R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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Platform: x86_64-w64-mingw32/x64

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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, 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 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

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

> 
> test_check("cBioPortalData")
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in .invoke_fun(api, name, use_cache, ...) : Bad Request (HTTP 400).
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in TCGAutils::uniformBuilds(x[[BCOL]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in save(full, file = cacheloc) : error writing to connection
Error in vec_init(value, nrow * ncol) : 
  `n` must be a single number, not an integer `NA`.
Error in .checkBarcodes(barcodes) : Barcodes must start with 'TCGA'
Error in .checkBarcodes(barcodes) : Barcodes must start with 'TCGA'
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in TCGAutils::uniformBuilds(x[[BCOL]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in .checkBarcodes(barcodes) : Barcodes must start with 'TCGA'
Error in save(full, file = cacheloc) : error writing to connection
Error in .invoke_fun(api, name, use_cache, ...) : 
  Internal Server Error (HTTP 500).
Error in .invoke_fun(api, name, use_cache, ...) : Bad Request (HTTP 400).
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in save(full, file = cacheloc) : error writing to connection
Error in .checkFixSampleMap(sampleMap) : 
  'sampleMap' does not have required columns
Error in save(full, file = cacheloc) : error writing to connection
Error in .normarg_genome(value, seqnames(x)) : 
  when the length of the supplied 'genome' vector is not 1, then it must
  be equal to the number of sequences
Error in save(full, file = cacheloc) : error writing to connection
Error : database or disk is full
[ FAIL 2 | WARN 420 | SKIP 0 | PASS 6 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_cBioDataPack.R:14:9'): cBioDataPack works on at least 70% of studies ──
Error: database or disk is full
Backtrace:
     ▆
  1. └─cBioPortalData::removePackCache(cancer_study_id = stud, dry.run = FALSE) at test_cBioDataPack.R:14:9
  2.   ├─BiocFileCache::bfcremove(bfc, rid)
  3.   └─BiocFileCache::bfcremove(bfc, rid)
  4.     └─BiocFileCache:::.sql_remove_resource(x, rids)
  5.       └─BiocFileCache:::.sql_db_execute(bfc, cmd)
  6.         ├─DBI::dbExecute(con, sql, params = param)
  7.         └─DBI::dbExecute(con, sql, params = param)
  8.           ├─DBI::dbSendStatement(conn, statement, ...)
  9.           └─DBI::dbSendStatement(conn, statement, ...)
 10.             ├─DBI::dbSendQuery(conn, statement, ...)
 11.             └─RSQLite::dbSendQuery(conn, statement, ...)
 12.               └─RSQLite (local) .local(conn, statement, ...)
 13.                 ├─methods::new(...)
 14.                 │ ├─methods::initialize(value, ...)
 15.                 │ └─methods::initialize(value, ...)
 16.                 └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_cBioPortalData.R:19:9'): cBioPortal API is working with most studies ──
Error: database or disk is full
Backtrace:
     ▆
  1. └─cBioPortalData::removeDataCache(...) at test_cBioPortalData.R:19:9
  2.   ├─base::do.call(.molDataCache, exargs)
  3.   └─cBioPortalData (local) `<fn>`(...)
  4.     └─cBioPortalData:::.getHashCache(digi)
  5.       ├─BiocFileCache::bfcnew(bfc, hashtag, ext = ".rda")
  6.       └─BiocFileCache::bfcnew(bfc, hashtag, ext = ".rda")
  7.         └─BiocFileCache:::.sql_add_resource(...)
  8.           └─BiocFileCache:::.sql_db_execute(...)
  9.             ├─DBI::dbExecute(con, sql, params = param)
 10.             └─DBI::dbExecute(con, sql, params = param)
 11.               ├─DBI::dbSendStatement(conn, statement, ...)
 12.               └─DBI::dbSendStatement(conn, statement, ...)
 13.                 ├─DBI::dbSendQuery(conn, statement, ...)
 14.                 └─RSQLite::dbSendQuery(conn, statement, ...)
 15.                   └─RSQLite (local) .local(conn, statement, ...)
 16.                     ├─DBI::dbBind(rs, params)
 17.                     └─RSQLite::dbBind(rs, params)
 18.                       └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
 19.                         └─RSQLite:::result_bind(res@ptr, params)

[ FAIL 2 | WARN 420 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/cBioPortalData.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 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 '2.17.0'
* 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 '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 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 ... 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:
    9.             ├─DBI::dbExecute(con, sql, params = param)
   10.             └─DBI::dbExecute(con, sql, params = param)
   11.               ├─DBI::dbSendStatement(conn, statement, ...)
   12.               └─DBI::dbSendStatement(conn, statement, ...)
   13.                 ├─DBI::dbSendQuery(conn, statement, ...)
   14.                 └─RSQLite::dbSendQuery(conn, statement, ...)
   15.                   └─RSQLite (local) .local(conn, statement, ...)
   16.                     ├─DBI::dbBind(rs, params)
   17.                     └─RSQLite::dbBind(rs, params)
   18.                       └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
   19.                         └─RSQLite:::result_bind(res@ptr, params)
  
  [ FAIL 2 | WARN 420 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR
See
  'F:/biocbuild/bbs-3.20-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)