| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).
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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 1140/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| minfi 1.38.0 (landing page) Kasper Daniel Hansen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: minfi |
| Version: 1.38.0 |
| 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_1.38.0.tar.gz |
| StartedAt: 2021-10-14 21:10:14 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:20:12 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 598.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: minfi.Rcheck |
| Warnings: 0 |
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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_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/minfi.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.38.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 ... 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 (user + system) or elapsed time > 5s
user system elapsed
combineArrays 74.838 1.983 76.891
bumphunter 31.400 4.059 35.519
read.metharray.exp 16.150 0.071 16.234
read.metharray 9.158 0.131 9.294
preprocessFunnorm 5.149 0.123 5.277
* 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
‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/library’ * installing *source* package ‘minfi’ ... ** using staged installation ** 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 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)
minfi.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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
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: locfit
locfit 1.5-9.4 2020-03-24
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 Oct 14 21:20:02 2021
***********************************************
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
Warning messages:
1: 'colGrid' is deprecated.
Use 'colAutoGrid' instead.
See help("Deprecated")
2: 'colGrid' is deprecated.
Use 'colAutoGrid' instead.
See help("Deprecated")
>
> proc.time()
user system elapsed
50.037 1.598 51.653
minfi.Rcheck/minfi-Ex.timings
| name | user | system | elapsed | |
| GenomicMethylSet-class | 0.002 | 0.001 | 0.002 | |
| GenomicRatioSet-class | 0.001 | 0.000 | 0.001 | |
| IlluminaMethylationManifest-class | 4.338 | 0.180 | 4.554 | |
| MethylSet-class | 0.001 | 0.001 | 0.002 | |
| RGChannelSet-class | 0.001 | 0.001 | 0.003 | |
| RatioSet-class | 0.001 | 0.001 | 0.002 | |
| bumphunter | 31.400 | 4.059 | 35.519 | |
| combineArrays | 74.838 | 1.983 | 76.891 | |
| compartments | 3.905 | 0.330 | 4.240 | |
| controlStripPlot | 1.798 | 0.017 | 1.815 | |
| convertArray | 2.367 | 0.054 | 2.425 | |
| densityBeanPlot | 4.414 | 0.108 | 4.527 | |
| densityPlot | 4.375 | 0.076 | 4.453 | |
| detectionP | 0.599 | 0.004 | 0.604 | |
| dmpFinder | 0.116 | 0.004 | 0.120 | |
| estimateCellCounts | 0 | 0 | 0 | |
| fixMethOutliers | 1.881 | 0.087 | 1.969 | |
| gaphunter | 0.134 | 0.004 | 0.138 | |
| getAnnotation | 1.168 | 0.007 | 1.175 | |
| getGenomicRatioSetFromGEO | 0.000 | 0.000 | 0.001 | |
| getQC | 0.261 | 0.004 | 0.266 | |
| getSex | 3.056 | 0.077 | 3.134 | |
| logit2 | 0 | 0 | 0 | |
| makeGenomicRatioSetFromMatrix | 0.523 | 0.016 | 0.539 | |
| mapToGenome-methods | 0.346 | 0.003 | 0.349 | |
| mdsPlot | 0.215 | 0.011 | 0.227 | |
| minfiQC | 3.233 | 0.096 | 3.331 | |
| plotBetasByType | 0 | 0 | 0 | |
| plotCpg | 0.129 | 0.003 | 0.133 | |
| preprocessFunnorm | 5.149 | 0.123 | 5.277 | |
| preprocessIllumina | 3.710 | 0.009 | 3.722 | |
| preprocessNoob | 2.747 | 0.059 | 2.808 | |
| preprocessQuantile | 1.634 | 0.014 | 1.648 | |
| preprocessRaw | 3.072 | 0.011 | 3.086 | |
| preprocessSwan | 2.388 | 0.069 | 2.459 | |
| qcReport | 0.062 | 0.002 | 0.065 | |
| ratioConvert-methods | 0.134 | 0.002 | 0.136 | |
| read.metharray | 9.158 | 0.131 | 9.294 | |
| read.metharray.exp | 16.150 | 0.071 | 16.234 | |
| read.metharray.sheet | 0.081 | 0.005 | 0.085 | |
| readGEORawFile | 0.000 | 0.001 | 0.001 | |
| readTCGA | 0.001 | 0.000 | 0.000 | |
| subsetByLoci | 1.064 | 0.006 | 1.071 | |
| utils | 0.148 | 0.003 | 0.151 | |