Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1539/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
phenomis 1.8.0 (landing page) Etienne A. Thevenot
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: phenomis |
Version: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2024-11-20 01:08:31 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:17:04 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 513.1 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/phenomis.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘phenomis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘phenomis’ version ‘1.8.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 code 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 5.392 0.051 5.459 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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/4.4-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)
phenomis.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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, saveRDS, setdiff, 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 [01:16:22.027] Loading definitions from package biodb version 1.14.0. INFO [01:16:24.005] Loading definitions from package biodbChebi version 1.12.0. INFO [01:16:24.032] Loading definitions from package biodbExpasy version 1.10.0. INFO [01:16:24.039] Loading definitions from package biodbHmdb version 1.12.0. INFO [01:16:24.070] Loading definitions from package biodbKegg version 1.12.0. INFO [01:16:24.114] Loading definitions from package biodbNcbi version 1.10.0. INFO [01:16:24.136] Loading definitions from package biodbNci version 1.10.0. INFO [01:16:24.143] Loading definitions from package biodbUniprot version 1.12.0. INFO [01:16:26.157] Closing BiodbMain instance... INFO [01:16:26.158] 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 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 110 ] > > proc.time() user system elapsed 40.307 6.266 41.604
phenomis.Rcheck/phenomis-Ex.timings
name | user | system | elapsed | |
annotating | 3.568 | 0.709 | 4.327 | |
clustering | 2.081 | 0.042 | 2.130 | |
correcting | 1.361 | 0.019 | 1.383 | |
filtering | 1.254 | 0.033 | 1.290 | |
gg_barplot | 0.516 | 0.009 | 0.527 | |
gg_boxplot | 0.702 | 0.010 | 0.715 | |
gg_pie | 0.357 | 0.004 | 0.362 | |
gg_volcanoplot | 1.397 | 0.054 | 1.461 | |
hypotesting | 5.392 | 0.051 | 5.459 | |
inspecting | 3.091 | 0.059 | 3.172 | |
normalizing | 0.148 | 0.004 | 0.154 | |
phenomis-package | 0 | 0 | 0 | |
reading | 0.957 | 0.018 | 0.979 | |
reducing | 0.221 | 0.004 | 0.226 | |
transforming | 1.243 | 0.019 | 1.268 | |
vennplot | 1.522 | 0.019 | 1.548 | |
writing | 0.359 | 0.007 | 0.366 | |