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BioC 3.4: CHECK report for bioCancer on morelia

This page was generated on 2016-09-21 03:56:01 -0700 (Wed, 21 Sep 2016).

Package 106/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioCancer 1.0.0
Karim Mezhoud
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bioCancer
Last Changed Rev: 120186 / Revision: 121152
Last Changed Date: 2016-08-16 14:02:36 -0700 (Tue, 16 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bioCancer
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioCancer_1.0.0.tar.gz
StartedAt: 2016-09-20 03:39:36 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:42:27 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 170.7 seconds
RetCode: 0
Status:  OK 
CheckDir: bioCancer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioCancer_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/bioCancer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.3Mb
  sub-directories of 1Mb or more:
    base        6.1Mb
    bioCancer   3.1Mb
    doc         1.8Mb
    quant       7.7Mb
* 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/bioCancer.Rcheck/00check.log’
for details.


bioCancer.Rcheck/00install.out:

* 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
* DONE (bioCancer)

bioCancer.Rcheck/bioCancer-Ex.timings:

nameusersystemelapsed
Edges_Diseases_obj0.0050.0000.005
Mutation_obj0.0180.0010.019
Node_Diseases_obj0.0040.0000.004
Node_df_FreqIn0.0010.0000.001
Node_obj_CNA_ProfData0.0020.0000.002
Node_obj_FreqIn0.0000.0000.001
Node_obj_Met_ProfData0.0010.0000.001
Node_obj_mRNA_Classifier0.0020.0000.002
Studies_obj0.0080.0010.009
UnifyRowNames0.0010.0000.001
attriColorGene0.0010.0000.001
attriColorValue0.0010.0000.001
attriColorVector0.0010.0000.002
attriShape2Gene0.0000.0010.000
attriShape2Node0.0010.0000.000
bioCancer0.0000.0000.001
checkDimensions0.0010.0000.001
coffeewheel000
coffeewheelOutput000
displayTable0.0060.0010.676
getFreqMutData0.0020.0000.002
getListProfData0.0020.0000.001
grepRef0.0000.0000.001
metabologram0.0010.0000.001
reStrColorGene0.0020.0010.002
reStrDimension0.0020.0000.002
reStrDisease0.0020.0000.002
renderCoffeewheel0.0000.0000.001
sampleWheelData000
whichGeneList0.0010.0000.001