| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:11 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 MAGAR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGAR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1067/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAGAR 1.7.0 (landing page) Michael Scherer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: MAGAR |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAGAR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAGAR_1.7.0.tar.gz |
| StartedAt: 2023-02-07 06:32:53 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 06:42:26 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 573.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MAGAR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MAGAR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MAGAR_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MAGAR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MAGAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGAR’ version ‘1.7.0’
* package encoding: UTF-8
* 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:
.travis.yml
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 ‘MAGAR’ 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 ... WARNING
Loading required package: HDF5Array
Loading required package: methods
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: utils
Attaching package: ‘utils’
The following objects are masked from ‘package:Matrix’:
head, tail
Loading required package: graphics
Attaching package: ‘graphics’
The following object is masked from ‘package:Matrix’:
image
The following object is masked from ‘package:stats4’:
plot
Loading required package: stats
Attaching package: ‘stats’
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cov2cor, toeplitz, update
The following objects are masked from ‘package:stats4’:
AIC, BIC, coef, confint, logLik, nobs, profile, update, vcov
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, aperm, 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: 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: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:Matrix’:
expand, unname
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I, expand.grid, unname
Loading required package: IRanges
Attaching package: ‘DelayedArray’
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apply, rowsum, scale, sweep
Loading required package: rhdf5
Attaching package: ‘HDF5Array’
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h5ls
Loading required package: RnBeads
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: MASS
Loading required package: grDevices
Loading required package: cluster
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Loading required package: bit
Attaching package: ‘bit’
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xor
Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpE6u4om/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package: ‘ff’
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maxlength
The following objects are masked from ‘package:utils’:
write.csv, write.csv2
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is.factor, is.ordered
Loading required package: fields
Loading required package: spam
Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: ‘spam’
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det
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mle
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backsolve, forwardsolve
Loading required package: viridis
Loading required package: viridisLite
Try help(fields) to get started.
Loading required package: ggplot2
Loading required package: gplots
Attaching package: ‘gplots’
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lowess
Loading required package: grid
Attaching package: ‘grid’
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Loading required package: gridExtra
Attaching package: ‘gridExtra’
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combine
Loading required package: limma
Attaching package: ‘limma’
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plotMA
Loading required package: illuminaio
Loading required package: methylumi
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’
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Loading required package: scales
Attaching package: ‘scales’
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Loading required package: reshape2
Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Attaching package: ‘AnnotationDbi’
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Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db
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Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
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Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: locfit
locfit 1.5-9.7 2023-01-02
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: plyr
Attaching package: ‘plyr’
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desc
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rename
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Loading required package: snpStats
Loading required package: survival
Loading required package: crlmm
Loading required package: oligoClasses
Welcome to oligoClasses version 1.61.0
