InterMine Team
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/InterMineR |
| Branch: RELEASE_3_7 |
| Last Commit: 978b6c2 |
| Last Changed Date: 2018-08-21 16:01:13 -0400 (Tue, 21 Aug 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:40 -0400 (Wed, 17 Oct 2018).
| Package 743/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| InterMineR 1.2.1 InterMine Team
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: InterMineR |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings InterMineR_1.2.1.tar.gz |
| StartedAt: 2018-10-16 01:20:17 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:24:12 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 234.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: InterMineR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings InterMineR_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/InterMineR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.1’
* 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 13.688 0.068 22.205
simplifyResult 7.520 0.328 8.909
doEnrichment 6.408 0.040 52.867
runQuery 3.476 0.108 5.662
listDatasets 3.204 0.172 6.230
convertToRangedSummarizedExperiment 2.648 0.008 10.236
* 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-3.7-bioc/meat/InterMineR.Rcheck/00check.log’
for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL InterMineR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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 | 0.228 | 0.000 | 0.744 | |
| PL_DiabetesGenes | 0.000 | 0.000 | 0.004 | |
| PL_FlyTF_site_specific_TFs | 0.000 | 0.000 | 0.002 | |
| convertToGRanges | 1.084 | 0.028 | 1.718 | |
| convertToGeneAnswers | 13.688 | 0.068 | 22.205 | |
| convertToRangedSummarizedExperiment | 2.648 | 0.008 | 10.236 | |
| doEnrichment | 6.408 | 0.040 | 52.867 | |
| getDatasets | 0.148 | 0.000 | 2.861 | |
| getGeneIds | 0.488 | 0.004 | 3.131 | |
| getModel | 1.304 | 0.008 | 2.270 | |
| getRelease | 0.028 | 0.000 | 0.340 | |
| getTemplateQuery | 0.032 | 0.000 | 0.388 | |
| getTemplates | 0.040 | 0.000 | 0.399 | |
| getVersion | 0.032 | 0.000 | 0.351 | |
| getWidgets | 0.064 | 0.000 | 0.709 | |
| initInterMine | 0.016 | 0.000 | 0.226 | |
| listDatasets | 3.204 | 0.172 | 6.230 | |
| listMines | 0.008 | 0.008 | 0.234 | |
| newQuery | 0.000 | 0.000 | 0.001 | |
| runQuery | 3.476 | 0.108 | 5.662 | |
| setConstraints | 0.040 | 0.008 | 0.640 | |
| setQuery | 0.040 | 0.012 | 0.717 | |
| simplifyResult | 7.520 | 0.328 | 8.909 | |
| summary | 0.032 | 0.000 | 0.387 | |