Kasper Daniel Hansen
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/minfi |
| Branch: RELEASE_3_7 |
| Last Commit: ebb07b7 |
| Last Changed Date: 2018-06-15 16:54:00 -0400 (Fri, 15 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:50:01 -0400 (Wed, 17 Oct 2018).
| Package 909/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| minfi 1.26.2 Kasper Daniel Hansen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: minfi |
| Version: 1.26.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings minfi_1.26.2.tar.gz |
| StartedAt: 2018-10-16 22:39:49 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 23:02:51 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 1382.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: minfi.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:minfi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings minfi_1.26.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/minfi.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 ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.26.2’
* 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 ... WARNING
Problems with news in ‘inst/NEWS.Rd’:
inst/NEWS.Rd:6: unknown macro '\item'
inst/NEWS.Rd:9: unknown macro '\item'
inst/NEWS.Rd:13: unknown macro '\item'
inst/NEWS.Rd:17: unexpected '}'
Malformed NEWS.Rd file:
Chunk starting
\item Fix bug in \code{preprocessQuantile()} that arose when
contains no \itemize.
* 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 objects imported by ':::' calls:
‘DelayedArray:::.as_array_or_matrix’ ‘DelayedArray:::.normarg_grid’
‘DelayedArray:::extract_block’ ‘DelayedArray:::get_max_block_length’
‘DelayedArray:::get_spacings_for_hypercube_capped_length_blocks’
‘DelayedArray:::get_spacings_for_linear_capped_length_blocks’
‘DelayedArray:::get_verbose_block_processing’
‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessFunnorm 291.244 0.947 295.427
preprocessNoob 148.352 0.462 152.587
bumphunter 137.476 7.916 146.364
preprocessQuantile 103.667 0.205 104.821
getAnnotation 95.987 0.283 97.073
combineArrays 75.929 4.464 80.962
compartments 50.723 0.794 51.818
minfiQC 15.223 0.869 16.239
getSex 15.413 0.574 16.098
mapToGenome-methods 11.917 0.034 12.057
makeGenomicRatioSetFromMatrix 11.807 0.080 11.957
read.metharray.exp 9.006 0.379 9.465
densityBeanPlot 6.955 0.702 7.716
fixMethOutliers 6.294 0.497 6.834
read.metharray 5.856 0.215 6.116
densityPlot 5.222 0.548 5.821
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/minfi.Rcheck/00check.log’
for details.
minfi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL minfi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘minfi’ ... ** 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 (minfi)
minfi.Rcheck/tests/runTests.Rout
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.
> 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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, 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
RUNIT TEST PROTOCOL -- Tue Oct 16 23:02:44 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
50.839 2.986 54.325
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0.003 | 0.001 | 0.003 | |
| GenomicRatioSet-class | 0.002 | 0.000 | 0.003 | |
| IlluminaMethylationManifest-class | 3.696 | 0.148 | 3.882 | |
| MethylSet-class | 0.003 | 0.000 | 0.004 | |
| RGChannelSet-class | 0.003 | 0.000 | 0.004 | |
| RatioSet-class | 0.003 | 0.001 | 0.003 | |
| bumphunter | 137.476 | 7.916 | 146.364 | |
| combineArrays | 75.929 | 4.464 | 80.962 | |
| compartments | 50.723 | 0.794 | 51.818 | |
| controlStripPlot | 4.253 | 0.447 | 4.721 | |
| convertArray | 1.694 | 0.100 | 1.806 | |
| densityBeanPlot | 6.955 | 0.702 | 7.716 | |
| densityPlot | 5.222 | 0.548 | 5.821 | |
| detectionP | 0.289 | 0.018 | 0.312 | |
| dmpFinder | 0.137 | 0.014 | 0.154 | |
| estimateCellCounts | 0.001 | 0.001 | 0.001 | |
| fixMethOutliers | 6.294 | 0.497 | 6.834 | |
| gaphunter | 0.089 | 0.001 | 0.091 | |
| getAnnotation | 95.987 | 0.283 | 97.073 | |
| getGenomicRatioSetFromGEO | 0.002 | 0.000 | 0.001 | |
| getQC | 0.251 | 0.060 | 0.443 | |
| getSex | 15.413 | 0.574 | 16.098 | |
| logit2 | 0.001 | 0.000 | 0.001 | |
| makeGenomicRatioSetFromMatrix | 11.807 | 0.080 | 11.957 | |
| mapToGenome-methods | 11.917 | 0.034 | 12.057 | |
| mdsPlot | 0.275 | 0.077 | 0.355 | |
| minfiQC | 15.223 | 0.869 | 16.239 | |
| plotBetasByType | 0.002 | 0.000 | 0.002 | |
| plotCpg | 0.117 | 0.005 | 0.124 | |
| preprocessFunnorm | 291.244 | 0.947 | 295.427 | |
| preprocessIllumina | 3.429 | 0.475 | 3.952 | |
| preprocessNoob | 148.352 | 0.462 | 152.587 | |
| preprocessQuantile | 103.667 | 0.205 | 104.821 | |
| preprocessRaw | 2.432 | 0.247 | 2.707 | |
| preprocessSwan | 0.435 | 0.022 | 0.464 | |
| qcReport | 0.049 | 0.002 | 0.052 | |
| ratioConvert-methods | 1.118 | 0.153 | 1.280 | |
| read.metharray | 5.856 | 0.215 | 6.116 | |
| read.metharray.exp | 9.006 | 0.379 | 9.465 | |
| read.metharray.sheet | 0.047 | 0.002 | 0.049 | |
| readGEORawFile | 0.003 | 0.000 | 0.003 | |
| readTCGA | 0.002 | 0.000 | 0.002 | |
| subsetByLoci | 0.453 | 0.026 | 0.484 | |
| utils | 0.225 | 0.133 | 0.362 | |