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This page was generated on 2016-04-23 10:22:29 -0700 (Sat, 23 Apr 2016).
| Package 608/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| MEAL 1.0.4 Carlos Ruiz
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK | ||||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
| Package: MEAL |
| Version: 1.0.4 |
| Command: rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.0.4.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.0.4.tar.gz |
| StartedAt: 2016-04-23 04:21:02 -0700 (Sat, 23 Apr 2016) |
| EndedAt: 2016-04-23 04:37:56 -0700 (Sat, 23 Apr 2016) |
| EllapsedTime: 1013.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MEAL.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.0.4.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.0.4.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/MEAL.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAL/DESCRIPTION' ... OK
* this is package 'MEAL' version '1.0.4'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
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 ... NOTE
plotVolcano,AnalysisResults: no visible binding for global variable
'adj.p'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [130s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 21.31 0.67 22.65
plotRDA-methods 13.82 0.39 14.22
plotRegion-methods 11.91 0.33 12.24
add.methy-methods 10.51 0.66 15.82
DARegionAnalysis 7.86 0.11 8.45
** running examples for arch 'x64' ... [141s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 23.45 0.76 24.38
add.methy-methods 14.48 0.61 15.09
plotRegion-methods 12.08 0.45 12.52
plotRDA-methods 10.47 0.45 10.92
DARegionAnalysis 9.38 0.14 9.51
plotEWAS-methods 5.14 0.21 5.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [59s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data
coercing object of mode numeric to SnpMatrix
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Error in eval(expr, envir, enclos) : could not find function "add_methy"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
testthat results ================================================================
OK: 217 SKIPPED: 0 FAILED: 0
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R' [79s]
Warning message:
running command '"D:/biocbld/BBS-3˜1.2-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data
coercing object of mode numeric to SnpMatrix
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Error in eval(expr, envir, enclos) : could not find function "add_methy"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
testthat results ================================================================
OK: 217 SKIPPED: 0 FAILED: 0
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: 2 ERRORs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/MEAL.Rcheck/00check.log'
for details.
testthat.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
Warning message:
package 'testthat' was built under R version 3.2.5
> 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, as.vector, 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, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("MEAL")
[cpgCollapse] Creating annotation.
[cpgCollapseAnnotation] Clustering islands and clusters of probes.
[cpgCollapseAnnotation] Computing new annotation.
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data
coercing object of mode numeric to SnpMatrix
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Error in eval(expr, envir, enclos) : could not find function "add_methy"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
testthat results ================================================================
OK: 217 SKIPPED: 0 FAILED: 0
Execution halted
testthat.Rout.fail:
R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
Warning message:
package 'testthat' was built under R version 3.2.5
> 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, as.vector, 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, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("MEAL")
[cpgCollapse] Creating annotation.
[cpgCollapseAnnotation] Clustering islands and clusters of probes.
[cpgCollapseAnnotation] Computing new annotation.
[cpgCollapseAnnotation] Defining blocks.
