
translate_data           13.34   0.59   14.05
node_color               13.33   0.48   13.89
load_pathways            13.20   0.50   16.39
get_path_names           13.16   0.42   13.63
visualize_report         13.05   0.47   15.06
get_pathways_summary     13.04   0.48   13.72
get_pathways_list        13.00   0.50   13.71
node_color_per_de        13.03   0.44   13.66
save_results             12.84   0.53   13.54
pathway_comparison_plot  12.60   0.57   13.25
get_node_names           12.31   0.31   12.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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-3.17-bioc-rtools43/meat/hipathia.Rcheck/00check.log'
for details.