Kasper Daniel Hansen
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/minfi |
| git_branch: master |
| git_last_commit: 77d3345 |
| git_last_commit_date: 2021-11-02 00:11:19 -0400 (Tue, 02 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:02 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the minfi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/minfi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1161/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| minfi 1.41.1 (landing page) Kasper Daniel Hansen
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: minfi |
| Version: 1.41.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:minfi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings minfi_1.41.1.tar.gz |
| StartedAt: 2022-03-17 19:35:53 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:43:20 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 447.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: minfi.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:minfi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings minfi_1.41.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/minfi.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'minfi/DESCRIPTION' ... OK
* this is package 'minfi' version '1.41.1'
* 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 '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 objects imported by ':::' calls:
'DelayedArray:::get_verbose_block_processing'
'DelayedArray:::normarg_grid' 'bumphunter:::.getEstimate'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.guessArrayTypes'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'minfi/R/IlluminaMethylationManifest-class.R':
unlockBinding(name, env = object@data)
* 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 (user + system) or elapsed time > 5s
user system elapsed
combineArrays 59.22 5.57 66.45
bumphunter 25.81 11.07 36.88
read.metharray.exp 8.34 0.33 8.68
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/minfi.Rcheck/00check.log'
for details.
minfi.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL minfi
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'minfi' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'minfi'
finding HTML links ... done
DelayedArray_utils html
GenomicMethylSet-class html
GenomicRatioSet-class html
IlluminaMethylationAnnotation-class html
IlluminaMethylationManifest-class html
MethylSet-class html
finding level-2 HTML links ... done
RGChannelSet-class html
RatioSet-class html
blockFinder html
bumphunter html
combineArrays html
compartments html
controlStripPlot html
convertArray html
cpgCollapse html
densityBeanPlot html
densityPlot html
detectionP html
dmpFinder html
estimateCellCounts html
fixMethOutliers html
gaphunter html
getAnnotation html
getGenomicRatioSetFromGEO html
getQC html
getSex html
logit2 html
makeGenomicRatioSetFromMatrix html
mapToGenome-methods html
mdsPlot html
minfi-defunct html
minfi-deprecated html
minfi-package html
minfiQC html
plotBetasByType html
plotCpg html
preprocessFunnorm html
preprocessIllumina html
preprocessNoob html
preprocessQuantile html
preprocessRaw html
preprocessSwan html
qcReport html
ratioConvert-methods html
read.metharray html
read.metharray.exp html
read.metharray.sheet html
readGEORawFile html
readTCGA html
subsetByLoci html
utils html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (minfi)
Making 'packages.html' ... done
minfi.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
> require("minfi") || stop("unable to load minfi")
Loading required package: minfi
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.5 2022-03-01
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
Loading required package: DelayedArray
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
RUNIT TEST PROTOCOL -- Thu Mar 17 19:43:04 2022
***********************************************
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
35.71 3.29 38.98
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0 | 0 | 0 | |
| GenomicRatioSet-class | 0 | 0 | 0 | |
| IlluminaMethylationManifest-class | 3.44 | 0.20 | 3.64 | |
| MethylSet-class | 0 | 0 | 0 | |
| RGChannelSet-class | 0 | 0 | 0 | |
| RatioSet-class | 0 | 0 | 0 | |
| bumphunter | 25.81 | 11.07 | 36.88 | |
| combineArrays | 59.22 | 5.57 | 66.45 | |
| compartments | 2.06 | 0.43 | 2.48 | |
| controlStripPlot | 2.14 | 0.29 | 2.44 | |
| convertArray | 1.25 | 0.11 | 1.36 | |
| densityBeanPlot | 2.35 | 0.35 | 2.69 | |
| densityPlot | 4.04 | 0.51 | 4.56 | |
| detectionP | 0.36 | 0.05 | 0.41 | |
| dmpFinder | 0.14 | 0.00 | 0.14 | |
| estimateCellCounts | 0 | 0 | 0 | |
| fixMethOutliers | 1.75 | 0.31 | 2.06 | |
| gaphunter | 0.11 | 0.02 | 0.12 | |
| getAnnotation | 1.03 | 0.06 | 1.10 | |
| getGenomicRatioSetFromGEO | 0 | 0 | 0 | |
| getQC | 0.19 | 0.00 | 0.19 | |
| getSex | 1.02 | 0.16 | 1.17 | |
| logit2 | 0 | 0 | 0 | |
| makeGenomicRatioSetFromMatrix | 1.42 | 0.25 | 1.68 | |
| mapToGenome-methods | 0.27 | 0.00 | 0.26 | |
| mdsPlot | 0.20 | 0.04 | 0.25 | |
| minfiQC | 1.99 | 0.33 | 2.31 | |
| plotBetasByType | 0 | 0 | 0 | |
| plotCpg | 0.12 | 0.03 | 0.16 | |
| preprocessFunnorm | 3.57 | 0.33 | 3.89 | |
| preprocessIllumina | 3.78 | 0.55 | 4.33 | |
| preprocessNoob | 0.78 | 0.04 | 0.83 | |
| preprocessQuantile | 0.69 | 0.07 | 0.75 | |
| preprocessRaw | 3.11 | 0.39 | 3.50 | |
| preprocessSwan | 0.41 | 0.00 | 0.41 | |
| qcReport | 0.04 | 0.00 | 0.05 | |
| ratioConvert-methods | 0.05 | 0.01 | 0.06 | |
| read.metharray | 4.30 | 0.19 | 4.48 | |
| read.metharray.exp | 8.34 | 0.33 | 8.68 | |
| read.metharray.sheet | 0.02 | 0.03 | 0.04 | |
| readGEORawFile | 0 | 0 | 0 | |
| readTCGA | 0 | 0 | 0 | |
| subsetByLoci | 0.70 | 0.01 | 0.72 | |
| utils | 0.14 | 0.04 | 0.17 | |