| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-01-16 13:29:29 -0500 (Thu, 16 Jan 2020).
| Package 167/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biomaRt 2.43.1 Mike Smith
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: biomaRt |
| Version: 2.43.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biomaRt_2.43.1.tar.gz |
| StartedAt: 2020-01-16 02:12:46 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:16:57 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 250.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biomaRt.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biomaRt_2.43.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/biomaRt.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.43.1’
* 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 ‘biomaRt’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
See the note in ?`:::` about the use of this operator.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
select 0.866 0.130 5.273
getBM 0.832 0.071 13.860
* 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:
3. biomaRt::listMarts(...)
4. biomaRt:::.listMarts(...)
5. biomaRt:::bmRequest(request = request, verbose = verbose)
6. httr::GET(request, content_type("text/plain"))
7. httr:::request_perform(req, hu$handle$handle)
9. httr:::request_fetch.write_memory(req$output, req$url, handle)
10. curl::curl_fetch_memory(url, handle = handle)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
1. Error: useEnsembl() options are respected (@test_ensemblFunctions.R#13)
2. Error: We find cache for previous query (@test_z_cache.R#21)
Error: testthat unit tests failed
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/biomaRt.Rcheck/00check.log’
for details.
biomaRt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL biomaRt ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘biomaRt’ ... ** 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 (biomaRt)
biomaRt.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(biomaRt)
>
> biomartCacheClear()
[1] TRUE
>
> test_check("biomaRt", encoding = "UTF-8")
── 1. Error: useEnsembl() options are respected (@test_ensemblFunctions.R#13) ─
Timeout was reached: [useast.ensembl.org:8443] Connection timed out after 10854 milliseconds
Backtrace:
1. testthat::expect_silent(...)
9. biomaRt::useEnsembl(biomart = "snp", mirror = "useast")
10. biomaRt:::.useMart(...)
11. biomaRt::listMarts(...)
12. biomaRt:::.listMarts(...)
13. biomaRt:::bmRequest(request = request, verbose = verbose)
14. httr::GET(request, content_type("text/plain"))
15. httr:::request_perform(req, hu$handle$handle)
17. httr:::request_fetch.write_memory(req$output, req$url, handle)
18. curl::curl_fetch_memory(url, handle = handle)
── 2. Error: We find cache for previous query (@test_z_cache.R#21) ────────────
Timeout was reached: [useast.ensembl.org:8443] Connection timed out after 10895 milliseconds
Backtrace:
1. biomaRt::useMart(...)
2. biomaRt:::.useMart(...)
3. biomaRt::listMarts(...)
4. biomaRt:::.listMarts(...)
5. biomaRt:::bmRequest(request = request, verbose = verbose)
6. httr::GET(request, content_type("text/plain"))
7. httr:::request_perform(req, hu$handle$handle)
9. httr:::request_fetch.write_memory(req$output, req$url, handle)
10. curl::curl_fetch_memory(url, handle = handle)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
1. Error: useEnsembl() options are respected (@test_ensemblFunctions.R#13)
2. Error: We find cache for previous query (@test_z_cache.R#21)
Error: testthat unit tests failed
Execution halted
biomaRt.Rcheck/biomaRt-Ex.timings
| name | user | system | elapsed | |
| NP2009code | 0 | 0 | 0 | |
| attributePages | 0.001 | 0.000 | 0.001 | |
| exportFASTA | 0.001 | 0.001 | 0.001 | |
| filterOptions | 0.001 | 0.000 | 0.000 | |
| filterType | 0.000 | 0.001 | 0.001 | |
| getBM | 0.832 | 0.071 | 13.860 | |
| getBMlist | 0.000 | 0.000 | 0.001 | |
| getGene | 0.001 | 0.000 | 0.002 | |
| getLDS | 0.001 | 0.000 | 0.002 | |
| getSequence | 0.002 | 0.000 | 0.002 | |
| getXML | 0.001 | 0.000 | 0.001 | |
| listAttributes | 0.002 | 0.000 | 0.003 | |
| listDatasets | 0.002 | 0.000 | 0.002 | |
| listEnsembl | 0.000 | 0.000 | 0.001 | |
| listEnsemblArchives | 0.017 | 0.003 | 0.330 | |
| listFilterValues | 0.002 | 0.000 | 0.002 | |
| listFilters | 0.001 | 0.000 | 0.001 | |
| listMarts | 0 | 0 | 0 | |
| select | 0.866 | 0.130 | 5.273 | |
| useDataset | 0 | 0 | 0 | |
| useEnsembl | 0.000 | 0.000 | 0.001 | |
| useMart | 0.000 | 0.000 | 0.001 | |