##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cBioPortalData.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cBioPortalData_2.21.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cBioPortalData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* this is package ‘cBioPortalData’ version ‘2.21.5’
* 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 ‘cBioPortalData’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
cBioDataPack   18.751  0.609  28.002
downloadStudy  14.727  0.538  40.490
cBioPortal      1.805  0.056  79.863
cBioPortalData  1.285  0.048  97.993
* 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:
   5.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
  ── Error ('test-cBioPortal.R:59:5'): allSamples returns a tibble structure ─────
  Error: '.service_get_api_file' failed:
    Service Unavailable (HTTP 503).
  Backtrace:
      ▆
   1. └─cBioPortalData::cBioPortal() at test-cBioPortal.R:59:5
   2.   ├─base::withCallingHandlers(...)
   3.   └─AnVIL::Service(...)
   4.     └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
   5.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
  
  [ FAIL 4 | WARN 0 | SKIP 1 | PASS 2 ]
  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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/cBioPortalData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cBioPortalData
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘cBioPortalData’ ...
** this is package ‘cBioPortalData’ version ‘2.21.5’
** using staged installation
** R
** 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 (cBioPortalData)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(cBioPortalData)
Loading required package: AnVIL
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: AnVILBase
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    count


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 object is masked from 'package:dplyr':

    explain

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 object is masked from 'package:dplyr':

    combine

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 objects are masked from 'package:dplyr':

    first, rename

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 objects are masked from 'package:dplyr':

    collapse, desc, slice

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("cBioPortalData")
<html>
<head><title>503 Service Temporarily Unavailable</title></head>
<body>
<center><h1>503 Service Temporarily Unavailable</h1></center>
<hr><center>nginx</center>
</body>
</html>
<html>
<head><title>503 Service Temporarily Unavailable</title></head>
<body>
<center><h1>503 Service Temporarily Unavailable</h1></center>
<hr><center>nginx</center>
</body>
</html>
<html>
<head><title>503 Service Temporarily Unavailable</title></head>
<body>
<center><h1>503 Service Temporarily Unavailable</h1></center>
<hr><center>nginx</center>
</body>
</html>
<html>
<head><title>503 Service Temporarily Unavailable</title></head>
<body>
<center><h1>503 Service Temporarily Unavailable</h1></center>
<hr><center>nginx</center>
</body>
</html>
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 2 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-cBioPortal.R:2:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cBioPortal.R:8:5'): cBioPortal integrity holds ─────────────────
Error: '.service_get_api_file' failed:
  Service Unavailable (HTTP 503).
Backtrace:
    ▆
 1. └─cBioPortalData::cBioPortal() at test-cBioPortal.R:8:5
 2.   ├─base::withCallingHandlers(...)
 3.   └─AnVIL::Service(...)
 4.     └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
 5.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
── Error ('test-cBioPortal.R:21:5'): getDataByGenes returns empty list when no data found ──
Error: '.service_get_api_file' failed:
  Service Unavailable (HTTP 503).
Backtrace:
    ▆
 1. └─cBioPortalData::cBioPortal() at test-cBioPortal.R:21:5
 2.   ├─base::withCallingHandlers(...)
 3.   └─AnVIL::Service(...)
 4.     └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
 5.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
── Error ('test-cBioPortal.R:42:5'): queryGeneTable returns a tibble structure ──
Error: '.service_get_api_file' failed:
  Service Unavailable (HTTP 503).
Backtrace:
    ▆
 1. └─cBioPortalData::cBioPortal() at test-cBioPortal.R:42:5
 2.   ├─base::withCallingHandlers(...)
 3.   └─AnVIL::Service(...)
 4.     └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
 5.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
── Error ('test-cBioPortal.R:59:5'): allSamples returns a tibble structure ─────
Error: '.service_get_api_file' failed:
  Service Unavailable (HTTP 503).
Backtrace:
    ▆
 1. └─cBioPortalData::cBioPortal() at test-cBioPortal.R:59:5
 2.   ├─base::withCallingHandlers(...)
 3.   └─AnVIL::Service(...)
 4.     └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
 5.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")

[ FAIL 4 | WARN 0 | SKIP 1 | PASS 2 ]
Error: Test failures
Execution halted