Back to Long Tests report for BioC 3.20

This page was generated on 2024-12-07 23:55 -0500 (Sat, 07 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4482
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4510
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 13/32HostnameOS / ArchCHECK
cBioPortalData 2.18.0  (landing page)
Marcel Ramos
Snapshot Date: 2024-12-07 09:55 -0500 (Sat, 07 Dec 2024)
git_url: https://git.bioconductor.org/packages/cBioPortalData
git_branch: RELEASE_3_20
git_last_commit: 5c2f01e
git_last_commit_date: 2024-10-29 10:47:10 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for cBioPortalData on merida1

To the developers/maintainers of the cBioPortalData package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cBioPortalData
Version: 2.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.18.0.tar.gz
StartedAt: 2024-12-07 16:03:53 -0500 (Sat, 07 Dec 2024)
EndedAt: 2024-12-07 19:41:41 -0500 (Sat, 07 Dec 2024)
EllapsedTime: 13068.0 seconds
RetCode: 0
Status:   OK  
CheckDir: cBioPortalData.Rcheck
Warnings: 0

Tests output

cBioPortalData.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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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

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, saveRDS, 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

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 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 TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in strsplit(hugos, "|", TRUE) : non-character argument
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    Non-unique names provided
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in strsplit(hugos, "|", TRUE) : non-character argument
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    ExperimentList elements must be named
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
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
sh: wget: command not found
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 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 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 read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
sh: wget: command not found
Error in utils::download.file(fileURL, destfile = tmpFile, quiet = TRUE,  : 
  'wget' call had nonzero exit status
Error in .invoke_fun(api, name, use_cache, ...) : Bad Request (HTTP 400).
Error in TCGAutils::uniformBuilds(x[[BCOL]]) : 
  Frequency of NA values higher than the cutoff tolerance
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 TCGAutils::uniformBuilds(x[[BCOL]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in .checkBarcodes(barcodes) : Barcodes must start with 'TCGA'
Error in .invoke_fun(api, name, use_cache, ...) : 
  Internal Server Error (HTTP 500).
Error in .checkFixSampleMap(sampleMap) : 
  'sampleMap' does not have required columns
Error in .invoke_fun(api, name, use_cache, ...) : Bad Request (HTTP 400).
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .invoke_fun(api, name, use_cache, ...) : Bad Request (HTTP 400).
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .checkBarcodes(barcodes) : Barcodes must start with 'TCGA'
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .validateNCBI(build) : Inconsistent build numbers found
Error in .invoke_fun(api, name, use_cache, ...) : Bad Request (HTTP 400).
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 .validateNCBI(build) : Inconsistent build numbers found
Error in TCGAutils::uniformBuilds(x[[BCOL]]) : 
  Only two build types at a time can be used
Error in vec_init(value, nrow * ncol) : 
  `n` must be a single number, not an integer `NA`.
[ FAIL 0 | WARN 1312 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 1312 | SKIP 0 | PASS 8 ]
> 
> proc.time()
     user    system   elapsed 
11148.907   489.721 12801.770

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/cBioPortalData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘2.18.0’
* 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 ‘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’
 OK
* DONE

Status: OK

Installation output

cBioPortalData.Rcheck/00install.out

* 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)