Attaching package: ‘oligoClasses’
The following object is masked from ‘package:minfi’:
getM
Loading required package: preprocessCore
Killed
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getOverlapUniverse: warning in overlapQTLs(meth.qtl.res = meth.qtl.res,
type = type): partial argument match of 'meth.qtl.res' to
'meth.qtl.result.list'
doGenoImport: no visible global function definition for
‘makeGRangesFromDataFrame’
doGenoImport: no visible global function definition for
‘seqlevelsStyle<-’
doGenoImport: no visible global function definition for ‘findOverlaps’
doGenoImport: no visible global function definition for ‘ggplot’
doGenoImport: no visible global function definition for ‘aes’
doGenoImport: no visible binding for global variable ‘PC1’
doGenoImport: no visible binding for global variable ‘PC2’
doGenoImport: no visible global function definition for ‘geom_point’
doGenoImport: no visible global function definition for ‘xlab’
doGenoImport: no visible global function definition for ‘ylab’
doGenoImport: no visible global function definition for ‘theme_bw’
doGenoImport: no visible global function definition for ‘theme’
doGenoImport: no visible global function definition for ‘element_blank’
doGenoImport: no visible global function definition for ‘element_text’
doGenoImport: no visible global function definition for ‘element_line’
doGenoImport: no visible global function definition for ‘ggsave’
doGenoImportIDAT: no visible global function definition for
‘featureData’
doGenoImportIDAT: no visible global function definition for
‘featureNames’
doGenoImportIDAT: no visible global function definition for
‘chromosome’
doGenoImportIDAT: no visible global function definition for ‘calls’
doGenoImportIDAT: no visible global function definition for
‘makeGRangesFromDataFrame’
doGenoImportIDAT: no visible global function definition for ‘GRanges’
doGenoImportIDAT: no visible global function definition for ‘Rle’
doGenoImportIDAT: no visible global function definition for ‘IRanges’
doGenoImportIDAT: no visible global function definition for
‘findOverlaps’
doGenoImportIDAT: no visible global function definition for ‘queryHits’
doGenoImportIDAT: no visible global function definition for
‘subjectHits’
doGenoImportImputed: no visible global function definition for ‘ggplot’
doGenoImportImputed: no visible global function definition for ‘aes’
doGenoImportImputed: no visible binding for global variable ‘PC1’
doGenoImportImputed: no visible binding for global variable ‘PC2’
doGenoImportImputed: no visible global function definition for
‘geom_point’
doGenoImportImputed: no visible global function definition for ‘xlab’
doGenoImportImputed: no visible global function definition for ‘ylab’
doGenoImportImputed: no visible global function definition for
‘theme_bw’
doGenoImportImputed: no visible global function definition for ‘theme’
doGenoImportImputed: no visible global function definition for
‘element_blank’
doGenoImportImputed: no visible global function definition for
‘element_text’
doGenoImportImputed: no visible global function definition for
‘element_line’
doGenoImportImputed: no visible global function definition for ‘ggsave’
doImport: no visible binding for global variable ‘anno’
doMethImport: no visible global function definition for ‘GRanges’
doMethImport: no visible global function definition for ‘Rle’
doMethImport: no visible global function definition for ‘IRanges’
doMethImport: no visible global function definition for
‘makeGRangesFromDataFrame’
doMethImport: no visible global function definition for ‘findOverlaps’
doMethImport: no visible global function definition for ‘queryHits’
doMethQTLChromosome: no visible global function definition for ‘ggplot’
doMethQTLChromosome: no visible global function definition for ‘aes’
doMethQTLChromosome: no visible binding for global variable ‘Size’
doMethQTLChromosome: no visible binding for global variable ‘..count..’
doMethQTLChromosome: no visible global function definition for
‘geom_histogram’
doMethQTLChromosome: no visible global function definition for
‘geom_vline’
doMethQTLChromosome: no visible global function definition for
‘theme_bw’
doMethQTLChromosome: no visible global function definition for ‘theme’
doMethQTLChromosome: no visible global function definition for
‘element_blank’
doMethQTLChromosome: no visible global function definition for
‘element_text’
doMethQTLChromosome: no visible global function definition for
‘element_line’
doMethQTLChromosome: no visible global function definition for ‘ggsave’
doMethQTLChromosome: no visible global function definition for
‘mclapply’
getOverlapUniverse: no visible global function definition for
‘makeGRangesFromDataFrame’
qtlAnnotationEnrichment: no visible global function definition for
‘findOverlaps’
qtlCorrelateCorBlockStat: no visible global function definition for
‘ggplot’
qtlCorrelateCorBlockStat: no visible global function definition for
‘aes_string’
qtlCorrelateCorBlockStat: no visible global function definition for
‘geom_point’
qtlCorrelateCorBlockStat: no visible global function definition for
‘geom_smooth’
qtlCorrelateCorBlockStat: no visible global function definition for
‘ggtitle’
qtlCorrelateCorBlockStat: no visible global function definition for
‘ylab’
qtlDistanceScatterplot: no visible global function definition for
