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 13:26:23 -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: rm -rf ELMER.buildbin-libdir ELMER.Rcheck && mkdir ELMER.buildbin-libdir ELMER.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ELMER.buildbin-libdir ELMER_2.2.7.tar.gz >ELMER.Rcheck\00install.out 2>&1 && cp ELMER.Rcheck\00install.out ELMER-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ELMER.buildbin-libdir --install="check:ELMER-install.out" --force-multiarch --no-vignettes --timings ELMER_2.2.7.tar.gz |
| StartedAt: 2018-04-11 23:45:05 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-12 00:17:20 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 1935.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ELMER.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf ELMER.buildbin-libdir ELMER.Rcheck && mkdir ELMER.buildbin-libdir ELMER.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ELMER.buildbin-libdir ELMER_2.2.7.tar.gz >ELMER.Rcheck\00install.out 2>&1 && cp ELMER.Rcheck\00install.out ELMER-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ELMER.buildbin-libdir --install="check:ELMER-install.out" --force-multiarch --no-vignettes --timings ELMER_2.2.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ELMER.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'ELMER' can be installed ... OK
* checking installed package size ... NOTE
installed size is 34.2Mb
sub-directories of 1Mb or more:
doc 33.8Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createMAE 133.75 0.76 144.36
preAssociationProbeFiltering 68.09 0.31 72.15
get.enriched.motif 25.21 0.71 29.68
GetNearGenes 10.75 0.48 33.89
schematic.plot 10.95 0.06 31.95
get.feature.probe 8.17 0.52 11.75
scatter.plot 8.36 0.08 8.44
get.pair 7.00 0.19 13.18
TF.rank.plot 5.00 0.10 6.14
get.TFs 3.15 0.14 12.81
getTCGA 1.74 0.02 37.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createMAE 135.97 0.73 146.57
preAssociationProbeFiltering 63.38 0.29 66.58
get.enriched.motif 26.17 0.39 29.59
GetNearGenes 13.31 0.26 36.36
schematic.plot 12.06 0.08 32.48
get.pair 7.94 0.24 14.22
get.feature.probe 7.38 0.53 10.86
scatter.plot 7.56 0.08 7.64
TF.rank.plot 5.90 0.10 6.14
get.TFs 3.28 0.07 13.47
getTCGA 1.99 0.05 36.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.6-bioc/meat/ELMER.Rcheck/00check.log'
for details.
ELMER.Rcheck/00install.out
install for i386
* installing *source* package 'ELMER' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ELMER'
finding HTML links ... done
ELMER html
Get.Pvalue.p html
GetNearGenes html
Stat.diff.meth html
Stat.nonpara html
Stat.nonpara.permu html
TCGA.pipe html
TF.rank.plot html
TFsurvival.plot html
addDistNearestTSS html
addMutCol html
createMAE html
createMotifRelevantTfs html
createSummaryDocument html
createTSVTemplates html
get.TFs html
get.diff.meth html
get.enriched.motif html
get.feature.probe html
get.pair html
get.permu html
get450K html
getClinic html
getExp html
getExpSamples html
getGeneID html
getMet html
getMetSamples html
getRNAseq html
getSymbol html
getTCGA html
getTF html
getTSS html
heatmapPairs html
lm_eqn html
metBoxPlot html
motif.enrichment.plot html
preAssociationProbeFiltering html
promoterMeth html
scatter html
scatter.plot html
schematic.plot html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ELMER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ELMER' as ELMER_2.2.7.zip
* DONE (ELMER)
In R CMD INSTALL
In R CMD INSTALL
|
ELMER.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
244.15 3.85 338.21
|
ELMER.Rcheck/tests_x64/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-w64-mingw32/x64 (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
246.98 3.10 339.18
|
|
ELMER.Rcheck/examples_i386/ELMER-Ex.timings
|
ELMER.Rcheck/examples_x64/ELMER-Ex.timings
|