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This page was generated on 2016-04-16 11:34:26 -0700 (Sat, 16 Apr 2016).
| Package 686/1205 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| metagenomeFeatures 1.1.0 Nathan D. Olson
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: metagenomeFeatures |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.1.0.tar.gz |
| StartedAt: 2016-04-15 03:52:20 -0700 (Fri, 15 Apr 2016) |
| EndedAt: 2016-04-15 03:54:38 -0700 (Fri, 15 Apr 2016) |
| EllapsedTime: 137.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: metagenomeFeatures.Rcheck |
| Warnings: NA |
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###
### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeFeatures_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/metagenomeFeatures.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70434)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* this is package ‘metagenomeFeatures’ version ‘1.1.0’
* 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 ‘metagenomeFeatures’ can be installed ... [11s/12s] OK
* checking installed package size ... NOTE
installed size is 32.4Mb
sub-directories of 1Mb or more:
data 1.1Mb
extdata 30.9Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘metagenomeSeq’
All declared Imports should be used.
* 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 ... WARNING
Undocumented S4 methods:
generic 'split_by' and siglist 'metagenomeAnnotation'
generic 'taxa_columns' and siglist 'MgDb'
generic 'taxa_keys' and siglist 'MgDb'
generic 'taxa_keytypes' and siglist 'MgDb'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Duplicated \argument entries in documentation object 'annotate':
‘mgdb’ ‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
annotateMRexp(mgdb = testMgDb, MRobj = testMRobj) not equal to reference from `cache/MgDb_test_annotateMRexp.rds`.
Attributes: < Component ".__classVersion__": Component "R": Mean relative difference: 1 >
Attributes: < Component ".__classVersion__": Component "Biobase": Mean relative difference: 0.1176471 >
Attributes: < Component "featureData": Attributes: < Component ".__classVersion__": Component "R": Mean relative difference: 1 > >
Attributes: < Component "featureData": Attributes: < Component ".__classVersion__": Component "Biobase": Mean relative difference: 0.1176471 > >
testthat results ================================================================
OK: 73 SKIPPED: 0 FAILED: 1
1. Failure: MgDb-class annotateMRexp (@test_mgDb-class.R#223)
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, 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/metagenomeFeatures.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.3.0 beta (2016-04-06 r70434) -- "Supposedly Educational"
Copyright (C) 2016 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)
>
> test_check("metagenomeFeatures")
Loading required package: metagenomeFeatures
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Joining by: "Keys"
Using 'db_keys' for subset database
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5
Loading required package: RColorBrewer
Using 'db_keys' for subset database
1. Failure: MgDb-class annotateMRexp (@test_mgDb-class.R#223) ------------------
annotateMRexp(mgdb = testMgDb, MRobj = testMRobj) not equal to reference from `cache/MgDb_test_annotateMRexp.rds`.
Attributes: < Component ".__classVersion__": Component "R": Mean relative difference: 1 >
Attributes: < Component ".__classVersion__": Component "Biobase": Mean relative difference: 0.1176471 >
Attributes: < Component "featureData": Attributes: < Component ".__classVersion__": Component "R": Mean relative difference: 1 > >
Attributes: < Component "featureData": Attributes: < Component ".__classVersion__": Component "Biobase": Mean relative difference: 0.1176471 > >
testthat results ================================================================
OK: 73 SKIPPED: 0 FAILED: 1
1. Failure: MgDb-class annotateMRexp (@test_mgDb-class.R#223)
Error: testthat unit tests failed
Execution halted
metagenomeFeatures.Rcheck/00install.out:
* installing *source* package ‘metagenomeFeatures’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (metagenomeFeatures)
metagenomeFeatures.Rcheck/metagenomeFeatures-Ex.timings:
| name | user | system | elapsed | |
| MgDb-class | 0.059 | 0.000 | 0.064 | |
| annotate-MgDb-method | 0 | 0 | 0 | |
| annotateMRexp-MgDb-method | 0 | 0 | 0 | |
| get_demoMgDb | 0.023 | 0.000 | 0.027 | |
| metagenomeAnnotation-class | 0.003 | 0.000 | 0.003 | |
| mgQuery | 0.001 | 0.000 | 0.001 | |
| msd16s_metagenomeAnnotation | 0.001 | 0.000 | 0.001 | |
| msd16s_query_df | 0.003 | 0.000 | 0.003 | |
| select-MgDb-method | 0.321 | 0.004 | 0.334 | |
| split_by | 1.520 | 0.124 | 1.671 | |
| taxa_columns | 0.021 | 0.004 | 0.025 | |
| taxa_keys | 0.033 | 0.000 | 0.033 | |
| taxa_keytypes | 0.025 | 0.000 | 0.025 | |