##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hipathia_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/hipathia.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hipathia/DESCRIPTION’ ... OK
* this is package ‘hipathia’ version ‘3.13.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘hipathia’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      4.1Mb
    extdata   4.5Mb
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘hipathia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_report
> ### Title: Create visualization HTML
> ### Aliases: create_report
> 
> ### ** Examples
> 
> data(comp)
> pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
+ "hsa04012"))
Error: lexical error: invalid char in json text.
                                       <html><body><h1>504 Gateway Tim
                     (right here) ------^
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6.           └─zenodo$getRecordByDOI(doi)
    7.             └─self$getRecords(q = query, all_versions = TRUE, exact = TRUE)
    8.               └─zenReq$execute()
    9.                 └─private$GET(private$url, private$request, private$progress, accept = private$accept)
   10.                   └─httr::content(r, type = "application/json", encoding = "UTF-8")
   11.                     └─httr:::parse_auto(raw, type, encoding, ...)
   12.                       └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
   13.                         └─jsonlite::fromJSON(...)
   14.                           └─jsonlite:::parse_and_simplify(...)
   15.                             └─jsonlite:::parseJSON(txt, bigint_as_char)
   16.                               └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/hipathia.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL hipathia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘hipathia’ ...
** this is package ‘hipathia’ version ‘3.13.0’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: zen4R
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: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    components, union

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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

    normalize, path

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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

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
Loading required package: Seqinfo
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

> 
> test_check("hipathia")
[zen4R][INFO] ZenodoRecord - Download in sequential mode 
[zen4R][INFO] ZenodoRecord - Will download 1 file from record '18268423' (doi: '10.5281/zenodo.18268423') - total size: 10.9 MiB 
[zen4R][INFO] Downloading file 'meta_graph_info_hsa_v3.rda' - size: 10.9 MiB
trying URL 'https://zenodo.org/api/records/18268423/files/meta_graph_info_hsa_v3.rda/content'
Content type 'application/octet-stream' length 11383594 bytes (10.9 MB)
==================================================
downloaded 10.9 MB

[zen4R][INFO] File downloaded at '/home/biocbuild/R/R-4.5.0/site-library/hipathia/data/v3'.
[zen4R][INFO] ZenodoRecord - Verifying file integrity... 
[zen4R][INFO] File 'meta_graph_info_hsa_v3.rda': integrity verified (md5sum: 0a0994d7f99cf59f67a7985a43f9265c)
[zen4R][INFO] ZenodoRecord - End of download 
[zen4R][INFO] ZenodoRecord - Download in sequential mode 
[zen4R][INFO] ZenodoRecord - Will download 1 file from record '18268423' (doi: '10.5281/zenodo.18268423') - total size: 36.8 KiB 
[zen4R][INFO] Downloading file 'annofuns_uniprot_hsa_v3.rda' - size: 36.8 KiB
trying URL 'https://zenodo.org/api/records/18268423/files/annofuns_uniprot_hsa_v3.rda/content'
Content type 'application/octet-stream' length 37718 bytes (36 KB)
==================================================
downloaded 36 KB

[zen4R][INFO] File downloaded at '/home/biocbuild/R/R-4.5.0/site-library/hipathia/data/v3'.
[zen4R][INFO] ZenodoRecord - Verifying file integrity... 
[zen4R][INFO] File 'annofuns_uniprot_hsa_v3.rda': integrity verified (md5sum: 7672c4b3832e581798e34c8a396e512d)
[zen4R][INFO] ZenodoRecord - End of download 
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 84 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-color-node.R:10:1'): (code run outside of `test_that()`) ───────
Error: lexical error: invalid char in json text.
                                       <html><body><h1>504 Gateway Tim
                     (right here) ------^

Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-color-node.R:10:1
  2.   └─hipathia:::load_mgi(species)
  3.     └─hipathia:::get_file(file)
  4.       └─zen4R::download_zenodo(...)
  5.         └─zen4R::get_zenodo(doi = doi, sandbox = sandbox, logger = logger)
  6.           └─zenodo$getRecordByDOI(doi)
  7.             └─self$getRecords(q = query, all_versions = TRUE, exact = TRUE)
  8.               └─zenReq$execute()
  9.                 └─private$GET(private$url, private$request, private$progress, accept = private$accept)
 10.                   └─httr::content(r, type = "application/json", encoding = "UTF-8")
 11.                     └─httr:::parse_auto(raw, type, encoding, ...)
 12.                       └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
 13.                         └─jsonlite::fromJSON(...)
 14.                           └─jsonlite:::parse_and_simplify(...)
 15.                             └─jsonlite:::parseJSON(txt, bigint_as_char)
 16.                               └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('test-hipathia.R:8:1'): (code run outside of `test_that()`) ──────────
Error: lexical error: invalid char in json text.
                                       <html><body><h1>504 Gateway Tim
                     (right here) ------^

