| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:57 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 MultiAssayExperiment package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiAssayExperiment.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 1238/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MultiAssayExperiment 1.20.0 (landing page) Marcel Ramos
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MultiAssayExperiment |
| Version: 1.20.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiAssayExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MultiAssayExperiment_1.20.0.tar.gz |
| StartedAt: 2022-04-12 23:24:15 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:29:34 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 318.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MultiAssayExperiment.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiAssayExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MultiAssayExperiment_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MultiAssayExperiment/DESCRIPTION' ... OK * this is package 'MultiAssayExperiment' version '1.20.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'MultiAssayExperiment' 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 ... WARNING '::' or ':::' import not declared from: 'DelayedArray' Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'DelayedArray:::normarg_verbose' 'S4Vectors:::selectSome' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.Rcheck/00check.log' for details.
MultiAssayExperiment.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MultiAssayExperiment_1.20.0.tar.gz && rm -rf MultiAssayExperiment.buildbin-libdir && mkdir MultiAssayExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MultiAssayExperiment.buildbin-libdir MultiAssayExperiment_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MultiAssayExperiment_1.20.0.zip && rm MultiAssayExperiment_1.20.0.tar.gz MultiAssayExperiment_1.20.0.zip
###
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install for i386
* installing *source* package 'MultiAssayExperiment' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MultiAssayExperiment'
finding HTML links ... done
ExperimentList-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.buildbin-libdir/00LOCK-MultiAssayExperiment/00new/MultiAssayExperiment/help/coerce+2CList+2CExperimentList-method.html
finding level-2 HTML links ... done
ExperimentList html
HDF5MultiAssayExperiment html
MatchedAssayExperiment-class html
MultiAssayExperiment-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.buildbin-libdir/00LOCK-MultiAssayExperiment/00new/MultiAssayExperiment/help/coerce+2CList+2CMultiAssayExperiment-method.html
MultiAssayExperiment-helpers html
MultiAssayExperiment-methods html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.buildbin-libdir/00LOCK-MultiAssayExperiment/00new/MultiAssayExperiment/help/colnames+3C-+2CMultiAssayExperiment+2Clist-method.html
MultiAssayExperiment-package html
MultiAssayExperiment html
MultiAssayExperimentToMAF html
hasAssay html
mapToList html
miniACC html
prepMultiAssay html
reexports html
subsetBy html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.buildbin-libdir/00LOCK-MultiAssayExperiment/00new/MultiAssayExperiment/help/subsetByRow+2CExperimentList+2CList-method.html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/MultiAssayExperiment.buildbin-libdir/00LOCK-MultiAssayExperiment/00new/MultiAssayExperiment/help/subsetByColumn+2CExperimentList+2CList-method.html
upsetSamples 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
install for x64
* installing *source* package 'MultiAssayExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiAssayExperiment' as MultiAssayExperiment_1.20.0.zip
* DONE (MultiAssayExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MultiAssayExperiment' successfully unpacked and MD5 sums checked
|
MultiAssayExperiment.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> library(testthat)
> library(MultiAssayExperiment)
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: GenomicRanges
Loading required package: stats4
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: 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: 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
>
> example("MultiAssayExperiment")
MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")
ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:
ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+ dimnames = list(
ExprmL+ c("ENST00000294241", "ENST00000355076",
ExprmL+ "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+ c("array1", "array2", "array3", "array4")
ExprmL+ ))
ExprmL> colDat <- data.frame(slope53 = rnorm(4),
ExprmL+ row.names = c("array1", "array2", "array3", "array4"))
ExprmL> ## SummarizedExperiment constructor
ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat,
ExprmL+ colData = colDat)
ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+ dimnames = list(
ExprmL+ c("ENST00000355076", "ENST00000383706",
ExprmL+ "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+ c("methyl1", "methyl2", "methyl3",
ExprmL+ "methyl4", "methyl5")
ExprmL+ ))
ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+ ncol = 4,
ExprmL+ dimnames = list(
ExprmL+ c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+ c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+ ))
ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame
ExprmL> rangedat <- data.frame(chr="chr2", start = 11:15, end = 12:16,
