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CHECK report for LedPred on tokay2

This page was generated on 2018-10-17 08:40:53 -0400 (Wed, 17 Oct 2018).

Package 783/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LedPred 1.14.1
Aitor Gonzalez
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/LedPred
Branch: RELEASE_3_7
Last Commit: d752697
Last Changed Date: 2018-08-24 05:36:46 -0400 (Fri, 24 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LedPred
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LedPred.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings LedPred_1.14.1.tar.gz
StartedAt: 2018-10-17 02:57:07 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:58:29 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 81.5 seconds
RetCode: 0
Status:  OK  
CheckDir: LedPred.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LedPred.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings LedPred_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/LedPred.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 'LedPred/DESCRIPTION' ... OK
* this is package 'LedPred' version '1.14.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'LedPred' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotCostGamma: no visible global function definition for 'title'
.plotCostGamma: no visible global function definition for 'points'
mapFeaturesToCRMs: no visible global function definition for
  'write.table'
mapFeaturesToCRMs: no visible global function definition for
  'read.table'
mapFeaturesToCRMs: no visible global function definition for
  'download.file'
scoreData: no visible global function definition for 'write.table'
Undefined global functions or variables:
  download.file points read.table title write.table
Consider adding
  importFrom("graphics", "points", "title")
  importFrom("utils", "download.file", "read.table", "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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/LedPred.Rcheck/00check.log'
for details.



Installation output

LedPred.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/LedPred_1.14.1.tar.gz && rm -rf LedPred.buildbin-libdir && mkdir LedPred.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LedPred.buildbin-libdir LedPred_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL LedPred_1.14.1.zip && rm LedPred_1.14.1.tar.gz LedPred_1.14.1.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 1418k  100 1418k    0     0  15.9M      0 --:--:-- --:--:-- --:--:-- 17.3M

install for i386

* installing *source* package 'LedPred' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LedPred'
    finding HTML links ... done
    LedPred                                 html  
    createModel                             html  
    crm.features                            html  
    evaluateModelPerformance                html  
    feature.ranking                         html  
    mapFeaturesToCRMs                       html  
    mcTune                                  html  
    rankFeatures                            html  
    scoreData                               html  
    tuneFeatureNb                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'LedPred' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LedPred' as LedPred_1.14.1.zip
* DONE (LedPred)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'LedPred' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

LedPred.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(LedPred)
Loading required package: e1071
> 
> test_check("LedPred")
== testthat results  ===========================================================
OK: 45 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.17    0.57    9.73 

LedPred.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(LedPred)
Loading required package: e1071
> 
> test_check("LedPred")
== testthat results  ===========================================================
OK: 45 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  12.21    0.67   12.87 

Example timings

LedPred.Rcheck/examples_i386/LedPred-Ex.timings

nameusersystemelapsed
LedPred0.010.000.01
createModel000
evaluateModelPerformance000
mapFeaturesToCRMs0.020.000.01
mcTune000
rankFeatures000
scoreData0.010.000.02
tuneFeatureNb000

LedPred.Rcheck/examples_x64/LedPred-Ex.timings

nameusersystemelapsed
LedPred0.010.000.02
createModel0.020.000.01
evaluateModelPerformance0.000.010.02
mapFeaturesToCRMs000
mcTune0.020.000.01
rankFeatures000
scoreData0.000.020.02
tuneFeatureNb0.010.000.01