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BioC 3.1: CHECK report for missMethyl on morelia

This page was generated on 2015-10-09 09:42:02 -0700 (Fri, 09 Oct 2015).

Package 610/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.2.0
Belinda Phipson , Jovana Maksimovic
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/missMethyl
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: missMethyl
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings missMethyl_1.2.0.tar.gz
StartedAt: 2015-10-09 04:00:21 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:07:15 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 414.0 seconds
RetCode: 0
Status:  OK 
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings missMethyl_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/missMethyl.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘missMethyl’ can be installed ... [20s/20s] 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
* 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 ... NOTE
SWAN.MethyLumiSet: no visible global function definition for
  ‘phenoData’
SWAN.default: no visible global function definition for ‘phenoData’
SWAN.default: no visible global function definition for
  ‘featureNames<-’
SWAN.default: no visible global function definition for ‘sampleNames<-’
gometh: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
gometh: no visible global function definition for ‘toTable’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [214s/214s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gometh             59.347  6.281  65.696
SWAN               47.846  6.752  54.611
densityByProbeType 25.128  3.530  28.702
RUVadj             18.072  1.792  19.895
topRUV             16.648  1.911  18.568
RUVfit             14.221  1.801  16.029
* 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/missMethyl.Rcheck/00check.log’
for details.


missMethyl.Rcheck/00install.out:

* installing *source* package ‘missMethyl’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (missMethyl)

missMethyl.Rcheck/missMethyl-Ex.timings:

nameusersystemelapsed
RUVadj18.072 1.79219.895
RUVfit14.221 1.80116.029
SWAN47.846 6.75254.611
contrasts.varFit0.0790.0050.092
densityByProbeType25.128 3.53028.702
getINCs0.6390.0580.698
getLeveneResiduals0.0080.0000.010
gometh59.347 6.28165.696
topRUV16.648 1.91118.568
topVar0.0110.0000.010
varFit0.0100.0000.011