ExprmL+ strand = c("+", "-", "+", "*", "."),
ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0),
ExprmL+ row.names = c(paste0("ENST", "00000", 135411:135414), "ENST00000383323"))
ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat)
ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat,
ExprmL+ GISTIC = rangeSE)
ExprmL> ## Use the ExperimentList constructor
ExprmL> ExpList <- ExperimentList(assayList)
MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+ primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+ colname = c("array1", "array2", "array3", "array4"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> methylmap <- data.frame(
MltAsE+ primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+ colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> rnamap <- data.frame(
MltAsE+ primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+ colname = c("samparray1", "samparray2", "samparray3", "samparray4"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> gistmap <- data.frame(
MltAsE+ primary = c("Jack", "Bob", "Jill"),
MltAsE+ colname = c("samp0", "samp1", "samp2"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap,
MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap)
MltAsE> ## Create a sampleMap
MltAsE> sampMap <- listToMap(maplist)
MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"), age = 38:41,
MltAsE+ row.names = c("Jack", "Jill", "Bob", "Barbara"))
MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat,
MltAsE+ sampleMap = sampMap)
>
> test_check("MultiAssayExperiment")
[ FAIL 0 | WARN 33 | SKIP 1 | PASS 243 ]
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 33 | SKIP 1 | PASS 243 ]
>
> proc.time()
user system elapsed
39.60 2.17 41.78
|
MultiAssayExperiment.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> library(testthat)
> library(MultiAssayExperiment)
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: GenomicRanges
Loading required package: stats4
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: 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: 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
>
> example("MultiAssayExperiment")
MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")
ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:
ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+ dimnames = list(
ExprmL+ c("ENST00000294241", "ENST00000355076",
ExprmL+ "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+ c("array1", "array2", "array3", "array4")
ExprmL+ ))
ExprmL> colDat <- data.frame(slope53 = rnorm(4),
ExprmL+ row.names = c("array1", "array2", "array3", "array4"))
ExprmL> ## SummarizedExperiment constructor
ExprmL> exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat,
ExprmL+ colData = colDat)
ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+ dimnames = list(
ExprmL+ c("ENST00000355076", "ENST00000383706",
ExprmL+ "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+ c("methyl1", "methyl2", "methyl3",
ExprmL+ "methyl4", "methyl5")
ExprmL+ ))
ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+ data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+ 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+ ncol = 4,
ExprmL+ dimnames = list(
ExprmL+ c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+ c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+ ))
ExprmL> ## Create a mock RangedSummarizedExperiment from a data.frame
ExprmL> rangedat <- data.frame(chr="chr2", start = 11:15, end = 12:16,
ExprmL+ strand = c("+", "-", "+", "*", "."),
ExprmL+ samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0),
ExprmL+ row.names = c(paste0("ENST", "00000", 135411:135414), "ENST00000383323"))
ExprmL> rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat)
ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat,
ExprmL+ GISTIC = rangeSE)
ExprmL> ## Use the ExperimentList constructor
ExprmL> ExpList <- ExperimentList(assayList)
MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+ primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+ colname = c("array1", "array2", "array3", "array4"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> methylmap <- data.frame(
MltAsE+ primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+ colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> rnamap <- data.frame(
MltAsE+ primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+ colname = c("samparray1", "samparray2", "samparray3", "samparray4"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> gistmap <- data.frame(
MltAsE+ primary = c("Jack", "Bob", "Jill"),
MltAsE+ colname = c("samp0", "samp1", "samp2"),
MltAsE+ stringsAsFactors = FALSE)
MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> maplist <- list(Affy = exprmap, Methyl450k = methylmap,
MltAsE+ RNASeqGene = rnamap, GISTIC = gistmap)
MltAsE> ## Create a sampleMap
MltAsE> sampMap <- listToMap(maplist)
MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"), age = 38:41,
MltAsE+ row.names = c("Jack", "Jill", "Bob", "Barbara"))
MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> mae <- MultiAssayExperiment(experiments = ExpList, colData = colDat,
MltAsE+ sampleMap = sampMap)
>
> test_check("MultiAssayExperiment")
[ FAIL 0 | WARN 33 | SKIP 1 | PASS 243 ]
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 33 | SKIP 1 | PASS 243 ]
>
> proc.time()
user system elapsed
39.10 1.39 40.54
|
|
MultiAssayExperiment.Rcheck/examples_i386/MultiAssayExperiment-Ex.timings
|
MultiAssayExperiment.Rcheck/examples_x64/MultiAssayExperiment-Ex.timings
|