R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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: 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

Attaching package: 'BiocGenerics'

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

    combine, intersect, setdiff, 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, sort, table,
    tapply, union, 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 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: 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

> 
> test_check("cBioPortalData")
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in strsplit(hugos, "|", TRUE) : non-character argument
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in strsplit(hugos, "|", TRUE) : non-character argument
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    Non-unique names provided
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    Non-unique names provided
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in eval(args[["api"]]) : object 'cbio' not found
[ FAIL 1 | WARN 279 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_cBioPortalData.R:19:9'): cBioPortal API is working with most studies ──
Error in `eval(args[["api"]])`: object 'cbio' not found
Backtrace:
    ▆
 1. └─cBioPortalData::removeDataCache(...) at test_cBioPortalData.R:19:8
 2.   └─cBioPortalData:::update.args(exargs)

[ FAIL 1 | WARN 279 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc-longtests/meat/cBioPortalData.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* this is package ‘cBioPortalData’ version ‘2.10.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cBioPortalData’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
    'wget' call had nonzero exit status
  Error in eval(args[["api"]]) : object 'cbio' not found
  [ FAIL 1 | WARN 279 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_cBioPortalData.R:19:9'): cBioPortal API is working with most studies ──
  Error in `eval(args[["api"]])`: object 'cbio' not found
  Backtrace:
      ▆
   1. └─cBioPortalData::removeDataCache(...) at test_cBioPortalData.R:19:8
   2.   └─cBioPortalData:::update.args(exargs)
  
  [ FAIL 1 | WARN 279 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.16-bioc-longtests/meat/cBioPortalData.Rcheck/00check.log’
for details.

* installing *source* package ‘cBioPortalData’ ...
** 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)