[cpgCollapse] Collapsing data
coercing object of mode numeric to SnpMatrix
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Error in eval(expr, envir, enclos) : could not find function "add_methy"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In matrix(runif(6, max = 15), 4) :
data length [6] is not a sub-multiple or multiple of the number of rows [4]
testthat results ================================================================
OK: 217 SKIPPED: 0 FAILED: 0
Execution halted
MEAL.Rcheck/00install.out:
install for i386 * 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 install for x64 * installing *source* package 'MEAL' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MEAL' as MEAL_1.0.4.zip * DONE (MEAL)
MEAL.Rcheck/examples_i386/MEAL-Ex.timings:
| name | user | system | elapsed | |
| AnalysisRegionResults-class | 0.02 | 0.00 | 0.02 | |
| AnalysisResults-class | 0 | 0 | 0 | |
| DAPipeline | 21.31 | 0.67 | 22.65 | |
| DAProbe | 0.92 | 0.11 | 1.03 | |
| DARegion | 2.80 | 0.12 | 2.91 | |
| DARegionAnalysis | 7.86 | 0.11 | 8.45 | |
| MethylationSet-class | 0 | 0 | 0 | |
| RDAset | 1.64 | 0.09 | 1.73 | |
| add.genexp-methods | 0.07 | 0.00 | 0.06 | |
| add.methy-methods | 10.51 | 0.66 | 15.82 | |
| add.set-methods | 0.06 | 0.00 | 0.06 | |
| calculateRelevantSNPs | 0.02 | 0.00 | 0.02 | |
| checkProbes-methods | 2.17 | 0.08 | 2.24 | |
| checkSamples-methods | 2.28 | 0.03 | 2.31 | |
| chrNumToChar | 0 | 0 | 0 | |
| createRanges | 0.01 | 0.00 | 0.02 | |
| explainedVariance | 0.03 | 0.00 | 0.03 | |
| exportResults-methods | 2.09 | 0.11 | 2.23 | |
| filterSet-methods | 2.33 | 0.07 | 2.40 | |
| getGeneVals-methods | 2.27 | 0.07 | 2.32 | |
| getMs-methods | 1.70 | 0.07 | 1.78 | |
| normalSNP | 0 | 0 | 0 | |
| plotBestFeatures | 2.71 | 0.15 | 2.94 | |
| plotEWAS-methods | 2.43 | 0.06 | 2.50 | |
| plotFeature | 2.65 | 0.09 | 2.75 | |
| plotQQ-methods | 2.88 | 0.06 | 2.95 | |
| plotRDA-methods | 13.82 | 0.39 | 14.22 | |
| plotRegion-methods | 11.91 | 0.33 | 12.24 | |
| plotVolcano-methods | 3.37 | 0.13 | 3.49 | |
| prepareMethylationSet | 1.85 | 0.06 | 1.90 | |
| preparePhenotype | 0.02 | 0.00 | 0.01 | |
MEAL.Rcheck/examples_x64/MEAL-Ex.timings:
| name | user | system | elapsed | |
| AnalysisRegionResults-class | 0 | 0 | 0 | |
| AnalysisResults-class | 0 | 0 | 0 | |
| DAPipeline | 23.45 | 0.76 | 24.38 | |
| DAProbe | 0.95 | 0.09 | 1.50 | |
| DARegion | 3.87 | 0.11 | 3.97 | |
| DARegionAnalysis | 9.38 | 0.14 | 9.51 | |
| MethylationSet-class | 0.01 | 0.00 | 0.01 | |
| RDAset | 2.06 | 0.10 | 2.16 | |
| add.genexp-methods | 0.09 | 0.00 | 0.09 | |
| add.methy-methods | 14.48 | 0.61 | 15.09 | |
| add.set-methods | 0.06 | 0.00 | 0.06 | |
| calculateRelevantSNPs | 0 | 0 | 0 | |
| checkProbes-methods | 2.25 | 0.04 | 2.57 | |
| checkSamples-methods | 2.06 | 0.05 | 2.32 | |
| chrNumToChar | 0 | 0 | 0 | |
| createRanges | 0.03 | 0.00 | 0.03 | |
| explainedVariance | 0.03 | 0.00 | 0.03 | |
| exportResults-methods | 2.34 | 0.09 | 2.45 | |
| filterSet-methods | 2.11 | 0.05 | 2.77 | |
| getGeneVals-methods | 4.18 | 0.17 | 4.35 | |
| getMs-methods | 1.60 | 0.02 | 1.62 | |
| normalSNP | 0 | 0 | 0 | |
| plotBestFeatures | 3.14 | 0.07 | 3.21 | |
| plotEWAS-methods | 5.14 | 0.21 | 5.35 | |
| plotFeature | 2.14 | 0.11 | 2.25 | |
| plotQQ-methods | 3.17 | 0.15 | 3.32 | |
| plotRDA-methods | 10.47 | 0.45 | 10.92 | |
| plotRegion-methods | 12.08 | 0.45 | 12.52 | |
| plotVolcano-methods | 2.95 | 0.05 | 2.99 | |
| prepareMethylationSet | 2.15 | 0.06 | 2.21 | |
| preparePhenotype | 0.02 | 0.00 | 0.01 | |