Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:38 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1166/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetNet 1.17.1 (landing page) Thomas Naake
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: MetNet |
Version: 1.17.1 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MetNet.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MetNet_1.17.1.tar.gz |
StartedAt: 2022-12-29 01:20:05 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 01:23:38 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 213.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetNet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MetNet.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MetNet_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MetNet.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server 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 '1.17.1' * 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 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 46.94 0.14 47.1 * 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: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MetNet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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, 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 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 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 25.98 0.85 26.82
MetNet.Rcheck/MetNet-Ex.timings
name | user | system | elapsed | |
AdjacencyMatrix | 0.08 | 0.00 | 0.07 | |
MetNet-package | 46.94 | 0.14 | 47.10 | |
addSpectralSimilarity | 0.06 | 0.01 | 0.08 | |
addToList | 0.00 | 0.02 | 0.02 | |
aracne | 0.08 | 0.06 | 0.14 | |
bayes | 1.52 | 0.05 | 1.56 | |
clr | 0.08 | 0.07 | 0.16 | |
combine | 0.43 | 0.00 | 0.43 | |
correlation | 0.00 | 0.02 | 0.02 | |
getLinks | 0 | 0 | 0 | |
lasso | 0 | 0 | 0 | |
mz_summary | 0.21 | 0.05 | 0.25 | |
mz_vis | 0.28 | 0.00 | 0.28 | |
partialCorrelation | 0.00 | 0.01 | 0.01 | |
randomForest | 1.19 | 0.00 | 1.19 | |
rtCorrection | 0.24 | 0.00 | 0.23 | |
statistical | 0.09 | 0.00 | 0.10 | |
structural | 0.03 | 0.00 | 0.03 | |
threshold | 0.41 | 0.02 | 0.42 | |
topKnet | 0 | 0 | 0 | |