| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:08 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 1507/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phenomis 1.2.0 (landing page) Etienne A. Thevenot
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the phenomis package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: phenomis |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phenomis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phenomis_1.2.0.tar.gz |
| StartedAt: 2023-10-18 14:33:51 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 14:42:44 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 533.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: phenomis.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phenomis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phenomis_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/phenomis.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenomis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenomis’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘phenomis’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
hypotesting 8.810 0.115 13.683
annotating 4.974 0.687 8.497
inspecting 4.910 0.103 7.839
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: OK
phenomis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phenomis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘phenomis’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (phenomis)
phenomis.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> test_check("phenomis")
Loading required package: phenomis
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, 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: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
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
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
INFO [14:41:13.591] Loading definitions from package biodb version 1.8.1.
INFO [14:41:18.267] Loading definitions from package biodbChebi version 1.6.0.
INFO [14:41:18.327] Loading definitions from package biodbExpasy version 1.4.0.
INFO [14:41:18.342] Loading definitions from package biodbHmdb version 1.6.1.
INFO [14:41:18.401] Loading definitions from package biodbKegg version 1.6.1.
INFO [14:41:18.493] Loading definitions from package biodbLipidmaps version 1.6.0.
INFO [14:41:18.513] Loading definitions from package biodbMirbase version 1.4.1.
INFO [14:41:18.532] Loading definitions from package biodbNcbi version 1.4.0.
INFO [14:41:18.584] Loading definitions from package biodbNci version 1.4.0.
INFO [14:41:18.596] Loading definitions from package biodbUniprot version 1.6.0.
INFO [14:41:21.747] Closing BiodbMain instance...
INFO [14:41:21.750] Connector "mass.csv.file" deleted.
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
[2] proteo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
[2] proteo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
pearson_age_cor pearson_age_BH
Quinic acid 0.4242918 2.436280e-07
Dehydroepiandrosterone sulfate -0.4079105 5.622222e-07
Dehydroepiandrosterone 3-glucuronide -0.3790183 4.585238e-06
1,7-Dimethyluric acid 0.3550416 2.303726e-05
1,3-Dimethyluric acid 0.3319468 9.990338e-05
Aminosalicyluric acid 0.3197563 1.925875e-04
1-Methylxanthine 0.3098597 3.176562e-04
Testosterone glucuronide -0.3069249 3.359986e-04
Aspartic acid -0.3034885 3.719846e-04
FMNH2 -0.3016243 3.766947e-04
Fumaric acid 0.2929663 5.860747e-04
1-Methyluric acid 0.2799157 1.169543e-03
Dimethylguanosine -0.2763133 1.329293e-03
5-Hydroxyindoleacetic acid -0.2739204 1.415079e-03
N4-Acetylcytidine -0.2642178 2.269409e-03
N-Acetyl-aspartic acid -0.2598694 2.694028e-03
6-(carboxymethoxy)-hexanoic acid -0.2563962 3.052851e-03
Threonic acid/Erythronic acid -0.2506358 3.901083e-03
Pentose 0.2445172 5.056935e-03
Methylinosine -0.2381169 6.614290e-03
Tryptophan -0.2335902 7.858311e-03
4-Hydroxybenzoic acid -0.2221771 1.286245e-02
N-Acetyltryptophan isomer 3 -0.2153012 1.681538e-02
Pyridylacetylglycine -0.2140805 1.701743e-02
3-Methylcrotonylglycine -0.2058001 2.346467e-02
Pyrroledicarboxylic acid 0.2017568 2.417414e-02
Acetylphenylalanine 0.2012786 2.417414e-02
N-Acetyltryptophan 0.2010813 2.417414e-02
(gamma)Glu-Leu/Ile -0.2009143 2.417414e-02
Methoxysalicylic acid isomer 0.2008038 2.417414e-02
Pantothenic acid -0.1987920 2.544600e-02
Pyridoxic acid isomer 1 -0.1958688 2.781563e-02
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 100 28
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(100): isobutyric acid oxalic acid ... UDP-alpha-D-galactose
GDP-L-fucose
rowData names(23): chromato name ... redund_group redund_iso_add_frag
colnames(28): L818f L819f ... W633f W634m
colData names(3): gene mouse_id sex
class: SummarizedExperiment
dim: 100 28
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(100): isobutyric acid oxalic acid ... UDP-alpha-D-galactose
GDP-L-fucose
rowData names(23): chromato name ... redund_group redund_iso_add_frag
colnames(28): L818f L819f ... W633f W634m
colData names(3): gene mouse_id sex
class: SummarizedExperiment
dim: 100 28
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(100): isobutyric acid oxalic acid ... UDP-alpha-D-galactose
GDP-L-fucose
rowData names(23): chromato name ... redund_group redund_iso_add_frag
colnames(28): L818f L819f ... W633f W634m
colData names(3): gene mouse_id sex
class: SummarizedExperiment
dim: 100 28
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(100): isobutyric acid oxalic acid ... UDP-alpha-D-galactose
GDP-L-fucose
rowData names(23): chromato name ... redund_group redund_iso_add_frag
colnames(28): L818f L819f ... W633f W634m
colData names(3): gene mouse_id sex
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 100 28
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(100): Q8C196_Carbamoyl-phosphate synt. Q9DBM2_Peroxisomal
bifunctional. ... Q8CII2_Cell division cycle prot. Q61553_Fascin
rowData names(3): accession description uniprot_id
colnames(28): L818f L819f ... W633f W634m
colData names(3): gene mouse_id sex
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
[2] proteo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
ExpressionSet (storageMode: lockedEnvironment)
assayData: 113 features, 210 samples
element names: exprs
protocolData: none
phenoData
sampleNames: QC1_001 HU_neg_017 ... QC1_012_b2 (210 total)
varLabels: subset full ... gender (10 total)
varMetadata: labelDescription
featureData
featureNames: (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Xanthosine (113 total)
fvarLabels: database_identifier chemical_formula ... reliability (10
total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
ExpressionSet (storageMode: lockedEnvironment)
assayData: 100 features, 28 samples
element names: exprs
protocolData: none
phenoData
sampleNames: L818f L819f ... W634m (28 total)
varLabels: gene mouse_id sex
varMetadata: labelDescription
featureData
featureNames: Q8C196_Carbamoyl-phosphate synt. Q9DBM2_Peroxisomal
bifunctional. ... Q61553_Fascin (100 total)
fvarLabels: accession description uniprot_id
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
[2] proteo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
[2] proteo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
A MultiAssayExperiment object of 1 listed
experiment with a user-defined name and respective class.
Containing an ExperimentList class object of length 1:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
Object of class 'MultiDataSet'
. assayData: 1 elements
. metabo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. rowRanges:
. metabo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
Object of class 'MultiDataSet'
. assayData: 1 elements
. metabo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. rowRanges:
. metabo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 1 cols (id)
. proteo: 28 samples, 4 cols (gene, ..., sex)
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
class: SummarizedExperiment
dim: 113 210
metadata(3): experimentData annotation protocolData
assays(1): exprs
rownames(113): (2-methoxyethoxy)propanoic acid isomer
(gamma)Glu-Leu/Ile ... Valerylglycine isomer 2 Xanthosine
rowData names(10): database_identifier chemical_formula ...
retention_time reliability
colnames(210): QC1_001 HU_neg_017 ... HU_neg_146_b2 QC1_012_b2
colData names(10): subset full ... bmi gender
A MultiAssayExperiment object of 2 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 2:
[1] metabo: SummarizedExperiment with 100 rows and 28 columns
[2] proteo: SummarizedExperiment with 100 rows and 28 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save data to flat files
Object of class 'MultiDataSet'
. assayData: 2 elements
. metabo: 100 features, 28 samples
. proteo: 100 features, 28 samples
. featureData:
. metabo: 100 rows, 23 cols (chromato, ..., redund_group)
. proteo: 100 rows, 3 cols (accession, ..., description)
. rowRanges:
. metabo: NO
. proteo: NO
. phenoData:
. metabo: 28 samples, 4 cols (gene, ..., sex)
. proteo: 28 samples, 4 cols (gene, ..., sex)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 108 ]
>
> proc.time()
user system elapsed
57.293 3.062 91.855
phenomis.Rcheck/phenomis-Ex.timings
| name | user | system | elapsed | |
| annotating | 4.974 | 0.687 | 8.497 | |
| clustering | 3.293 | 0.068 | 4.877 | |
| correcting | 1.332 | 0.021 | 1.741 | |
| filtering | 2.095 | 0.051 | 2.750 | |
| gg_barplot | 0.883 | 0.019 | 1.153 | |
| gg_boxplot | 1.145 | 0.022 | 1.525 | |
| gg_pie | 0.433 | 0.009 | 0.622 | |
| gg_volcanoplot | 2.948 | 0.077 | 4.423 | |
| hypotesting | 8.810 | 0.115 | 13.683 | |
| inspecting | 4.910 | 0.103 | 7.839 | |
| normalizing | 0.219 | 0.005 | 0.355 | |
| phenomis-package | 0.001 | 0.000 | 0.000 | |
| reading | 1.494 | 0.029 | 2.221 | |
| reducing | 0.385 | 0.007 | 0.581 | |
| transforming | 1.984 | 0.033 | 2.886 | |
| vennplot | 2.400 | 0.036 | 3.647 | |
| writing | 0.567 | 0.013 | 0.898 | |