| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-06 11:32 -0500 (Fri, 06 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4857 |
| 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 184/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bioCancer 1.39.0 (landing page) Karim Mezhoud
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for bioCancer in R Universe. | ||||||||||||||
|
To the developers/maintainers of the bioCancer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioCancer.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
| Package: bioCancer |
| Version: 1.39.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bioCancer_1.39.0.tar.gz |
| StartedAt: 2026-02-05 21:30:29 -0500 (Thu, 05 Feb 2026) |
| EndedAt: 2026-02-05 21:36:57 -0500 (Thu, 05 Feb 2026) |
| EllapsedTime: 387.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bioCancer.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bioCancer_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bioCancer.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.39.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘bioCancer’ can be installed ... OK
* checking installed package size ... INFO
installed size is 6.4Mb
sub-directories of 1Mb or more:
app 3.3Mb
extdata 2.6Mb
* 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 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 ... NOTE
Invalid package aliases in Rd file 'bioCancer.Rd':
‘-package’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘bioCancer-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mutation_obj
> ### Title: Atribute mutation frequency to nodes
> ### Aliases: Mutation_obj
>
> ### ** Examples
>
> cgds <- cBioPortal(
+ hostname = "www.cbioportal.org",
+ protocol = "https",
+ api = "/api/v2/api-docs"
+ )
No encoding supplied: defaulting to UTF-8.
<html>
<head><title>429 Too Many Requests</title></head>
<body>
<center><h1>429 Too Many Requests</h1></center>
<hr><center>nginx</center>
</body>
</html>
Error: '.service_get_api_file' failed:
Too Many Requests (RFC 6585) (HTTP 429).
Execution halted
* 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:
── Error ('test_funs.R:11:23'): cBioPortal connection ──────────────────────────
Error: '.service_get_api_file' failed:
Too Many Requests (RFC 6585) (HTTP 429).
Backtrace:
▆
1. └─cBioPortalData::cBioPortal(...) at test_funs.R:11:23
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 1 | WARN 0 | SKIP 1 | PASS 0 ]
Error:
! Test failures.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/bioCancer.Rcheck/00check.log’
for details.
bioCancer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bioCancer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘bioCancer’ ... ** this is package ‘bioCancer’ version ‘1.39.0’ ** 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 (bioCancer)
bioCancer.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
Loading required package: ggplot2
Loading required package: lubridate
Attaching package: 'lubridate'
The following objects are masked from 'package:base':
date, intersect, setdiff, union
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:magrittr':
extract
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'radiant.data'
The following objects are masked from 'package:lubridate':
month, wday
The following object is masked from 'package:ggplot2':
diamonds
The following object is masked from 'package:magrittr':
set_attr
The following object is masked from 'package:testthat':
describe
The following object is masked from 'package:base':
date
Loading required package: cBioPortalData
Loading required package: AnVIL
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 objects are masked from 'package:radiant.data':
explore, visualize
The following object is masked from 'package:dplyr':
explain
The following object is masked from 'package:lubridate':
as.difftime
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:radiant.data':
normalize
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:tidyr':
expand
The following objects are masked from 'package:lubridate':
second, second<-
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:lubridate':
%within%
Loading required package: Seqinfo
Attaching package: 'GenomicRanges'
The following object is masked from 'package:magrittr':
subtract
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
Loading required package: XML
>
> test_check("bioCancer")
<html>
<head><title>429 Too Many Requests</title></head>
<body>
<center><h1>429 Too Many Requests</h1></center>
<hr><center>nginx</center>
</body>
</html>
Saving _problems/test_funs-15.R
ReactomeFI connection... OK
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_funs.R:20:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_funs.R:11:23'): cBioPortal connection ──────────────────────────
Error: '.service_get_api_file' failed:
Too Many Requests (RFC 6585) (HTTP 429).
Backtrace:
▆
1. └─cBioPortalData::cBioPortal(...) at test_funs.R:11:23
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 1 | WARN 0 | SKIP 1 | PASS 0 ]
Error:
! Test failures.
Execution halted
bioCancer.Rcheck/bioCancer-Ex.timings
| name | user | system | elapsed | |
| AnnotationFuncs | 0.146 | 0.014 | 0.164 | |
| Edges_Diseases_obj | 0.002 | 0.000 | 0.002 | |