Michael Scherer
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MAGAR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 7901096 |
| git_last_commit_date: 2021-07-06 11:44:06 -0400 (Tue, 06 Jul 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
|
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? 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 1022/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAGAR 1.0.1 (landing page) Michael Scherer
| 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: MAGAR |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MAGAR_1.0.1.tar.gz |
| StartedAt: 2021-10-15 01:17:22 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:27:55 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 632.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGAR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAGAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MAGAR_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MAGAR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAGAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGAR' version '1.0.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
doMethQTL 10.33 1.52 12.25
doMethQTLChromosome 8.96 0.10 9.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
doMethQTL 11.60 0.22 12.17
doMethQTLChromosome 9.98 0.11 10.47
computeCorrelationBlocks 5.11 0.01 5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/MAGAR.Rcheck/00check.log'
for details.
MAGAR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MAGAR_1.0.1.tar.gz && rm -rf MAGAR.buildbin-libdir && mkdir MAGAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAGAR.buildbin-libdir MAGAR_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MAGAR_1.0.1.zip && rm MAGAR_1.0.1.tar.gz MAGAR_1.0.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
3 395k 3 13289 0 0 101k 0 0:00:03 --:--:-- 0:00:03 101k
100 395k 100 395k 0 0 1010k 0 --:--:-- --:--:-- --:--:-- 1010k
install for i386
* 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
converting help for package 'MAGAR'
finding HTML links ... done
MethQTLInput-class html
finding level-2 HTML links ... done
MethQTLResult-class html
QTL.OPTIONS html
computeCorrelationBlocks html
doImport html
doMethQTL html
doMethQTLChromosome html
filterPval html
getAnno html
getCorrelationBlocks html
getGeno html
getMethData html
getOverlapUniverse html
getOverlappingQTL html
getPheno html
getResult html
getResultGWASMap html
getSamples html
getSpecificQTL html
imputeMeth html
joinMethQTLResult html
loadMethQTLInput html
loadMethQTLResult html
overlapInputs html
overlapQTLs html
qtlAnnotationEnrichment html
qtlBaseSubstitutionEnrichment html
qtlDistanceScatterplot html
qtlGetOption html
qtlJSON2options html
qtlManhattanPlot html
qtlOptions2JSON html
qtlPlotBaseSubstitution html
qtlPlotClusterSize html
qtlPlotSNPCpGInteraction html
qtlSetOption html
qtlTFBSMotifEnrichment html
qtlUpSetPlotCorBlocks html
qtlUpSetPlotTagCpGs html
qtlUpsetPlot html
qtlVennPlot html
saveMethQTLInput html
saveMethQTLResult html
** 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
install for x64
* installing *source* package 'MAGAR' ...
** testing if installed package can be loaded
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
* MD5 sums
packaged installation of 'MAGAR' as MAGAR_1.0.1.zip
* DONE (MAGAR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MAGAR' successfully unpacked and MD5 sums checked
|
MAGAR.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: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
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: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
Attaching package: 'HDF5Array'
The following object is masked from 'package:rhdf5':
h5ls
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpCwxYFR/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")==37570478.08 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system
Attaching package: 'ff'
The following object is masked from 'package:DelayedArray':
maxlength
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Attaching package: 'grid'
The following object is masked from 'package:ff':
pattern
Spam version 2.7-0 (2021-06-25) 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'
The following object is masked from 'package:Matrix':
det
The following object is masked from 'package:stats4':
mle
The following objects are masked from 'package:base':
backsolve, forwardsolve
See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
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
Attaching package: 'scales'
The following object is masked from 'package:viridis':
viridis_pal
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following objects are masked from 'package:ff':
mismatch, pattern
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:matrixStats':
count
Welcome to oligoClasses version 1.54.0
