| Back to Long Tests report for BioC 3.11 |
This page was generated on 2020-10-10 17:30:04 -0400 (Sat, 10 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE cBioPortalData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 3/7 | Hostname | OS / Arch | CHECK | |||||
| cBioPortalData 2.0.10 Marcel Ramos
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | ERROR | |||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | [ ERROR ] |
| Package: cBioPortalData |
| Version: 2.0.10 |
| Command: /Library/Frameworks/R.framework/Versions/Current/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_2.0.10.tar.gz |
| StartedAt: 2020-10-10 10:04:12 -0400 (Sat, 10 Oct 2020) |
| EndedAt: 2020-10-10 11:03:48 -0400 (Sat, 10 Oct 2020) |
| EllapsedTime: 3575.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: cBioPortalData.Rcheck |
| Warnings: NA |
cBioPortalData.Rcheck/tests/testthat.Rout.fail
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, 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:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:dplyr':
count
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("cBioPortalData")
── 1. Failure: cBioPortal API is working with most studies (@test_cBioPortalData
successrate > 90 isn't true.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 271 | FAILED: 1 ]
1. Failure: cBioPortal API is working with most studies (@test_cBioPortalData.R#24)
Error: testthat unit tests failed
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/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_2.0.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/cBioPortalData.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.0.10’
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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:
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("cBioPortalData")
── 1. Failure: cBioPortal API is working with most studies (@test_cBioPortalData
successrate > 90 isn't true.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 271 | FAILED: 1 ]
1. Failure: cBioPortal API is working with most studies (@test_cBioPortalData.R#24)
Error: testthat unit tests failed
Execution halted
* DONE
Status: 1 ERROR
See
‘/Users/biocbuild/bbs-3.11-bioc-longtests/meat/cBioPortalData.Rcheck/00check.log’
for details.
cBioPortalData.Rcheck/00install.out
* installing *source* package ‘cBioPortalData’ ... ** 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 (cBioPortalData)