Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:26:46 -0400 (Tue, 09 Apr 2019).
Package 665/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GGBase 3.45.0 VJ Carey
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: GGBase |
Version: 3.45.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GGBase.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GGBase_3.45.0.tar.gz |
StartedAt: 2019-04-09 00:51:50 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 00:55:35 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 224.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GGBase.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GGBase.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GGBase_3.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GGBase.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GGBase/DESCRIPTION’ ... OK * this is package ‘GGBase’ version ‘3.45.0’ * 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 ‘GGBase’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 getSS: no visible global function definition for ‘installed.packages’ Undefined global functions or variables: installed.packages Consider adding importFrom("utils", "installed.packages") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘MAFfilter.R’ Running ‘make.R’ Running ‘plot_EvG.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 ‘/home/biocbuild/bbs-3.9-bioc/meat/GGBase.Rcheck/00check.log’ for details.
GGBase.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GGBase ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘GGBase’ ... ** using staged installation ** R ** 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 (GGBase)
GGBase.Rcheck/tests/MAFfilter.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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(GGBase) Loading required package: snpStats Loading required package: survival Loading required package: Matrix > if ("GGtools" %in% installed.packages()[,1]) { + s20 = getSS("GGtools", "20") + nsnp = ncol(smList(s20)[[1]]) + s20f = MAFfilter(s20, lower=.1) + nsnp2 = ncol(smList(s20f)[[1]]) + ( nsnp == 119921 & nsnp2 == 46755 ) + } [1] FALSE > > proc.time() user system elapsed 13.151 0.445 13.588
GGBase.Rcheck/tests/make.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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(GGBase) Loading required package: snpStats Loading required package: survival Loading required package: Matrix > if ("GGtools" %in% installed.packages()[,1]) { + s20 = getSS("GGtools", "20") + remk = make_smlSet( as(s20, "ExpressionSet"), smList(s20) ) + validObject(s20) & validObject(remk) + } [1] TRUE > > proc.time() user system elapsed 11.570 0.396 11.958
GGBase.Rcheck/tests/plot_EvG.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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(GGBase) Loading required package: snpStats Loading required package: survival Loading required package: Matrix > if ("GGtools" %in% installed.packages()[,1]) { + s20 = getSS("GGtools", "20") + plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20) + } 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:Matrix': colMeans, colSums, rowMeans, rowSums, which 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, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, 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")'. Attaching package: 'S4Vectors' The following object is masked from 'package:Matrix': expand The following object is masked from 'package:base': expand.grid > > proc.time() user system elapsed 12.643 0.471 13.135
GGBase.Rcheck/GGBase-Ex.timings
name | user | system | elapsed | |
MAFfilter | 4.414 | 0.175 | 4.677 | |
clipPCs | 0.000 | 0.000 | 0.001 | |
externalize | 0 | 0 | 0 | |
make_smlSet | 3.153 | 0.044 | 3.200 | |
plot_EvG | 4.507 | 0.115 | 4.649 | |
rsid-class | 0.002 | 0.000 | 0.002 | |
smlSet-class | 0.001 | 0.000 | 0.001 | |