Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:53 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the EGSEA package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 536/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EGSEA 1.18.1 (landing page) Monther Alhamdoosh
| 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: EGSEA |
Version: 1.18.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EGSEA_1.18.1.tar.gz |
StartedAt: 2021-05-06 01:25:04 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:34:56 -0400 (Thu, 06 May 2021) |
EllapsedTime: 591.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EGSEA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EGSEA_1.18.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/EGSEA.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 ‘EGSEA/DESCRIPTION’ ... OK * this is package ‘EGSEA’ version ‘1.18.1’ * 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 ‘EGSEA’ 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 ... NOTE buildGeneSetDBIdx: no visible binding for global variable ‘GOTERM’ buildMSigDBIdx: no visible binding for global variable ‘msigdb’ generateSummaryPlots: no visible binding for global variable ‘x.data’ generateSummaryPlots: no visible binding for global variable ‘y.data’ generateSummaryPlots: no visible binding for global variable ‘gsSize’ generateSummaryPlots: no visible binding for global variable ‘id’ generateSummaryPlots: no visible binding for global variable ‘sig’ loadKeggData: no visible binding for global variable ‘kegg.pathways’ Undefined global functions or variables: GOTERM gsSize id kegg.pathways msigdb sig x.data y.data * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed egsea-main 99.607 12.761 85.000 EGSEAResults-methods 96.998 4.281 105.154 egsea-index 52.449 4.833 57.366 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.12-bioc/meat/EGSEA.Rcheck/00check.log’ for details.
EGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EGSEA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘EGSEA’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (EGSEA)
EGSEA.Rcheck/tests/testthat.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. > library(testthat) > library(EGSEA) Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: gage Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: topGO Loading required package: graph Loading required package: GO.db Loading required package: SparseM Attaching package: 'SparseM' The following object is masked from 'package:base': backsolve groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members The following object is masked from 'package:gage': geneData Loading required package: pathview ############################################################################## Pathview is an open source software package distributed under GNU General Public License version 3 (GPLv3). Details of GPLv3 is available at http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to formally cite the original Pathview paper (not just mention it) in publications or products. For details, do citation("pathview") within R. The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG license agreement (details at http://www.kegg.jp/kegg/legal.html). ############################################################################## > > test_check("EGSEA") [1] "Created the User-Defined Gene Sets collection ... " [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 16.496 0.818 17.385
EGSEA.Rcheck/EGSEA-Ex.timings
name | user | system | elapsed | |
EGSEAResults-methods | 96.998 | 4.281 | 105.154 | |
GSCollectionIndex-methods | 2.655 | 0.240 | 2.915 | |
egsea-aux | 0.000 | 0.001 | 0.001 | |
egsea-index | 52.449 | 4.833 | 57.366 | |
egsea-main | 99.607 | 12.761 | 85.000 | |