Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-22 11:37:39 -0400 (Fri, 22 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 1507/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenomis 1.2.0  (landing page)
Etienne A. Thevenot
Snapshot Date: 2023-09-21 14:00:15 -0400 (Thu, 21 Sep 2023)
git_url: https://git.bioconductor.org/packages/phenomis
git_branch: RELEASE_3_17
git_last_commit: ccf2bb6
git_last_commit_date: 2023-04-25 11:39:57 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for phenomis on merida1


To the developers/maintainers of the phenomis package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phenomis.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

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: 2023-09-22 05:54:31 -0400 (Fri, 22 Sep 2023)
EndedAt: 2023-09-22 06:07:55 -0400 (Fri, 22 Sep 2023)
EllapsedTime: 804.2 seconds
RetCode: 0
Status:   OK  
CheckDir: phenomis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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/meat/phenomis.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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    15.115  0.126  20.149
annotating      9.048  1.205  13.788
inspecting      9.031  0.133  12.151
clustering      6.166  0.087   8.379
vennplot        4.412  0.047   6.218
gg_volcanoplot  3.980  0.115   5.782
filtering       3.969  0.069   5.400
* 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


Installation output

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-x86_64/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)

Tests output

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: x86_64-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  [06:05:47.413] Loading definitions from package biodb version 1.8.1.
INFO  [06:05:54.103] Loading definitions from package biodbChebi version 1.6.0.
INFO  [06:05:54.214] Loading definitions from package biodbExpasy version 1.4.0.
INFO  [06:05:54.237] Loading definitions from package biodbHmdb version 1.6.1.
INFO  [06:05:54.353] Loading definitions from package biodbKegg version 1.6.1.
INFO  [06:05:54.540] Loading definitions from package biodbLipidmaps version 1.6.0.
INFO  [06:05:54.571] Loading definitions from package biodbMirbase version 1.4.1.
INFO  [06:05:54.595] Loading definitions from package biodbNcbi version 1.4.0.
INFO  [06:05:54.690] Loading definitions from package biodbNci version 1.4.0.
INFO  [06:05:54.717] Loading definitions from package biodbUniprot version 1.6.0.
INFO  [06:06:00.403] Closing BiodbMain instance...
INFO  [06:06:00.406] 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 
103.544   8.973 138.169 

Example timings

phenomis.Rcheck/phenomis-Ex.timings

nameusersystemelapsed
annotating 9.048 1.20513.788
clustering6.1660.0878.379
correcting2.1910.0282.994
filtering3.9690.0695.400
gg_barplot1.5380.0212.012
gg_boxplot2.0540.0202.734
gg_pie0.8230.0091.140
gg_volcanoplot3.9800.1155.782
hypotesting15.115 0.12620.149
inspecting 9.031 0.13312.151
normalizing0.4140.0060.544
phenomis-package0.0000.0000.001
reading2.7540.0303.645
reducing0.6280.0060.854
transforming3.6040.0384.994
vennplot4.4120.0476.218
writing1.0650.0151.435