Backtrace:
     ▆
  1. └─hipathia::load_pathways(...) at test-hipathia.R:8:1
  2.   └─hipathia:::load_mgi(species)
  3.     └─hipathia:::get_file(file)
  4.       └─zen4R::download_zenodo(...)
  5.         └─zen4R::get_zenodo(doi = doi, sandbox = sandbox, logger = logger)
  6.           └─zenodo$getRecordByDOI(doi)
  7.             └─self$getRecords(q = query, all_versions = TRUE, exact = TRUE)
  8.               └─zenReq$execute()
  9.                 └─private$GET(private$url, private$request, private$progress, accept = private$accept)
 10.                   └─httr::content(r, type = "application/json", encoding = "UTF-8")
 11.                     └─httr:::parse_auto(raw, type, encoding, ...)
 12.                       └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
 13.                         └─jsonlite::fromJSON(...)
 14.                           └─jsonlite:::parse_and_simplify(...)
 15.                             └─jsonlite:::parseJSON(txt, bigint_as_char)
 16.                               └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('test-quantify.R:10:1'): (code run outside of `test_that()`) ─────────
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html> <!-- This "appl
                     (right here) ------^

Backtrace:
     ▆
  1. └─hipathia::quantify_terms(results, pathways, "GO") at test-quantify.R:10:1
  2.   └─hipathia:::quantify_funs(...)
  3.     └─hipathia:::load_annofuns(dbannot, species)
  4.       └─hipathia:::get_file(file)
  5.         └─zen4R::download_zenodo(...)
  6.           └─zen4R::get_zenodo(doi = doi, sandbox = sandbox, logger = logger)
  7.             └─zenodo$getRecordByDOI(doi)
  8.               └─self$getRecords(q = query, all_versions = TRUE, exact = TRUE)
  9.                 └─zenReq$execute()
 10.                   └─private$GET(private$url, private$request, private$progress, accept = private$accept)
 11.                     └─httr::content(r, type = "application/json", encoding = "UTF-8")
 12.                       └─httr:::parse_auto(raw, type, encoding, ...)
 13.                         └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
 14.                           └─jsonlite::fromJSON(...)
 15.                             └─jsonlite:::parse_and_simplify(...)
 16.                               └─jsonlite:::parseJSON(txt, bigint_as_char)
 17.                                 └─jsonlite:::parse_string(txt, bigint_as_char)
── Error ('test-translate-matrix.R:8:1'): (code run outside of `test_that()`) ──
Error: lexical error: invalid char in json text.
                                       <html><body><h1>504 Gateway Tim
                     (right here) ------^

Backtrace:
     ▆
  1. └─hipathia:::translate_matrix(brca_data, "hsa") at test-translate-matrix.R:8:1
  2.   └─hipathia:::load_xref(species)
  3.     └─hipathia:::get_file(file)
  4.       └─zen4R::download_zenodo(...)
  5.         └─zen4R::get_zenodo(doi = doi, sandbox = sandbox, logger = logger)
  6.           └─zenodo$getRecordByDOI(doi)
  7.             └─self$getRecords(q = query, all_versions = TRUE, exact = TRUE)
  8.               └─zenReq$execute()
  9.                 └─private$GET(private$url, private$request, private$progress, accept = private$accept)
 10.                   └─httr::content(r, type = "application/json", encoding = "UTF-8")
 11.                     └─httr:::parse_auto(raw, type, encoding, ...)
 12.                       └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
 13.                         └─jsonlite::fromJSON(...)
 14.                           └─jsonlite:::parse_and_simplify(...)
 15.                             └─jsonlite:::parseJSON(txt, bigint_as_char)
 16.                               └─jsonlite:::parse_string(txt, bigint_as_char)

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted