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CHECK report for BEclear on tokay2

This page was generated on 2018-10-17 08:40:36 -0400 (Wed, 17 Oct 2018).

Package 110/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BEclear 1.12.1
David Rasp
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BEclear
Branch: RELEASE_3_7
Last Commit: 4ec4f42
Last Changed Date: 2018-09-26 13:32:10 -0400 (Wed, 26 Sep 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: BEclear
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BEclear_1.12.1.tar.gz
StartedAt: 2018-10-17 00:40:30 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:43:25 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 175.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BEclear.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:BEclear.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BEclear_1.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BEclear.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 'BEclear/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEclear' version '1.12.1'
* 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 'BEclear' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BEclear : BEclear: no visible global function definition for 'as'
BEclear : BEclear: no visible global function definition for 'rnorm'
BEclear: no visible global function definition for 'write.table'
calcMedians : calcMedians: no visible global function definition for
  'median'
calcPvalues : calcPvals: no visible global function definition for
  'ks.test'
calcPvalues: no visible global function definition for 'p.adjust'
makeBoxplot: no visible global function definition for 'par'
makeBoxplot: no visible global function definition for 'boxplot'
makeBoxplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  as boxplot ks.test median mtext p.adjust par rnorm write.table
Consider adding
  importFrom("graphics", "boxplot", "mtext", "par")
  importFrom("methods", "as")
  importFrom("stats", "ks.test", "median", "p.adjust", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
correctBatchEffect   0.29   0.09   15.83
BEclear              0.26   0.06   16.51
makeBoxplot          0.19   0.01    5.89
countValuesToPredict 0.17   0.00    6.17
clearBEgenes         0.07   0.03    5.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
correctBatchEffect   0.32   0.11   18.88
BEclear              0.33   0.03   19.53
makeBoxplot          0.19   0.04    6.08
countValuesToPredict 0.16   0.02    6.17
clearBEgenes         0.11   0.04    6.14
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/BEclear.Rcheck/00check.log'
for details.



Installation output

BEclear.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/BEclear_1.12.1.tar.gz && rm -rf BEclear.buildbin-libdir && mkdir BEclear.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEclear.buildbin-libdir BEclear_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BEclear_1.12.1.zip && rm BEclear_1.12.1.tar.gz BEclear_1.12.1.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  173k  100  173k    0     0  2855k      0 --:--:-- --:--:-- --:--:-- 3152k

install for i386

* installing *source* package 'BEclear' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BEclear'
    finding HTML links ... done
    BEclear-package                         html  
    BEclear                                 html  
    finding level-2 HTML links ... done

    BEclearData                             html  
    calcMedians                             html  
    calcPvalues                             html  
    calcScore                               html  
    calcSummary                             html  
    clearBEgenes                            html  
    correctBatchEffect                      html  
    countValuesToPredict                    html  
    ex.corrected.data                       html  
    findWrongValues                         html  
    makeBoxplot                             html  
    replaceWrongValues                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BEclear' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEclear' as BEclear_1.12.1.zip
* DONE (BEclear)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BEclear' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

BEclear.Rcheck/examples_i386/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package2.450.022.47
BEclear 0.26 0.0616.51
BEclearData000
calcMedians0.090.000.09
calcPvalues0.140.020.16
calcScore0.240.000.23
calcSummary0.190.000.19
clearBEgenes0.070.035.98
correctBatchEffect 0.29 0.0915.83
countValuesToPredict0.170.006.17
findWrongValues0.540.020.57
makeBoxplot0.190.015.89
replaceWrongValues0.560.020.57

BEclear.Rcheck/examples_x64/BEclear-Ex.timings

nameusersystemelapsed
BEclear-package2.250.002.25
BEclear 0.33 0.0319.53
BEclearData000
calcMedians0.130.020.14
calcPvalues0.150.000.16
calcScore0.290.000.28
calcSummary0.260.000.27
clearBEgenes0.110.046.14
correctBatchEffect 0.32 0.1118.88
countValuesToPredict0.160.026.17
findWrongValues0.550.000.55
makeBoxplot0.190.046.08
replaceWrongValues0.450.000.45