| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:21:23 -0400 (Wed, 17 Oct 2018).
| Package 140/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biomaRt 2.36.1 Mike Smith
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: biomaRt |
| Version: 2.36.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings biomaRt_2.36.1.tar.gz |
| StartedAt: 2018-10-15 22:48:28 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 22:50:47 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 138.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biomaRt.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings biomaRt_2.36.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/biomaRt.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.36.1’
* 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
getBM 0.656 0.008 5.262
select 0.236 0.048 56.952
* 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:
1: getBM(filter = "ensembl_gene_id", values = "ENSMUSG00000000103", attributes = attributes,
mart = mart) at testthat/test_colnames.R:37
2: read.table(con, sep = "\t", header = callHeader, quote = quote, comment.char = "",
check.names = FALSE, stringsAsFactors = FALSE)
3: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows,
skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white,
blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char,
allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 9 SKIPPED: 0 FAILED: 1
1. Error: Renaming columns - real data (@test_colnames.R#37)
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
‘/home/biocbuild/bbs-3.7-bioc/meat/biomaRt.Rcheck/00check.log’
for details.
biomaRt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL biomaRt ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: Renaming columns - real data (@test_colnames.R#37) ───────────────
line 1 did not have 3 elements
1: getBM(filter = "ensembl_gene_id", values = "ENSMUSG00000000103", attributes = attributes,
mart = mart) at testthat/test_colnames.R:37
2: read.table(con, sep = "\t", header = callHeader, quote = quote, comment.char = "",
check.names = FALSE, stringsAsFactors = FALSE)
3: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows,
skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white,
blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char,
allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)
══ testthat results ═══════════════════════════════════════════════════════════
OK: 9 SKIPPED: 0 FAILED: 1
1. Error: Renaming columns - real data (@test_colnames.R#37)
Error: testthat unit tests failed
Execution halted
biomaRt.Rcheck/biomaRt-Ex.timings
| name | user | system | elapsed | |
| NP2009code | 0 | 0 | 0 | |
| attributePages | 0 | 0 | 0 | |
| exportFASTA | 0 | 0 | 0 | |
| filterOptions | 0.000 | 0.000 | 0.001 | |
| filterType | 0.004 | 0.000 | 0.000 | |
| getBM | 0.656 | 0.008 | 5.262 | |
| getBMlist | 0.004 | 0.000 | 0.001 | |
| getGene | 0.000 | 0.000 | 0.002 | |
| getLDS | 0.000 | 0.000 | 0.001 | |
| getSequence | 0.000 | 0.000 | 0.002 | |
| getXML | 0.000 | 0.000 | 0.001 | |
| listAttributes | 0.004 | 0.000 | 0.001 | |
| listDatasets | 0.004 | 0.000 | 0.003 | |
| listEnsembl | 0.000 | 0.000 | 0.001 | |
| listEnsemblArchives | 0.024 | 0.000 | 0.494 | |
| listFilters | 0.004 | 0.000 | 0.001 | |
| listMarts | 0.000 | 0.000 | 0.001 | |
| select | 0.236 | 0.048 | 56.952 | |
| useDataset | 0.000 | 0.000 | 0.001 | |
| useEnsembl | 0.000 | 0.000 | 0.001 | |
| useMart | 0.000 | 0.000 | 0.001 | |