Attaching package: 'oligoClasses'
The following object is masked from 'package:minfi':
getM
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.50.0
Attaching package: 'MAGAR'
The following object is masked from 'package:foreach':
getResult
2021-10-15 01:26:57 0.5 STATUS STARTED Unit Testing
2021-10-15 01:26:57 0.5 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
2021-10-15 01:26:57 0.5 STATUS COMPLETED Testing constructors
2021-10-15 01:26:57 0.5 STATUS STARTED Testing options
2021-10-15 01:26:57 0.5 STATUS COMPLETED Testing options
2021-10-15 01:26:58 0.5 STATUS STARTED Testing cor blocks
2021-10-15 01:26:58 0.5 STATUS STARTED Compute correlation blocks
2021-10-15 01:26:58 0.5 STATUS STARTED Compute correlation matrix
2021-10-15 01:26:58 0.5 STATUS COMPLETED Compute correlation matrix
2021-10-15 01:26:58 0.5 STATUS STARTED Compute pairwise distances
2021-10-15 01:26:59 0.5 STATUS COMPLETED Compute pairwise distances
2021-10-15 01:27:00 0.5 STATUS STARTED Weight distances
2021-10-15 01:27:00 0.5 STATUS COMPLETED Weight distances
2021-10-15 01:27:01 0.5 STATUS STARTED Compute graph
2021-10-15 01:27:01 0.5 STATUS COMPLETED Compute graph
2021-10-15 01:27:01 0.5 STATUS STARTED Compute clustering
2021-10-15 01:27:02 0.5 STATUS COMPLETED Compute clustering
2021-10-15 01:27:02 0.5 STATUS COMPLETED Compute correlation blocks
2021-10-15 01:27:02 0.5 STATUS COMPLETED Testing cor blocks
2021-10-15 01:27:02 0.5 STATUS STARTED Test methQTL calling
2021-10-15 01:27:03 0.5 INFO Loading default option setting
2021-10-15 01:27:03 0.5 STATUS STARTED Imputation procedure knn
2021-10-15 01:27:03 0.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 01:27:03 0.5 STATUS STARTED Computing methQTLs
2021-10-15 01:27:03 0.5 STATUS STARTED Computing methQTL for chromosome chr18
2021-10-15 01:27:03 0.5 STATUS STARTED Compute methQTL per correlation block
2021-10-15 01:27:03 0.5 STATUS STARTED Setting up Multicore
2021-10-15 01:27:03 0.5 INFO Using 1 cores
2021-10-15 01:27:03 0.5 STATUS COMPLETED Setting up Multicore
2021-10-15 01:27:04 0.6 STATUS COMPLETED Compute methQTL per correlation block
2021-10-15 01:27:04 0.6 STATUS COMPLETED Computing methQTL for chromosome chr18
2021-10-15 01:27:05 0.5 STATUS COMPLETED Computing methQTLs
2021-10-15 01:27:05 0.5 STATUS COMPLETED Test methQTL calling
2021-10-15 01:27:05 0.5 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
2021-10-15 01:27:05 0.5 INFO Loading default option setting
2021-10-15 01:27:05 0.5 STATUS STARTED Imputation procedure knn
2021-10-15 01:27:05 0.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 01:27:06 0.5 STATUS STARTED Computing methQTLs
2021-10-15 01:27:06 0.5 STATUS STARTED Computing methQTL for chromosome chr18
2021-10-15 01:27:06 0.5 STATUS STARTED Compute methQTL per correlation block
2021-10-15 01:27:06 0.5 STATUS STARTED Setting up Multicore
2021-10-15 01:27:06 0.5 INFO Using 1 cores
2021-10-15 01:27:06 0.5 STATUS COMPLETED Setting up Multicore
2021-10-15 01:27:07 0.6 STATUS COMPLETED Compute methQTL per correlation block
2021-10-15 01:27:07 0.6 STATUS COMPLETED Computing methQTL for chromosome chr18
2021-10-15 01:27:08 0.6 STATUS COMPLETED Computing methQTLs
2021-10-15 01:27:08 0.6 STATUS STARTED Compute correlation blocks
2021-10-15 01:27:08 0.6 STATUS STARTED Compute correlation matrix
2021-10-15 01:27:08 0.6 STATUS COMPLETED Compute correlation matrix
2021-10-15 01:27:08 0.6 STATUS STARTED Compute pairwise distances
2021-10-15 01:27:09 0.6 STATUS COMPLETED Compute pairwise distances
2021-10-15 01:27:10 0.6 STATUS STARTED Weight distances
2021-10-15 01:27:10 0.6 STATUS COMPLETED Weight distances
2021-10-15 01:27:11 0.6 STATUS STARTED Compute graph
2021-10-15 01:27:11 0.6 STATUS COMPLETED Compute graph
2021-10-15 01:27:11 0.6 STATUS STARTED Compute clustering
2021-10-15 01:27:12 0.6 STATUS COMPLETED Compute clustering
2021-10-15 01:27:12 0.6 STATUS COMPLETED Compute correlation blocks
RUNIT TEST PROTOCOL -- Fri Oct 15 01:27:12 2021
***********************************************
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
32.51 2.73 36.10
|
MAGAR.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
> BiocGenerics:::testPackage("MAGAR")
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
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: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
Attaching package: 'HDF5Array'
The following object is masked from 'package:rhdf5':
h5ls
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpiUILoL/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")==685831618.56 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system
Attaching package: 'ff'
The following object is masked from 'package:DelayedArray':
maxlength
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Attaching package: 'grid'
The following object is masked from 'package:ff':
pattern
