Kasper Daniel Hansen
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/minfi |
| Branch: RELEASE_3_6 |
| Last Commit: a4df428 |
| Last Changed Date: 2017-10-30 12:39:36 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:09:57 -0400 (Thu, 12 Apr 2018).
| Package 859/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| minfi 1.24.0 Kasper Daniel Hansen
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: minfi |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.24.0.tar.gz |
| StartedAt: 2018-04-12 01:08:20 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:17:45 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 564.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: minfi.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/minfi.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.24.0’
* 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 ‘minfi’ 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: ‘bumphunter:::.getEstimate’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
combineArrays 62.392 2.156 66.589
bumphunter 30.708 1.272 32.139
read.metharray.exp 7.484 0.008 7.494
minfiQC 6.124 0.040 6.165
densityPlot 5.716 0.032 5.753
read.metharray 5.076 0.012 5.094
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* 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 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/minfi.Rcheck/00check.log’
for details.
minfi.Rcheck/00install.out
* installing *source* package ‘minfi’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (minfi)
minfi.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.
> require("minfi") || stop("unable to load minfi")
Loading required package: minfi
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
[1] TRUE
> BiocGenerics:::testPackage("minfi")
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
[preprocessFunnorm] Normalization
RUNIT TEST PROTOCOL -- Thu Apr 12 01:17:41 2018
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
minfi RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
202.348 2.556 205.405
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0.000 | 0.000 | 0.002 | |
| GenomicRatioSet-class | 0.000 | 0.000 | 0.001 | |
| IlluminaMethylationManifest-class | 3.016 | 0.084 | 3.103 | |
| MethylSet-class | 0.000 | 0.000 | 0.001 | |
| RGChannelSet-class | 0.000 | 0.000 | 0.001 | |
| RatioSet-class | 0.000 | 0.000 | 0.001 | |
| bumphunter | 30.708 | 1.272 | 32.139 | |
| combineArrays | 62.392 | 2.156 | 66.589 | |
| compartments | 4.516 | 0.148 | 4.667 | |
| controlStripPlot | 2.324 | 0.028 | 2.666 | |
| convertArray | 2.164 | 0.032 | 2.197 | |
| densityBeanPlot | 3.544 | 0.028 | 3.577 | |
| densityPlot | 5.716 | 0.032 | 5.753 | |
| detectionP | 0.220 | 0.004 | 0.225 | |
| dmpFinder | 0.296 | 0.000 | 0.294 | |
| estimateCellCounts | 0 | 0 | 0 | |
| fixMethOutliers | 1.640 | 0.000 | 1.641 | |
| gaphunter | 0.100 | 0.004 | 0.104 | |
| getAnnotation | 1.100 | 0.000 | 1.099 | |
| getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
| getQC | 0.244 | 0.000 | 0.243 | |
| getSex | 1.960 | 0.000 | 1.961 | |
| logit2 | 0 | 0 | 0 | |
| makeGenomicRatioSetFromMatrix | 1.436 | 0.000 | 1.436 | |
| mapToGenome-methods | 0.268 | 0.000 | 0.269 | |
| mdsPlot | 0.168 | 0.000 | 0.167 | |
| minfiQC | 6.124 | 0.040 | 6.165 | |
| plotBetasByType | 0.000 | 0.000 | 0.001 | |
| plotCpg | 0.104 | 0.000 | 0.105 | |
| preprocessFunnorm | 3.420 | 0.104 | 3.532 | |
| preprocessIllumina | 3.208 | 0.120 | 3.329 | |
| preprocessNoob | 0.840 | 0.004 | 0.844 | |
| preprocessQuantile | 0.516 | 0.008 | 0.521 | |
| preprocessRaw | 2.160 | 0.012 | 2.170 | |
| preprocessSwan | 0.436 | 0.020 | 0.456 | |
| qcReport | 0.068 | 0.000 | 0.068 | |
| ratioConvert-methods | 0.076 | 0.000 | 0.078 | |
| read.metharray | 5.076 | 0.012 | 5.094 | |
| read.metharray.exp | 7.484 | 0.008 | 7.494 | |
| read.metharray.sheet | 0.072 | 0.000 | 0.071 | |
| readGEORawFile | 0.000 | 0.000 | 0.001 | |
| readTCGA | 0.000 | 0.000 | 0.001 | |
| subsetByLoci | 0.368 | 0.000 | 0.366 | |
| utils | 0.14 | 0.00 | 0.14 | |