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This page was generated on 2021-05-06 12:35:11 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the GRmetrics package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 787/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRmetrics 1.16.0 (landing page) Nicholas Clark
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GRmetrics |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRmetrics_1.16.0.tar.gz |
StartedAt: 2021-05-06 02:26:48 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 02:30:05 -0400 (Thu, 06 May 2021) |
EllapsedTime: 196.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRmetrics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GRmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GRmetrics_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GRmetrics.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRmetrics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GRmetrics’ version ‘1.16.0’ * 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 ‘GRmetrics’ 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 ... NOTE Package in Depends field not imported from: ‘SummarizedExperiment’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .GRlogisticFit: no visible binding for global variable ‘experiment’ GRdrawDRC: no visible binding for global variable ‘GRvalue’ Undefined global functions or variables: GRvalue experiment * 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 GRfit 12.712 0.083 12.809 GRscatter 7.174 0.065 7.248 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.12-bioc/meat/GRmetrics.Rcheck/00check.log’ for details.
GRmetrics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GRmetrics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘GRmetrics’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (GRmetrics)
GRmetrics.Rcheck/tests/test.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > # Case C (example 4) test > #install.packages('readr') # un-comment and install these packages if necessary > #install.packages('devtools') # un-comment and install these packages if necessary > ## try http:// if https:// URLs are not supported > #if (!requireNamespace("BiocManager", quietly=TRUE)) > #install.packages("BiocManager") > #BiocManager::install("SummarizedExperiment") > > # Load GRmetrics functions > library(GRmetrics) 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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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 > # Load Case C (example 4) input > data("inputCaseC") > # Run GRfit function with case = "C" > output4 = GRfit(inputData = inputCaseC, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "C") There were 50 or more warnings (use warnings() to see the first 50) > > # Load Case A (example 1) input > data("inputCaseA") > # Run GRfit function with case = "A" > output1 = GRfit(inputData = inputCaseA, groupingVariables = c('cell_line','agent', 'perturbation','replicate', 'time'), case = "A") There were 50 or more warnings (use warnings() to see the first 50) > > # change type integer to numeric for the sake of testing > metadata(output1)[[1]]$replicate = as.numeric(metadata(output1)[[1]]$replicate) > all.equal(output1, output4) [1] "Attributes: < Component \"metadata\": Component 1: Attributes: < Component \"class\": Lengths (3, 1) differ (string compare on first 1) > >" [2] "Attributes: < Component \"metadata\": Component 1: Attributes: < Component \"class\": 1 string mismatch > >" > #[1] TRUE > # Test passed - output from Case C matches output from Case A > > proc.time() user system elapsed 22.986 0.565 26.451
GRmetrics.Rcheck/GRmetrics-Ex.timings
name | user | system | elapsed | |
GRbox | 0.001 | 0.000 | 0.001 | |
GRdrawDRC | 4.719 | 0.268 | 4.997 | |
GRfit | 12.712 | 0.083 | 12.809 | |
GRgetDefs | 1.087 | 0.048 | 1.136 | |
GRgetGroupVars | 1.108 | 0.028 | 1.136 | |
GRgetMetrics | 1.092 | 0.031 | 1.124 | |
GRgetValues | 1.067 | 0.039 | 1.107 | |
GRscatter | 7.174 | 0.065 | 7.248 | |