InterMine Team
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/InterMineR |
| Branch: RELEASE_3_8 |
| Last Commit: 1fdb15b |
| Last Changed Date: 2018-12-06 07:14:37 -0400 (Thu, 06 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
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 |
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### Running command:
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### /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
###
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* 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 | |