Tiago Chedraoui Silva
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ELMER |
| Branch: RELEASE_3_6 |
| Last Commit: 969aa0f |
| Last Changed Date: 2017-12-26 10:21:36 -0400 (Tue, 26 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:43 -0400 (Thu, 12 Apr 2018).
| Package 417/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ELMER 2.2.7 Tiago Chedraoui Silva
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ELMER |
| Version: 2.2.7 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ELMER_2.2.7.tar.gz |
| StartedAt: 2018-04-11 23:11:02 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:28:16 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 1034.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ELMER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ELMER_2.2.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ELMER.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.2.7’
* 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 ... NOTE
installed size is 34.8Mb
sub-directories of 1Mb or more:
doc 34.6Mb
* 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 ... NOTE
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'
get.diff.meth: no visible binding for global variable 'x'
get.enriched.motif : <anonymous>: no visible global function definition
for 'fisher.test'
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'
Undefined global functions or variables:
Gene GeneID Hugo_Symbol OR Probe Target fisher.test label lowerOR
motif pvalue upperOR value x y z
Consider adding
importFrom("stats", "fisher.test")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createMAE 129.412 0.704 142.299
preAssociationProbeFiltering 62.668 0.296 66.983
get.enriched.motif 28.656 0.240 31.672
schematic.plot 11.420 0.032 38.176
GetNearGenes 8.232 0.148 31.421
get.pair 7.676 0.032 14.761
get.feature.probe 7.080 0.212 10.860
scatter.plot 6.864 0.008 6.892
get.TFs 3.784 0.020 12.762
getTCGA 2.016 0.028 36.488
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘devtools’
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/ELMER.Rcheck/00check.log’
for details.
ELMER.Rcheck/00install.out
* installing *source* package ‘ELMER’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 96 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
224.324 1.764 332.560
ELMER.Rcheck/ELMER-Ex.timings
| name | user | system | elapsed | |
| GetNearGenes | 8.232 | 0.148 | 31.421 | |
| TCGA.pipe | 0.000 | 0.000 | 0.001 | |
| TF.rank.plot | 4.840 | 0.016 | 4.877 | |
| addDistNearestTSS | 0.000 | 0.000 | 0.001 | |
| addMutCol | 0 | 0 | 0 | |
| createMAE | 129.412 | 0.704 | 142.299 | |
| createTSVTemplates | 0.008 | 0.000 | 0.008 | |
| get.TFs | 3.784 | 0.020 | 12.762 | |
| get.diff.meth | 1.104 | 0.004 | 1.192 | |
| get.enriched.motif | 28.656 | 0.240 | 31.672 | |
| get.feature.probe | 7.080 | 0.212 | 10.860 | |
| get.pair | 7.676 | 0.032 | 14.761 | |
| get.permu | 3.9 | 0.0 | 3.9 | |
| getGeneID | 0.640 | 0.000 | 0.641 | |
| getSymbol | 0.632 | 0.000 | 0.629 | |
| getTCGA | 2.016 | 0.028 | 36.488 | |
| getTSS | 0.000 | 0.000 | 0.001 | |
| heatmapPairs | 0.000 | 0.000 | 0.001 | |
| metBoxPlot | 0.004 | 0.000 | 0.001 | |
| motif.enrichment.plot | 0.972 | 0.000 | 0.973 | |
| preAssociationProbeFiltering | 62.668 | 0.296 | 66.983 | |
| promoterMeth | 0.000 | 0.000 | 0.001 | |
| scatter.plot | 6.864 | 0.008 | 6.892 | |
| schematic.plot | 11.420 | 0.032 | 38.176 | |