Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:31 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the MetNet package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1161/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetNet 1.14.0 (landing page) Thomas Naake
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MetNet |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MetNet.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MetNet_1.14.0.tar.gz |
StartedAt: 2022-10-18 20:33:11 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 20:38:42 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 330.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MetNet.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MetNet_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MetNet.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetNet’ version ‘1.14.0’ * 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 ‘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 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 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 55.466 0.404 55.87 * 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
MetNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MetNet ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("testthat") > library("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, 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 Attaching package: 'S4Vectors' 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 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): 0.1024 Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 [1] "randomForest finished." [1] "clr finished." [1] "aracne finished." [1] "pearson finished." [1] "pearson_partial finished." [1] "spearman finished." [1] "spearman_partial finished." Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 [1] "ggm finished." 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 141.040 79.600 118.841
MetNet.Rcheck/MetNet-Ex.timings
name | user | system | elapsed | |
AdjacencyMatrix | 0.087 | 0.004 | 0.091 | |
MetNet-package | 55.466 | 0.404 | 55.870 | |
addSpectralSimilarity | 0.09 | 0.00 | 0.09 | |
addToList | 0.016 | 0.003 | 0.018 | |
aracne | 0.074 | 0.136 | 0.184 | |
bayes | 1.578 | 0.069 | 1.646 | |
clr | 0.084 | 0.116 | 0.175 | |
combine | 0.514 | 0.004 | 0.517 | |
correlation | 0.010 | 0.000 | 0.009 | |
getLinks | 0.003 | 0.000 | 0.003 | |
lasso | 0.004 | 0.000 | 0.004 | |
mz_summary | 0.262 | 0.004 | 0.266 | |
mz_vis | 0.317 | 0.000 | 0.318 | |
partialCorrelation | 0.009 | 0.024 | 0.033 | |
randomForest | 1.746 | 0.024 | 1.770 | |
rtCorrection | 0.257 | 0.000 | 0.256 | |
statistical | 0.124 | 0.004 | 0.127 | |
structural | 0.044 | 0.000 | 0.044 | |
threshold | 0.514 | 0.024 | 0.538 | |
topKnet | 0.003 | 0.000 | 0.003 | |