Tiago Chedraoui Silva
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ELMER |
| Branch: RELEASE_3_7 |
| Last Commit: a667145 |
| Last Changed Date: 2018-06-26 15:13:01 -0400 (Tue, 26 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:54:55 -0400 (Wed, 17 Oct 2018).
| Package 441/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ELMER 2.4.4 Tiago Chedraoui Silva
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: ELMER |
| Version: 2.4.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ELMER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ELMER_2.4.4.tar.gz |
| StartedAt: 2018-10-16 21:09:40 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:28:13 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 1113.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ELMER.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ELMER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ELMER_2.4.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ELMER.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.4.4’
* 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 ‘ELMER’ 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'data.table'
':::' call which should be '::': 'TCGAbiolinks:::TCGAVisualize_volcano'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'TCGAbiolinks:::colDataPrepare' 'TCGAbiolinks:::get.GRCh.bioMart'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TF.rank.plot: no visible binding for global variable 'pvalue'
TF.rank.plot: no visible binding for global variable 'label'
TF.rank.plot: no visible binding for global variable 'Gene'
addDistNearestTSS: no visible binding for global variable 'Target'
addDistNearestTSS: no visible binding for global variable 'GeneID'
addDistNearestTSS: no visible binding for global variable 'Probe'
addMutCol: no visible binding for global variable 'Hugo_Symbol'
calculateEnrichement : <anonymous>: no visible global function
definition for 'fisher.test'
findMotifRegion: no visible binding for global variable 'gr'
findMotifRegion: no visible global function definition for
'write.table'
get.diff.meth: no visible binding for global variable 'x'
get.enriched.motif : <anonymous>: no visible global function definition
for 'fisher.test'
getRandomPairs: no visible binding for global variable
'hm450.hg38.manifest'
getTFtargets: no visible binding for global variable 'TF'
heatmapGene: no visible global function definition for 'precede'
heatmapGene: no visible global function definition for
'subsetByOverlaps'
heatmapGene: no visible binding for global variable 'mae'
motif.enrichment.plot: no visible binding for global variable 'y'
motif.enrichment.plot: no visible binding for global variable 'x'
motif.enrichment.plot: no visible binding for global variable 'z'
motif.enrichment.plot: no visible binding for global variable 'upperOR'
motif.enrichment.plot: no visible binding for global variable 'lowerOR'
motif.enrichment.plot: no visible binding for global variable 'motif'
motif.enrichment.plot: no visible binding for global variable 'OR'
scatter: no visible binding for global variable 'value'
scatter: no visible global function definition for 'cor.test'
scatter: no visible binding for global variable 'mae'
Undefined global functions or variables:
Gene GeneID Hugo_Symbol OR Probe TF Target cor.test fisher.test gr
hm450.hg38.manifest label lowerOR mae motif precede pvalue
subsetByOverlaps upperOR value write.table x y z
Consider adding
importFrom("stats", "cor.test", "fisher.test")
importFrom("utils", "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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get.enriched.motif 26.937 0.816 30.689
createMAE 20.380 0.583 41.312
getRandomPairs 19.497 0.643 39.371
schematic.plot 15.048 0.184 25.042
get.feature.probe 9.839 0.507 16.678
get.pair 9.290 0.273 28.407
preAssociationProbeFiltering 8.695 0.289 22.923
GetNearGenes 8.108 0.311 46.713
scatter.plot 7.931 0.120 8.121
TF.rank.plot 4.842 0.255 5.168
getTCGA 2.998 0.533 10.358
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/ELMER.Rcheck/00check.log’
for details.
ELMER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ELMER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ELMER’ ... ** R ** 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 (ELMER)
ELMER.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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.
> library(testthat)
> library(ELMER)
Loading required package: ELMER.data
>
> test_check("ELMER")
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══ testthat results ═══════════════════════════════════════════════════════════
OK: 95 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
121.439 4.995 471.789
ELMER.Rcheck/ELMER-Ex.timings
| name | user | system | elapsed | |
| GetNearGenes | 8.108 | 0.311 | 46.713 | |
| TCGA.pipe | 0.002 | 0.000 | 0.003 | |
| TF.rank.plot | 4.842 | 0.255 | 5.168 | |
| addDistNearestTSS | 0.001 | 0.000 | 0.001 | |
| addMutCol | 0.001 | 0.000 | 0.001 | |
| calculateEnrichement | 0.055 | 0.008 | 0.062 | |
| createMAE | 20.380 | 0.583 | 41.312 | |
| createTSVTemplates | 0.012 | 0.001 | 0.012 | |
| findMotifRegion | 0.002 | 0.000 | 0.002 | |
| get.TFs | 4.584 | 0.179 | 4.813 | |
| get.diff.meth | 1.669 | 0.065 | 1.746 | |
| get.enriched.motif | 26.937 | 0.816 | 30.689 | |
| get.feature.probe | 9.839 | 0.507 | 16.678 | |
| get.pair | 9.290 | 0.273 | 28.407 | |
| get.permu | 4.312 | 0.179 | 4.523 | |
| getGeneID | 0.723 | 0.050 | 0.785 | |
| getRandomPairs | 19.497 | 0.643 | 39.371 | |
| getSymbol | 0.683 | 0.054 | 0.738 | |
| getTCGA | 2.998 | 0.533 | 10.358 | |
| getTFtargets | 0.029 | 0.082 | 0.010 | |
| getTSS | 0.004 | 0.013 | 0.001 | |
| heatmapGene | 0.011 | 0.030 | 0.003 | |
| heatmapPairs | 0.007 | 0.020 | 0.002 | |
| metBoxPlot | 0.006 | 0.018 | 0.003 | |
| motif.enrichment.plot | 2.225 | 0.605 | 2.178 | |
| preAssociationProbeFiltering | 8.695 | 0.289 | 22.923 | |
| promoterMeth | 0.001 | 0.000 | 0.001 | |
| render_report | 0.001 | 0.000 | 0.002 | |
| scatter.plot | 7.931 | 0.120 | 8.121 | |
| schematic.plot | 15.048 | 0.184 | 25.042 | |