Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:46:31 -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: /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_2.36.1.tar.gz |
StartedAt: 2018-10-16 20:07:38 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 20:10:24 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 166.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biomaRt.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running 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_2.36.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/biomaRt.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘2.36.1’ * 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 0.305 0.043 6.651 select 0.282 0.033 57.382 * 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 ‘/Users/biocbuild/bbs-3.7-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/3.5/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" 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: 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 | 0.002 | 0.000 | 0.001 | |
attributePages | 0.002 | 0.001 | 0.002 | |
exportFASTA | 0.001 | 0.000 | 0.002 | |
filterOptions | 0.002 | 0.000 | 0.001 | |
filterType | 0.002 | 0.000 | 0.002 | |
getBM | 0.305 | 0.043 | 6.651 | |
getBMlist | 0.002 | 0.000 | 0.002 | |
getGene | 0.003 | 0.000 | 0.004 | |
getLDS | 0.002 | 0.000 | 0.002 | |
getSequence | 0.003 | 0.000 | 0.002 | |
getXML | 0.002 | 0.001 | 0.002 | |
listAttributes | 0.002 | 0.000 | 0.001 | |
listDatasets | 0.002 | 0.000 | 0.001 | |
listEnsembl | 0.001 | 0.000 | 0.001 | |
listEnsemblArchives | 0.026 | 0.002 | 0.269 | |
listFilters | 0.002 | 0.000 | 0.002 | |
listMarts | 0.002 | 0.000 | 0.002 | |
select | 0.282 | 0.033 | 57.382 | |
useDataset | 0.002 | 0.000 | 0.002 | |
useEnsembl | 0.002 | 0.000 | 0.002 | |
useMart | 0.002 | 0.001 | 0.002 | |