##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hipathia.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings hipathia_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck'
* using R version 4.4.1 (2024-06-14 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
* using option '--no-vignettes'
* checking for file 'hipathia/DESCRIPTION' ... OK
* this is package 'hipathia' version '3.5.0'
* 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           19.87   2.73   23.89
create_report            18.36   0.80   19.92
get_pathways_annotations 15.11   0.86   16.72
normalize_data           15.06   0.70   16.31
hipathia                 14.14   0.96   15.78
load_pathways            11.72   2.64   14.70
get_pathways_summary     13.29   0.83   14.57
get_node_names           13.29   0.67   14.35
visualize_report         13.22   0.60   14.35
pathway_comparison_plot  12.96   0.80   14.03
node_color               12.89   0.75   14.01
translate_data           12.96   0.67   13.95
get_pathways_list        12.79   0.70   13.53
get_path_names           12.74   0.58   13.93
node_color_per_de        12.50   0.63   13.46
save_results             10.60   1.05   11.89
normalize_paths          10.89   0.64   12.01
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL hipathia
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'hipathia' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hipathia)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(hipathia)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: AnnotationHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

The following object is masked from 'package:AnnotationHub':

    cache

> 
> test_check("hipathia")
Computing pathway...
hsa03320 - PPAR signaling pathway 
hsa04012 - ErbB signaling pathway 
Computing pathway...
hsa03320 - PPAR signaling pathway 
hsa04012 - ErbB signaling pathway 
translated ids = 3184 (1) 
untranslated ids = 3 (0.00094) 
multihit ids = 0 (0) 
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 119 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 119 ]
> 
> proc.time()
   user  system elapsed 
 176.26   12.28  195.25