‘ggplot’
qtlDistanceScatterplot: no visible global function definition for ‘aes’
qtlDistanceScatterplot: no visible binding for global variable
‘Distance’
qtlDistanceScatterplot: no visible binding for global variable
‘P.value’
qtlDistanceScatterplot: no visible global function definition for
‘geom_point’
qtlDistanceScatterplot: no visible global function definition for
‘ggtitle’
qtlDistanceScatterplot: no visible global function definition for
‘xlab’
qtlDistanceScatterplot: no visible global function definition for
‘ylab’
qtlDistanceScatterplot: no visible binding for global variable ‘Beta’
qtlDistanceScatterplot: no visible global function definition for
‘labs’
qtlDistanceScatterplot: no visible global function definition for
‘scale_color_gradient2’
qtlDistanceScatterplot: no visible global function definition for
‘scale_color_continuous’
qtlDistanceScatterplot: no visible global function definition for
‘annotate’
qtlDistanceScatterplot: no visible global function definition for
‘ggsave’
qtlLOLAEnrichment: no visible global function definition for
‘loadRegionDB’
qtlLOLAEnrichment: no visible global function definition for ‘runLOLA’
qtlPlotAnnotationEnrichment: no visible global function definition for
‘ggplot’
qtlPlotAnnotationEnrichment: no visible global function definition for
‘aes’
qtlPlotAnnotationEnrichment: no visible binding for global variable
‘Type’
qtlPlotAnnotationEnrichment: no visible binding for global variable
‘Annotation’
qtlPlotAnnotationEnrichment: no visible binding for global variable
‘OddsRatio’
qtlPlotAnnotationEnrichment: no visible global function definition for
‘geom_tile’
qtlPlotAnnotationEnrichment: no visible global function definition for
‘scale_fill_gradient2’
qtlPlotBaseSubstitution: no visible global function definition for
‘ggplot’
qtlPlotBaseSubstitution: no visible global function definition for
‘aes’
qtlPlotBaseSubstitution: no visible binding for global variable
‘Substitution’
qtlPlotBaseSubstitution: no visible binding for global variable
‘OddsRatio’
qtlPlotBaseSubstitution: no visible global function definition for
‘geom_tile’
qtlPlotBaseSubstitution: no visible global function definition for
‘scale_fill_gradient2’
qtlPlotClusterSize: no visible global function definition for ‘ggplot’
qtlPlotClusterSize: no visible global function definition for ‘aes’
qtlPlotClusterSize: no visible binding for global variable ‘Size’
qtlPlotClusterSize: no visible binding for global variable ‘..count..’
qtlPlotClusterSize: no visible global function definition for
‘geom_histogram’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘ggplot’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘aes’
qtlPlotSNPCorrelationBlock: no visible binding for global variable
‘SNP’
qtlPlotSNPCorrelationBlock: no visible binding for global variable
‘CpG’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘geom_point’
qtlPlotSNPCorrelationBlock: no visible binding for global variable
‘Representative’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘geom_smooth’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘facet_grid’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘theme’
qtlPlotSNPCorrelationBlock: no visible global function definition for
‘scale_color_manual’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘ggplot’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘aes’
qtlPlotSNPCpGInteraction: no visible binding for global variable ‘SNP’
qtlPlotSNPCpGInteraction: no visible binding for global variable ‘CpG’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘geom_boxplot’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘theme_bw’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘ylab’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘xlab’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘ggsave’
qtlPlotSNPCpGInteraction: no visible binding for global variable
‘SNPDosage’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘geom_point’
qtlPlotSNPCpGInteraction: no visible global function definition for
‘geom_smooth’
Undefined global functions or variables:
..count.. Annotation Beta CpG Distance GRanges IRanges OddsRatio
P.value PC1 PC2 Representative Rle SNP SNPDosage Size Substitution
Type aes aes_string anno annotate calls chromosome element_blank
element_line element_text facet_grid featureData featureNames
findOverlaps geom_boxplot geom_histogram geom_point geom_smooth
geom_tile geom_vline ggplot ggsave ggtitle labs loadRegionDB
makeGRangesFromDataFrame mclapply queryHits runLOLA
scale_color_continuous scale_color_gradient2 scale_color_manual
scale_fill_gradient2 seqlevelsStyle<- subjectHits theme theme_bw xlab
ylab
* 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 ... ERROR
Running examples in ‘MAGAR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qtlPlotBaseSubstitution
> ### Title: qtlPlotBaseSubstitution
> ### Aliases: qtlPlotBaseSubstitution
>
> ### ** Examples
>
> meth.qtl.res <- loadMethQTLResult(system.file("extdata","MethQTLResult_chr18",package="MAGAR"))
> qtlPlotBaseSubstitution(meth.qtl.res)
Killed
* 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 ...
‘MAGAR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘MAGAR.Rmd’ using rmarkdown
Killed
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MAGAR.Rcheck/00check.log’
for details.
MAGAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MAGAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘MAGAR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** testing if installed package can be loaded from final location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** testing if installed package keeps a record of temporary installation path * DONE (MAGAR)
MAGAR.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> BiocGenerics:::testPackage("MAGAR")
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, aperm, 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
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'DelayedArray'
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- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
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Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
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Try help(fields) to get started.
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Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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Welcome to oligoClasses version 1.61.0
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2023-02-07 06:41:18 1.2 STATUS STARTED Unit Testing
2023-02-07 06:41:18 1.2 STATUS STARTED Testing constructors
Object of class MethQTLInput
Contains 3 samples
Methylation data for 5 CpGs
Genotyping data for 4 SNPs
Genome assembly: hg19
Object of class MethQTLResult
Contains 10 methQTL
Contains 0 correlation blocks
methQTL called using classical.linear
representative CpGs computed with row.medians
2023-02-07 06:41:18 1.2 STATUS COMPLETED Testing constructors
2023-02-07 06:41:18 1.2 STATUS STARTED Testing options
2023-02-07 06:41:18 1.2 STATUS COMPLETED Testing options
2023-02-07 06:41:18 1.2 STATUS STARTED Testing cor blocks
2023-02-07 06:41:18 1.2 STATUS STARTED Compute correlation blocks
2023-02-07 06:41:18 1.2 STATUS STARTED Compute correlation matrix
2023-02-07 06:41:18 1.2 STATUS COMPLETED Compute correlation matrix
2023-02-07 06:41:18 1.2 STATUS STARTED Compute pairwise distances
2023-02-07 06:41:19 1.2 STATUS COMPLETED Compute pairwise distances
2023-02-07 06:41:21 1.2 STATUS STARTED Weight distances
2023-02-07 06:41:21 1.2 STATUS COMPLETED Weight distances
2023-02-07 06:41:22 1.2 STATUS STARTED Compute graph
2023-02-07 06:41:22 1.2 STATUS COMPLETED Compute graph
2023-02-07 06:41:22 1.2 STATUS STARTED Compute clustering
2023-02-07 06:41:23 1.2 STATUS COMPLETED Compute clustering
2023-02-07 06:41:23 1.2 STATUS COMPLETED Compute correlation blocks
2023-02-07 06:41:23 1.2 STATUS COMPLETED Testing cor blocks
2023-02-07 06:41:23 1.2 STATUS STARTED Test methQTL calling
2023-02-07 06:41:23 1.2 INFO Loading default option setting
2023-02-07 06:41:23 1.2 STATUS STARTED Imputation procedure knn
2023-02-07 06:41:23 1.2 STATUS COMPLETED Imputation procedure knn
2023-02-07 06:41:24 1.2 STATUS STARTED Computing methQTLs
2023-02-07 06:41:24 1.2 STATUS STARTED Computing methQTL for chromosome chr18
2023-02-07 06:41:24 1.2 STATUS STARTED Compute methQTL per correlation block
2023-02-07 06:41:24 1.2 STATUS STARTED Setting up Multicore
2023-02-07 06:41:24 1.2 INFO Using 1 cores
2023-02-07 06:41:24 1.2 STATUS COMPLETED Setting up Multicore
2023-02-07 06:41:24 1.2 STATUS COMPLETED Compute methQTL per correlation block
2023-02-07 06:41:24 1.2 STATUS COMPLETED Computing methQTL for chromosome chr18
2023-02-07 06:41:25 1.2 STATUS COMPLETED Computing methQTLs
2023-02-07 06:41:25 1.2 STATUS COMPLETED Test methQTL calling
