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BioC 3.5: CHECK report for bioCancer on tokay2

This page was generated on 2017-10-18 14:26:06 -0400 (Wed, 18 Oct 2017).

Package 113/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioCancer 1.4.0
Karim Mezhoud
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/bioCancer
Branch: RELEASE_3_5
Last Commit: 631ed60
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bioCancer
Version: 1.4.0
Command: rm -rf bioCancer.buildbin-libdir bioCancer.Rcheck && mkdir bioCancer.buildbin-libdir bioCancer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bioCancer.buildbin-libdir bioCancer_1.4.0.tar.gz >bioCancer.Rcheck\00install.out 2>&1 && cp bioCancer.Rcheck\00install.out bioCancer-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=bioCancer.buildbin-libdir --install="check:bioCancer-install.out" --force-multiarch --no-vignettes --timings bioCancer_1.4.0.tar.gz
StartedAt: 2017-10-17 22:17:02 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:22:05 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 303.4 seconds
RetCode: 0
Status:  OK  
CheckDir: bioCancer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bioCancer.buildbin-libdir bioCancer.Rcheck && mkdir bioCancer.buildbin-libdir bioCancer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bioCancer.buildbin-libdir bioCancer_1.4.0.tar.gz >bioCancer.Rcheck\00install.out 2>&1 && cp bioCancer.Rcheck\00install.out bioCancer-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=bioCancer.buildbin-libdir --install="check:bioCancer-install.out" --force-multiarch --no-vignettes --timings bioCancer_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/bioCancer.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bioCancer/DESCRIPTION' ... OK
* this is package 'bioCancer' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'magrittr' 'ggplot2' 'lubridate' 'tidyr' 'cgdsr' 'RCurl' 'XML'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'bioCancer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.2Mb
  sub-directories of 1Mb or more:
    base        6.8Mb
    bioCancer   3.1Mb
    doc         2.8Mb
    quant       7.8Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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
** 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-3.5-bioc/meat/bioCancer.Rcheck/00check.log'
for details.


bioCancer.Rcheck/00install.out:


install for i386

* installing *source* package 'bioCancer' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'bioCancer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bioCancer' as bioCancer_1.4.0.zip
* DONE (bioCancer)

bioCancer.Rcheck/examples_i386/bioCancer-Ex.timings:

nameusersystemelapsed
Edges_Diseases_obj000
Mutation_obj0.050.000.05
Node_Diseases_obj000
Node_df_FreqIn000
Node_obj_CNA_ProfData000
Node_obj_FreqIn000
Node_obj_Met_ProfData000
Node_obj_mRNA_Classifier000
Studies_obj000
UnifyRowNames000
attriColorGene0.010.000.02
attriColorValue000
attriColorVector000
attriShape2Gene000
attriShape2Node000
bioCancer000
checkDimensions000
coffeewheel000
coffeewheelOutput000
displayTable0.300.100.45
getFreqMutData000
getGenesClassification0.250.080.37
getListProfData000
getList_Cases0.190.110.35
getList_GenProfs0.220.090.34
getMegaProfData000
grepRef000
metabologram000
reStrColorGene000
reStrDimension0.010.000.02
reStrDisease000
renderCoffeewheel000
sampleWheelData000
whichGeneList000

bioCancer.Rcheck/examples_x64/bioCancer-Ex.timings:

nameusersystemelapsed
Edges_Diseases_obj0.020.000.01
Mutation_obj0.040.000.05
Node_Diseases_obj0.010.000.02
Node_df_FreqIn000
Node_obj_CNA_ProfData000
Node_obj_FreqIn000
Node_obj_Met_ProfData000
Node_obj_mRNA_Classifier000
Studies_obj0.020.000.02
UnifyRowNames000
attriColorGene000
attriColorValue000
attriColorVector000
attriShape2Gene000
attriShape2Node000
bioCancer000
checkDimensions0.020.000.01
coffeewheel000
coffeewheelOutput000
displayTable0.210.170.45
getFreqMutData000
getGenesClassification0.190.130.36
getListProfData000
getList_Cases0.170.170.37
getList_GenProfs0.060.250.36
getMegaProfData000
grepRef000
metabologram000
reStrColorGene000
reStrDimension000
reStrDisease000
renderCoffeewheel0.010.000.01
sampleWheelData000
whichGeneList000