Mike Smith
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/biomaRt |
| Branch: master |
| Last Commit: 4b2f4b1 |
| Last Changed Date: 2018-11-07 10:14:45 -0400 (Wed, 07 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:22:53 -0400 (Tue, 09 Apr 2019).
| Package 156/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biomaRt 2.39.2 Mike Smith
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: biomaRt |
| Version: 2.39.2 |
| 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_2.39.2.tar.gz |
| StartedAt: 2019-04-08 23:31:38 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:38:45 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 426.7 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_2.39.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/biomaRt.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.39.2’
* 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 or elapsed time > 5s
user system elapsed
select 0.424 0.078 49.782
getBM 0.336 0.047 56.217
* 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: listMarts(host = host, path = path, port = port, includeHosts = TRUE, archive = archive,
ssl.verifypeer = ssl.verifypeer)
4: stop("Unexpected format to the list of available marts.\n", "Please check the following URL manually, ",
"and try ?listMarts for advice.\n", request)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 5
1. Error: (unknown) (@test_getLDS.R#4)
2. Error: (unknown) (@test_listAndSearch.R#6)
3. Error: listMarts retruns a data.frame (@test_listMarts.R#9)
4. Error: martCheck() catches bad input (@test_martCheck.R#8)
5. Error: martCheck() is quiet for valid input (@test_martCheck.R#19)
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-3.9-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/3.6/Resources/library’ * installing *source* package ‘biomaRt’ ... ** 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 * DONE (biomaRt)
biomaRt.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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)
>
> test_check("biomaRt", encoding = "UTF-8")
── 1. Error: (unknown) (@test_getLDS.R#4) ─────────────────────────────────────
biomaRt error: looks like we're connecting to incompatible version of BioMart suite.
1: useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") at testthat/test_getLDS.R:4
2: useDataset(mart = mart, dataset = dataset, verbose = verbose)
3: bmAttrFilt("filters", mart, verbose = verbose)
4: stop("biomaRt error: looks like we're connecting to incompatible version of BioMart suite.")
── 2. Error: (unknown) (@test_listAndSearch.R#6) ──────────────────────────────
The given dataset: xtropicalis_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.
1: useDataset(ensembl, dataset = "xtropicalis_gene_ensembl") at testthat/test_listAndSearch.R:6
2: checkDataset(dataset = dataset, mart = mart)
3: stop(paste("The given dataset: ", dataset, ", is not valid. Correct dataset names can be obtained with the listDatasets() function."))
── 3. Error: listMarts retruns a data.frame (@test_listMarts.R#9) ─────────────
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
1: listMarts(host = "www.ensembl.org") at testthat/test_listMarts.R:9
2: stop("Unexpected format to the list of available marts.\n", "Please check the following URL manually, ",
"and try ?listMarts for advice.\n", request)
── 4. Error: martCheck() catches bad input (@test_martCheck.R#8) ──────────────
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
1: useMart("ensembl") at testthat/test_martCheck.R:8
2: listMarts(host = host, path = path, port = port, includeHosts = TRUE, archive = archive,
ssl.verifypeer = ssl.verifypeer)
3: stop("Unexpected format to the list of available marts.\n", "Please check the following URL manually, ",
"and try ?listMarts for advice.\n", request)
── 5. Error: martCheck() is quiet for valid input (@test_martCheck.R#19) ──────
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
https://www.ensembl.org:443/biomart/martservice?type=registry&requestid=biomaRt
1: useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl") at testthat/test_martCheck.R:19
2: useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose, port = port)
3: listMarts(host = host, path = path, port = port, includeHosts = TRUE, archive = archive,
ssl.verifypeer = ssl.verifypeer)
4: stop("Unexpected format to the list of available marts.\n", "Please check the following URL manually, ",
"and try ?listMarts for advice.\n", request)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 5
1. Error: (unknown) (@test_getLDS.R#4)
2. Error: (unknown) (@test_listAndSearch.R#6)
3. Error: listMarts retruns a data.frame (@test_listMarts.R#9)
4. Error: martCheck() catches bad input (@test_martCheck.R#8)
5. Error: martCheck() is quiet for valid input (@test_martCheck.R#19)
Error: testthat unit tests failed
Execution halted
biomaRt.Rcheck/biomaRt-Ex.timings
| name | user | system | elapsed | |
| NP2009code | 0.000 | 0.000 | 0.001 | |
| attributePages | 0.000 | 0.000 | 0.001 | |
| exportFASTA | 0.000 | 0.000 | 0.001 | |
| filterOptions | 0.001 | 0.000 | 0.000 | |
| filterType | 0.001 | 0.000 | 0.001 | |
| getBM | 0.336 | 0.047 | 56.217 | |
| getBMlist | 0.001 | 0.000 | 0.000 | |
| getGene | 0.000 | 0.000 | 0.001 | |
| getLDS | 0.001 | 0.000 | 0.001 | |
| getSequence | 0.001 | 0.001 | 0.002 | |
| getXML | 0.001 | 0.000 | 0.001 | |
| listAttributes | 0.002 | 0.001 | 0.002 | |
| listDatasets | 0.001 | 0.000 | 0.002 | |
| listEnsembl | 0 | 0 | 0 | |
| listEnsemblArchives | 0.026 | 0.003 | 0.630 | |
| listFilterValues | 0.001 | 0.000 | 0.001 | |
| listFilters | 0.001 | 0.000 | 0.001 | |
| listMarts | 0.000 | 0.000 | 0.001 | |
| select | 0.424 | 0.078 | 49.782 | |
| useDataset | 0.000 | 0.001 | 0.000 | |
| useEnsembl | 0 | 0 | 0 | |
| useMart | 0.000 | 0.000 | 0.001 | |