2023-02-07 06:41:25 1.2 STATUS COMPLETED Unit Testing
Object of class MethQTLInput
Contains 3 samples
Methylation data for 5 CpGs
Genotyping data for 4 SNPs
Genome assembly: hg19
Object of class MethQTLResult
Contains 10 methQTL
Contains 0 correlation blocks
methQTL called using classical.linear
representative CpGs computed with row.medians
2023-02-07 06:41:26 1.2 INFO Loading default option setting
2023-02-07 06:41:26 1.2 STATUS STARTED Imputation procedure knn
2023-02-07 06:41:26 1.2 STATUS COMPLETED Imputation procedure knn
2023-02-07 06:41:26 1.2 STATUS STARTED Computing methQTLs
2023-02-07 06:41:26 1.2 STATUS STARTED Computing methQTL for chromosome chr18
2023-02-07 06:41:26 1.2 STATUS STARTED Compute methQTL per correlation block
2023-02-07 06:41:26 1.2 STATUS STARTED Setting up Multicore
2023-02-07 06:41:26 1.2 INFO Using 1 cores
2023-02-07 06:41:26 1.2 STATUS COMPLETED Setting up Multicore
2023-02-07 06:41:26 1.3 STATUS COMPLETED Compute methQTL per correlation block
2023-02-07 06:41:26 1.3 STATUS COMPLETED Computing methQTL for chromosome chr18
2023-02-07 06:41:27 1.3 STATUS COMPLETED Computing methQTLs
2023-02-07 06:41:28 1.3 STATUS STARTED Compute correlation blocks
2023-02-07 06:41:28 1.3 STATUS STARTED Compute correlation matrix
2023-02-07 06:41:28 1.3 STATUS COMPLETED Compute correlation matrix
2023-02-07 06:41:28 1.3 STATUS STARTED Compute pairwise distances
2023-02-07 06:41:29 1.3 STATUS COMPLETED Compute pairwise distances
2023-02-07 06:41:30 1.3 STATUS STARTED Weight distances
2023-02-07 06:41:30 1.3 STATUS COMPLETED Weight distances
2023-02-07 06:41:31 1.3 STATUS STARTED Compute graph
2023-02-07 06:41:31 1.3 STATUS COMPLETED Compute graph
2023-02-07 06:41:31 1.3 STATUS STARTED Compute clustering
2023-02-07 06:41:33 1.3 STATUS COMPLETED Compute clustering
2023-02-07 06:41:33 1.3 STATUS COMPLETED Compute correlation blocks
RUNIT TEST PROTOCOL -- Tue Feb 7 06:41:33 2023
***********************************************
Number of test functions: 4
Number of errors: 0
Number of failures: 0
1 Test Suite :
MAGAR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
39.029 0.856 40.684
MAGAR.Rcheck/MAGAR-Ex.timings
| name | user | system | elapsed | |
| computeCorrelationBlocks | 5.469 | 0.016 | 5.541 | |
| doImport | 0.078 | 0.000 | 0.078 | |
| doMethQTL | 13.037 | 0.243 | 13.338 | |
| doMethQTLChromosome | 11.05 | 0.12 | 11.18 | |
| filterPval | 0.020 | 0.004 | 0.029 | |
| getAnno | 0.102 | 0.004 | 0.108 | |
| getCorrelationBlocks | 0.036 | 0.000 | 0.037 | |
| getGeno | 0.124 | 0.004 | 0.127 | |
| getMethData | 0.101 | 0.003 | 0.105 | |
| getOverlapUniverse | 0.149 | 0.000 | 0.151 | |
| getOverlappingQTL | 0.026 | 0.001 | 0.025 | |
| getPheno | 0.073 | 0.000 | 0.073 | |
| getResult | 0.023 | 0.000 | 0.023 | |
| getResultGWASMap | 0.091 | 0.003 | 0.095 | |
| getSamples | 0.073 | 0.001 | 0.073 | |
| getSpecificQTL | 0.022 | 0.000 | 0.022 | |
| imputeMeth | 0.193 | 0.003 | 0.223 | |
| joinMethQTLResult | 0.074 | 0.008 | 0.082 | |
| loadMethQTLInput | 0.069 | 0.004 | 0.073 | |
| loadMethQTLResult | 0.021 | 0.000 | 0.021 | |
| overlapInputs | 0.069 | 0.004 | 0.073 | |
| overlapQTLs | 0.021 | 0.000 | 0.022 | |
| qtlAnnotationEnrichment | 1.046 | 0.040 | 1.099 | |
| qtlBaseSubstitutionEnrichment | 0.065 | 0.004 | 0.076 | |
| qtlDistanceScatterplot | 0.613 | 0.016 | 0.642 | |
| qtlGetOption | 0.000 | 0.000 | 0.001 | |
| qtlJSON2options | 0.000 | 0.002 | 0.004 | |
| qtlManhattanPlot | 0.036 | 0.005 | 0.058 | |
| qtlOptions2JSON | 0.006 | 0.000 | 0.024 | |