Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:24:41 -0400 (Thu, 12 Apr 2018).
Package 87/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ballgown 2.10.0 Jack Fu
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: ballgown |
Version: 2.10.0 |
Command: rm -rf ballgown.buildbin-libdir ballgown.Rcheck && mkdir ballgown.buildbin-libdir ballgown.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ballgown.buildbin-libdir ballgown_2.10.0.tar.gz >ballgown.Rcheck\00install.out 2>&1 && cp ballgown.Rcheck\00install.out ballgown-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ballgown.buildbin-libdir --install="check:ballgown-install.out" --force-multiarch --no-vignettes --timings ballgown_2.10.0.tar.gz |
StartedAt: 2018-04-11 22:20:10 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:25:54 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 343.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ballgown.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ballgown.buildbin-libdir ballgown.Rcheck && mkdir ballgown.buildbin-libdir ballgown.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ballgown.buildbin-libdir ballgown_2.10.0.tar.gz >ballgown.Rcheck\00install.out 2>&1 && cp ballgown.Rcheck\00install.out ballgown-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ballgown.buildbin-libdir --install="check:ballgown-install.out" --force-multiarch --no-vignettes --timings ballgown_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ballgown.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ballgown/DESCRIPTION' ... OK * this is package 'ballgown' version '2.10.0' * 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 whether package 'ballgown' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 .readExon: no visible global function definition for 'read.table' .readIntron: no visible global function definition for 'read.table' .readTranscript: no visible global function definition for 'read.table' assessSim: no visible global function definition for 'read.table' assessSim: no visible global function definition for 'lines' assessSim: no visible global function definition for 'legend' ballgown: no visible global function definition for 'read.table' ballgownrsem: no visible global function definition for 'read.table' ballgownrsem : <anonymous>: no visible global function definition for 'read.table' checkAssembledTx: no visible global function definition for 'par' checkAssembledTx: no visible global function definition for 'plot' checkAssembledTx: no visible global function definition for 'polygon' checkAssembledTx: no visible global function definition for 'lines' checkAssembledTx: no visible global function definition for 'abline' checkAssembledTx: no visible global function definition for 'title' checkAssembledTx: no visible global function definition for 'axis' closestColor: no visible global function definition for 'heat.colors' clusterTranscripts: no visible global function definition for 'cutree' clusterTranscripts: no visible global function definition for 'hclust' clusterTranscripts: no visible global function definition for 'as.dist' clusterTranscripts: no visible global function definition for 'kmeans' gffRead: no visible global function definition for 'read.table' plotMeans: no visible global function definition for 'par' plotMeans: no visible global function definition for 'plot' plotMeans: no visible global function definition for 'polygon' plotMeans: no visible global function definition for 'lines' plotMeans: no visible global function definition for 'heat.colors' plotMeans: no visible global function definition for 'text' plotMeans: no visible global function definition for 'axis' plotTranscripts: no visible global function definition for 'par' plotTranscripts: no visible global function definition for 'plot' plotTranscripts: no visible global function definition for 'title' plotTranscripts: no visible global function definition for 'polygon' plotTranscripts: no visible global function definition for 'lines' plotTranscripts: no visible global function definition for 'heat.colors' plotTranscripts: no visible global function definition for 'text' plotTranscripts: no visible global function definition for 'axis' stattest: no visible global function definition for 'model.matrix' stattest: no visible global function definition for 'p.adjust' writeFiles: no visible global function definition for 'write.table' subset,ballgown: no visible binding for global variable 'i_id' subset,ballgown: no visible binding for global variable 'e_id' subset,ballgown: no visible binding for global variable 't_id' Undefined global functions or variables: abline as.dist axis cutree e_id hclust heat.colors i_id kmeans legend lines model.matrix p.adjust par plot polygon read.table t_id text title write.table Consider adding importFrom("grDevices", "heat.colors") importFrom("graphics", "abline", "axis", "legend", "lines", "par", "plot", "polygon", "text", "title") importFrom("stats", "as.dist", "cutree", "hclust", "kmeans", "model.matrix", "p.adjust") importFrom("utils", "read.table", "write.table") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test-all.R' OK ** running tests for arch 'x64' ... Running 'test-all.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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ballgown.Rcheck/00check.log' for details.
ballgown.Rcheck/00install.out
install for i386 * installing *source* package 'ballgown' ... ** R ** data ** inst ** preparing package for lazy loading Creating a new generic function for 'structure' in package 'ballgown' ** help *** installing help indices converting help for package 'ballgown' finding HTML links ... done annotate_assembly html ballgown-class html ballgown-constructor html ballgown-package html ballgownrsem html bg html checkAssembledTx html clusterTranscripts html collapseTranscripts html contains html dirs html eexpr html expr-replace html expr html exprfilter html geneIDs html geneNames html getAttributeField html getGenes html gexpr html gffRead html gffReadGR html iexpr html indexes-replace html indexes html last html mergedDate html pData-replace html pData html pctOverlap html plotLatentTranscripts html plotMeans html plotTranscripts html sampleNames html seqnames html stattest html structure html subset html tGene html texpr html transcriptIDs html transcriptNames html writeFiles html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'ballgown' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ballgown' as ballgown_2.10.0.zip * DONE (ballgown) In R CMD INSTALL In R CMD INSTALL
ballgown.Rcheck/tests_i386/test-all.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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) > test_check('ballgown') Loading required package: ballgown Attaching package: 'ballgown' The following object is masked from 'package:base': structure == testthat results =========================================================== OK: 178 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 22.60 0.42 23.01 |
ballgown.Rcheck/tests_x64/test-all.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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) > test_check('ballgown') Loading required package: ballgown Attaching package: 'ballgown' The following object is masked from 'package:base': structure == testthat results =========================================================== OK: 178 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 32.21 0.25 32.45 |
ballgown.Rcheck/examples_i386/ballgown-Ex.timings
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ballgown.Rcheck/examples_x64/ballgown-Ex.timings
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