Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:37:55 -0400 (Thu, 12 Apr 2018).
Package 541/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GeneOverlap 1.14.0 Li Shen, Mount Sinai
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | ![]() |
Package: GeneOverlap |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneOverlap_1.14.0.tar.gz |
StartedAt: 2018-04-12 04:11:09 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 04:11:41 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 32.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneOverlap.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneOverlap_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GeneOverlap.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneOverlap/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneOverlap’ version ‘1.14.0’ * 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 ‘GeneOverlap’ 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 loading without being on the library search path ... 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 drawHeatmap,GeneOverlapMatrix: no visible global function definition for ‘p.adjust’ print,GeneOverlap: no visible global function definition for ‘head’ testGeneOverlap,GeneOverlap: no visible global function definition for ‘setNames’ Undefined global functions or variables: head p.adjust setNames Consider adding importFrom("stats", "p.adjust", "setNames") importFrom("utils", "head") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE The following files look like leftovers/mistakes: ‘Rplots.pdf’ Please remove them from your package. * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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-3.6-bioc/meat/GeneOverlap.Rcheck/00check.log’ for details.
GeneOverlap.Rcheck/00install.out
* installing *source* package ‘GeneOverlap’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GeneOverlap)
GeneOverlap.Rcheck/tests/runTests.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-apple-darwin15.6.0 (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. > BiocGenerics:::testPackage("GeneOverlap") RUNIT TEST PROTOCOL -- Thu Apr 12 04:11:37 2018 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : GeneOverlap RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 Warning messages: 1: In getPval(go.obj) : Test has not been performed yet. 2: In getOddsRatio(go.obj) : Test has not been performed yet. > > proc.time() user system elapsed 0.860 0.063 0.922
GeneOverlap.Rcheck/GeneOverlap-Ex.timings
name | user | system | elapsed | |
GeneOverlap | 0.063 | 0.004 | 0.067 | |
GeneOverlapMatrix | 0.330 | 0.016 | 0.358 | |
drawHeatmap | 1.410 | 0.015 | 1.454 | |
getGenomeSize | 0.084 | 0.005 | 0.089 | |
getList | 0.050 | 0.002 | 0.053 | |
getReadonly | 0.049 | 0.001 | 0.051 | |
getReadonlyMatrix | 0.255 | 0.008 | 0.268 | |
gs.RNASeq | 0.032 | 0.001 | 0.035 | |
hESC.ChIPSeq.list | 0.041 | 0.002 | 0.048 | |
hESC.RNASeq.list | 0.045 | 0.001 | 0.046 | |
newGOM | 0.202 | 0.002 | 0.207 | |
newGeneOverlap | 0.057 | 0.001 | 0.062 | |
testGeneOverlap | 0.043 | 0.001 | 0.045 | |