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 08:40:39 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELMER.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ELMER_2.4.4.tar.gz |
| StartedAt: 2018-10-17 01:47:39 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:10:08 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1348.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ELMER.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELMER.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ELMER_2.4.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ELMER.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.4.4'
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get.enriched.motif 26.16 1.54 30.39
createMAE 19.63 0.30 30.61
getRandomPairs 19.00 0.47 26.28
schematic.plot 13.00 0.14 23.61
GetNearGenes 10.94 0.69 32.13
get.feature.probe 10.12 0.49 15.58
preAssociationProbeFiltering 9.66 0.22 14.08
get.pair 8.72 0.22 18.28
scatter.plot 6.00 0.03 6.03
getTCGA 2.06 0.02 10.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get.enriched.motif 30.51 0.52 33.69
createMAE 21.54 0.55 34.02
getRandomPairs 20.55 0.39 27.80
schematic.plot 16.03 0.07 27.73
get.feature.probe 10.16 0.42 14.48
GetNearGenes 9.61 0.39 28.11
preAssociationProbeFiltering 9.70 0.29 13.38
get.pair 9.64 0.18 17.78
scatter.plot 7.05 0.07 7.55
getTCGA 3.19 0.04 10.59
* 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 ... 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/ELMER.Rcheck/00check.log'
for details.
ELMER.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ELMER_2.4.4.tar.gz && rm -rf ELMER.buildbin-libdir && mkdir ELMER.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ELMER.buildbin-libdir ELMER_2.4.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ELMER_2.4.4.zip && rm ELMER_2.4.4.tar.gz ELMER_2.4.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12.4M 100 12.4M 0 0 58.6M 0 --:--:-- --:--:-- --:--:-- 60.6M
install for i386
* installing *source* package 'ELMER' ...
** R
** inst
** byte-compile and prepare 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
calculateEnrichement html
createMAE html
createMotifRelevantTfs html
createSummaryDocument html
createTSVTemplates html
findMotifRegion 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
getRandomPairs html
getSymbol html
getTCGA html
getTF html
getTFtargets html
getTSS html
heatmapGene html
heatmapPairs html
lm_eqn html
metBoxPlot html
motif.enrichment.plot html
preAssociationProbeFiltering html
promoterMeth html
render_report 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_2.4.4.zip
* DONE (ELMER)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ELMER' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ELMER.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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: 95 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
127.64 5.64 209.12
|
ELMER.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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: 95 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
143.04 3.35 218.78
|
|
ELMER.Rcheck/examples_i386/ELMER-Ex.timings
|
ELMER.Rcheck/examples_x64/ELMER-Ex.timings
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