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This page was generated on 2016-09-05 02:36:32 -0700 (Mon, 05 Sep 2016).
| Package 703/1251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| MEAL 1.3.6 Carlos Ruiz
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped | ||||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: MEAL |
| Version: 1.3.6 |
| Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.3.6.tar.gz |
| StartedAt: 2016-09-04 08:28:07 -0700 (Sun, 04 Sep 2016) |
| EndedAt: 2016-09-04 08:36:00 -0700 (Sun, 04 Sep 2016) |
| EllapsedTime: 473.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MEAL.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.3.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MEAL.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.3.6’
* 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 ‘MEAL’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DARegion : <anonymous>: no visible binding for global variable
'proberes'
correlationMethExprs: no visible global function definition for
'rowRanges'
Undefined global functions or variables:
proberes rowRanges
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'DARegion':
DARegion
Code: function(set, model, methods = c("blockFinder", "bumphunter",
"DMRcate"), coefficient = 2, num_permutations = 0,
bumphunter_cutoff = 0.05, bumps_max = 30000, num_cores
= 1, verbose = FALSE, ...)
Docs: function(set, model, proberes, methods = c("blockFinder",
"bumphunter", "DMRcate"), coefficient = 2,
num_permutations = 0, bumphunter_cutoff = 0.05,
bumps_max = 30000, num_cores = 1, verbose = FALSE,
...)
Argument names in docs not in code:
proberes
Mismatches in argument names (first 3):
Position: 3 Code: methods Docs: proberes
Position: 4 Code: coefficient Docs: methods
Position: 5 Code: num_permutations Docs: coefficient
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotRegion-methods 40.600 0.024 40.628
plotRDA-methods 40.164 0.092 40.265
topRDAhits-methods 40.020 0.028 40.064
DAPipeline 15.480 0.904 16.957
* 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:
2: In add_eset(object, methySet, dataset.type = "methylation", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
3: In add_eset(object, snpSet, dataset.type = "snps", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
4: In add_eset(object, methySet, dataset.type = "methylation", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
5: In add_eset(object, snpSet, dataset.type = "snps", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
6: In add_eset(object, gexpSet, dataset.type = "expression", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
7: In add_eset(object, methySet, dataset.type = "methylation", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
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 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.4-bioc/meat/MEAL.Rcheck/00check.log’
for details.
testthat.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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)
> library(MEAL)
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, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("MEAL")
Loading required package: minfi
Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Your contrast returned 82 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrX...
Fitting chrY...
Demarcating regions...
Done!
1. Failure: Check Errors (@test_06regionAnalysis.R#70) -------------------------
error$message does not match "set must be a MethylationSet.".
Actual value: "The number of samples is different in the set and in the model."
2. Failure: Check Errors (@test_06regionAnalysis.R#71) -------------------------
error$message does not match "The set is empty.".
Actual value: "object 'emptyset' not found"
coercing object of mode numeric to SnpMatrix
Your contrast returned 10 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
Your contrast returned no individually significant probes. Set pcutoff manually in dmrcate() to return DMRs, but be warned there is an increased risk of Type I errors.
Fitting chrY...
Your contrast returned 10 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
Your contrast returned 10 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
Your contrast returned no individually significant probes. Set pcutoff manually in dmrcate() to return DMRs, but be warned there is an increased risk of Type I errors.
Fitting chrY...
Your contrast returned 10 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
Your contrast returned 5 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
coercing object of mode numeric to SnpMatrix
Your contrast returned 5 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Your contrast returned 5 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
Your contrast returned 5 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
coercing object of mode numeric to SnpMatrix
Your contrast returned 10 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
Your contrast returned no individually significant probes. Set pcutoff manually in dmrcate() to return DMRs, but be warned there is an increased risk of Type I errors.
Fitting chrY...
Your contrast returned 10 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chrY...
Demarcating regions...
Done!
testthat results ================================================================
OK: 239 SKIPPED: 0 FAILED: 2
1. Failure: Check Errors (@test_06regionAnalysis.R#70)
2. Failure: Check Errors (@test_06regionAnalysis.R#71)
Error: testthat unit tests failed
In addition: Warning messages:
1: In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
2: In add_eset(object, methySet, dataset.type = "methylation", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
3: In add_eset(object, snpSet, dataset.type = "snps", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
4: In add_eset(object, methySet, dataset.type = "methylation", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
5: In add_eset(object, snpSet, dataset.type = "snps", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
6: In add_eset(object, gexpSet, dataset.type = "expression", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
7: In add_eset(object, methySet, dataset.type = "methylation", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
Execution halted
MEAL.Rcheck/00install.out:
* installing *source* package ‘MEAL’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (MEAL)
MEAL.Rcheck/MEAL-Ex.timings:
| name | user | system | elapsed | |
| AnalysisRegionResults-class | 0.004 | 0.000 | 0.002 | |
| AnalysisResults-class | 0.000 | 0.000 | 0.001 | |
| DAPipeline | 15.480 | 0.904 | 16.957 | |
| DAProbe | 0.464 | 0.000 | 0.463 | |
| DARegion | 2.044 | 0.036 | 2.079 | |
| DARegionAnalysis | 2.524 | 0.000 | 2.525 | |
| RDAset | 2.004 | 0.020 | 2.024 | |
| calculateRelevantSNPs | 0.000 | 0.000 | 0.001 | |
| createRanges | 0.016 | 0.000 | 0.016 | |
| explainedVariance | 0.020 | 0.000 | 0.023 | |
| exportResults-methods | 1.896 | 0.000 | 1.908 | |
| filterSet-methods | 1.628 | 0.000 | 1.630 | |
| getGeneVals-methods | 1.904 | 0.004 | 1.908 | |
| multiCorrMethExprs | 0.004 | 0.000 | 0.001 | |
| normalSNP | 0.000 | 0.000 | 0.001 | |
| plotBestFeatures | 2.100 | 0.004 | 2.105 | |
| plotEWAS-methods | 2.348 | 0.004 | 2.354 | |
| plotFeature | 1.972 | 0.000 | 1.971 | |
| plotLM | 0.172 | 0.000 | 0.171 | |
| plotQQ-methods | 2.212 | 0.004 | 2.213 | |
| plotRDA-methods | 40.164 | 0.092 | 40.265 | |
| plotRegion-methods | 40.600 | 0.024 | 40.628 | |
| plotVolcano-methods | 2.512 | 0.008 | 2.522 | |
| preparePhenotype | 0.004 | 0.000 | 0.004 | |
| topRDAhits-methods | 40.020 | 0.028 | 40.064 | |