Spam version 2.7-0 (2021-06-25) 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'
The following object is masked from 'package:Matrix':
det
The following object is masked from 'package:stats4':
mle
The following objects are masked from 'package:base':
backsolve, forwardsolve
See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
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
Attaching package: 'scales'
The following object is masked from 'package:viridis':
viridis_pal
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following objects are masked from 'package:ff':
mismatch, pattern
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:matrixStats':
count
Welcome to oligoClasses version 1.54.0
Attaching package: 'oligoClasses'
The following object is masked from 'package:minfi':
getM
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.50.0
Attaching package: 'MAGAR'
The following object is masked from 'package:foreach':
getResult
2021-10-15 01:27:31 0.9 STATUS STARTED Unit Testing
2021-10-15 01:27:31 0.8 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
2021-10-15 01:27:31 0.8 STATUS COMPLETED Testing constructors
2021-10-15 01:27:31 0.8 STATUS STARTED Testing options
2021-10-15 01:27:31 0.8 STATUS COMPLETED Testing options
2021-10-15 01:27:31 0.8 STATUS STARTED Testing cor blocks
2021-10-15 01:27:32 0.8 STATUS STARTED Compute correlation blocks
2021-10-15 01:27:32 0.8 STATUS STARTED Compute correlation matrix
2021-10-15 01:27:32 0.9 STATUS COMPLETED Compute correlation matrix
2021-10-15 01:27:32 0.9 STATUS STARTED Compute pairwise distances
2021-10-15 01:27:33 0.9 STATUS COMPLETED Compute pairwise distances
2021-10-15 01:27:34 0.9 STATUS STARTED Weight distances
2021-10-15 01:27:34 0.9 STATUS COMPLETED Weight distances
2021-10-15 01:27:35 0.9 STATUS STARTED Compute graph
2021-10-15 01:27:35 0.9 STATUS COMPLETED Compute graph
2021-10-15 01:27:35 0.9 STATUS STARTED Compute clustering
2021-10-15 01:27:36 0.9 STATUS COMPLETED Compute clustering
2021-10-15 01:27:36 0.9 STATUS COMPLETED Compute correlation blocks
2021-10-15 01:27:36 0.9 STATUS COMPLETED Testing cor blocks
2021-10-15 01:27:36 0.9 STATUS STARTED Test methQTL calling
2021-10-15 01:27:36 0.9 INFO Loading default option setting
2021-10-15 01:27:36 0.9 STATUS STARTED Imputation procedure knn
2021-10-15 01:27:36 0.9 STATUS COMPLETED Imputation procedure knn
2021-10-15 01:27:36 0.9 STATUS STARTED Computing methQTLs
2021-10-15 01:27:36 0.9 STATUS STARTED Computing methQTL for chromosome chr18
2021-10-15 01:27:37 0.9 STATUS STARTED Compute methQTL per correlation block
2021-10-15 01:27:37 0.9 STATUS STARTED Setting up Multicore
2021-10-15 01:27:37 0.9 INFO Using 1 cores
2021-10-15 01:27:37 0.9 STATUS COMPLETED Setting up Multicore
2021-10-15 01:27:38 0.9 STATUS COMPLETED Compute methQTL per correlation block
2021-10-15 01:27:38 0.9 STATUS COMPLETED Computing methQTL for chromosome chr18
2021-10-15 01:27:39 0.9 STATUS COMPLETED Computing methQTLs
2021-10-15 01:27:39 0.9 STATUS COMPLETED Test methQTL calling
2021-10-15 01:27:39 0.9 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
2021-10-15 01:27:39 0.9 INFO Loading default option setting
2021-10-15 01:27:39 0.9 STATUS STARTED Imputation procedure knn
2021-10-15 01:27:39 0.9 STATUS COMPLETED Imputation procedure knn
2021-10-15 01:27:39 0.9 STATUS STARTED Computing methQTLs
2021-10-15 01:27:39 0.9 STATUS STARTED Computing methQTL for chromosome chr18
2021-10-15 01:27:39 0.9 STATUS STARTED Compute methQTL per correlation block
2021-10-15 01:27:39 0.9 STATUS STARTED Setting up Multicore
2021-10-15 01:27:40 0.9 INFO Using 1 cores
2021-10-15 01:27:40 0.9 STATUS COMPLETED Setting up Multicore
2021-10-15 01:27:40 0.9 STATUS COMPLETED Compute methQTL per correlation block
2021-10-15 01:27:40 0.9 STATUS COMPLETED Computing methQTL for chromosome chr18
2021-10-15 01:27:41 0.9 STATUS COMPLETED Computing methQTLs
2021-10-15 01:27:41 0.9 STATUS STARTED Compute correlation blocks
2021-10-15 01:27:41 0.9 STATUS STARTED Compute correlation matrix
2021-10-15 01:27:42 0.9 STATUS COMPLETED Compute correlation matrix
2021-10-15 01:27:42 0.9 STATUS STARTED Compute pairwise distances
2021-10-15 01:27:43 0.9 STATUS COMPLETED Compute pairwise distances
2021-10-15 01:27:44 0.9 STATUS STARTED Weight distances
2021-10-15 01:27:44 0.9 STATUS COMPLETED Weight distances
2021-10-15 01:27:45 0.9 STATUS STARTED Compute graph
2021-10-15 01:27:45 0.9 STATUS COMPLETED Compute graph
2021-10-15 01:27:45 0.9 STATUS STARTED Compute clustering
2021-10-15 01:27:46 0.9 STATUS COMPLETED Compute clustering
2021-10-15 01:27:46 0.9 STATUS COMPLETED Compute correlation blocks
RUNIT TEST PROTOCOL -- Fri Oct 15 01:27:46 2021
***********************************************
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
31.98 0.96 33.76
|
|
MAGAR.Rcheck/examples_i386/MAGAR-Ex.timings
|
MAGAR.Rcheck/examples_x64/MAGAR-Ex.timings
|