Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1240/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetNet 1.24.0 (landing page) Thomas Naake
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the MetNet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetNet.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: MetNet |
Version: 1.24.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MetNet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MetNet_1.24.0.tar.gz |
StartedAt: 2024-12-20 03:23:56 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:29:08 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 311.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MetNet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MetNet_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MetNet.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MetNet/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MetNet' version '1.24.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'MetNet' 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 ... NOTE checkRd: (-1) partialCorrelation.Rd:33: Lost braces; missing escapes or markup? 33 | The correlation coefficients $r_{ij|S}$ are obtained from `cor2pcor` | ^ checkRd: (-1) threshold.Rd:49: Lost braces; missing escapes or markup? 49 | a^*_{ij} = min(a_ij, a_ji) | ^ checkRd: (-1) threshold.Rd:50: Lost braces; missing escapes or markup? 50 | a^*_{ij} = max(a_ij, a_ji)} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MetNet-package 62.98 0.61 63.59 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/MetNet.Rcheck/00check.log' for details.
MetNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MetNet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MetNet' ... ** using staged installation ** R ** data ** 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 (MetNet)
MetNet.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("testthat") > library("MetNet") Loading required package: S4Vectors 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 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: 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: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'MetNet' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:BiocGenerics': combine, type > > test_check("MetNet") [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "spearman finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0987 [1] "ggm finished." [1] "pearson finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1038 [1] "ggm finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "spearman finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "spearman finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3859 [1] "ggm finished." [1] "bayes finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "spearman finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0761 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0806 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0211 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0222 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 [1] "randomForest finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0761 [1] "pearson_partial finished." [1] "spearman finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0806 [1] "spearman_partial finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 [1] "ggm finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0761 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0806 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 [1] "pearson finished." [1] "spearman finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0987 [1] "ggm finished." [1] "randomForest finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "spearman finished." [1] "bayes finished." [1] "pearson finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1139 [1] "ggm finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "spearman finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0461 [1] "ggm finished." [ FAIL 0 | WARN 0 | SKIP 0 | PASS 606 ] > > proc.time() user system elapsed 36.76 1.26 38.03
MetNet.Rcheck/MetNet-Ex.timings
name | user | system | elapsed | |
AdjacencyMatrix | 0.08 | 0.00 | 0.08 | |
MetNet-package | 62.98 | 0.61 | 63.59 | |
addSpectralSimilarity | 0.14 | 0.00 | 0.14 | |
addToList | 0.02 | 0.00 | 0.02 | |
aracne | 0.15 | 0.05 | 0.20 | |
bayes | 2.44 | 0.15 | 2.59 | |
clr | 0.14 | 0.08 | 0.22 | |
combine | 0.45 | 0.02 | 0.47 | |
correlation | 0.02 | 0.00 | 0.02 | |
getLinks | 0 | 0 | 0 | |
lasso | 0 | 0 | 0 | |
mz_summary | 0.23 | 0.00 | 0.23 | |
mz_vis | 0.32 | 0.01 | 0.33 | |
partialCorrelation | 0.00 | 0.03 | 0.03 | |
randomForest | 1.18 | 0.11 | 1.30 | |
rtCorrection | 0.29 | 0.02 | 0.29 | |
statistical | 0.12 | 0.00 | 0.13 | |
structural | 0.06 | 0.00 | 0.06 | |
threshold | 0.71 | 0.01 | 0.72 | |
topKnet | 0 | 0 | 0 | |