Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:53:00 -0400 (Tue, 16 Apr 2019).
Package 785/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
InterMineR 1.4.1 InterMine Team
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: InterMineR |
Version: 1.4.1 |
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings InterMineR_1.4.1.tar.gz |
StartedAt: 2019-04-16 00:50:14 -0400 (Tue, 16 Apr 2019) |
EndedAt: 2019-04-16 00:54:29 -0400 (Tue, 16 Apr 2019) |
EllapsedTime: 255.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: InterMineR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings InterMineR_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/InterMineR.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘InterMineR/DESCRIPTION’ ... OK * this is package ‘InterMineR’ version ‘1.4.1’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘InterMineR’ 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 ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 convertToGeneAnswers: no visible binding for global variable ‘geneExpProfile’ convertToRangedSummarizedExperiment: no visible global function definition for ‘reshape’ doEnrichment: no visible global function definition for ‘URLencode’ listDatasets: no visible binding for global variable ‘child_name’ runQuery,ANY-InterMineR: no visible global function definition for ‘URLencode’ runQuery,ANY-list: no visible global function definition for ‘URLencode’ Undefined global functions or variables: URLencode child_name geneExpProfile reshape Consider adding importFrom("stats", "reshape") importFrom("utils", "URLencode") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed convertToGeneAnswers 17.372 0.152 25.988 simplifyResult 9.928 0.288 11.241 doEnrichment 7.536 0.052 37.891 runQuery 4.088 0.140 5.330 convertToRangedSummarizedExperiment 4.212 0.000 7.605 listDatasets 3.652 0.156 5.120 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.8-bioc/meat/InterMineR.Rcheck/00check.log’ for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL InterMineR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘InterMineR’ ... ** 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 * DONE (InterMineR)
InterMineR.Rcheck/InterMineR-Ex.timings
name | user | system | elapsed | |
InterMineR-methods | 0.28 | 0.00 | 0.69 | |
PL_DiabetesGenes | 0.004 | 0.000 | 0.003 | |
PL_FlyTF_site_specific_TFs | 0.000 | 0.000 | 0.001 | |
convertToGRanges | 0.632 | 0.036 | 1.060 | |
convertToGeneAnswers | 17.372 | 0.152 | 25.988 | |
convertToRangedSummarizedExperiment | 4.212 | 0.000 | 7.605 | |
doEnrichment | 7.536 | 0.052 | 37.891 | |
getDatasets | 0.160 | 0.004 | 0.882 | |
getGeneIds | 0.656 | 0.004 | 3.061 | |
getModel | 1.612 | 0.028 | 2.546 | |
getRelease | 0.036 | 0.000 | 0.314 | |
getTemplateQuery | 0.036 | 0.000 | 0.320 | |
getTemplates | 0.036 | 0.008 | 0.332 | |
getVersion | 0.036 | 0.000 | 0.316 | |
getWidgets | 0.076 | 0.000 | 0.640 | |
initInterMine | 0.016 | 0.000 | 0.233 | |
listDatasets | 3.652 | 0.156 | 5.120 | |
listMines | 0.020 | 0.000 | 0.203 | |
newQuery | 0 | 0 | 0 | |
runQuery | 4.088 | 0.140 | 5.330 | |
setConstraints | 0.060 | 0.000 | 0.501 | |
setQuery | 0.060 | 0.004 | 0.508 | |
simplifyResult | 9.928 | 0.288 | 11.241 | |
summary | 0.036 | 0.000 | 0.308 | |