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BioC 3.2: CHECK report for ChAMP on oaxaca

This page was generated on 2016-04-23 10:27:17 -0700 (Sat, 23 Apr 2016).

Package 158/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 1.8.2
Tiffany Morris
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ChAMP
Last Changed Rev: 116669 / Revision: 116712
Last Changed Date: 2016-04-21 12:55:18 -0700 (Thu, 21 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChAMP
Version: 1.8.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMP_1.8.2.tar.gz
StartedAt: 2016-04-22 22:32:41 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:41:41 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 539.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChAMP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChAMP_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChAMP.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMP’ version ‘1.8.2’
* 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 ‘ChAMP’ can be installed ... [27s/27s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: replacing previous import ‘limma::ebayes’ by ‘RPMM::ebayes’ when loading ‘ChAMP’
  Warning: replacing previous import ‘plyr::desc’ by ‘IRanges::desc’ when loading ‘ChAMP’
  Warning: replacing previous import ‘wateRmelon::colnames’ by ‘IRanges::colnames’ when loading ‘ChAMP’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChAMP.Rcheck/00install.out’ for details.
* 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
champ.CNA: no visible binding for global variable ‘myLoad’
champ.CNA: no visible binding for global variable ‘probe.features’
champ.CNA: no visible binding for global variable ‘bloodCtl’
champ.MVP: no visible binding for global variable ‘myNorm’
champ.MVP: no visible binding for global variable ‘myLoad’
champ.MVP: no visible binding for global variable ‘probe.features’
champ.SVD: no visible binding for global variable ‘myNorm’
champ.SVD: no visible binding for global variable ‘myLoad’
champ.TrueMethyl: no visible binding for global variable ‘myNorm’
champ.TrueMethyl: no visible binding for global variable ‘myLoad’
champ.TrueMethyl: no visible binding for global variable
  ‘probe.features’
champ.lasso: no visible binding for global variable ‘myNorm’
champ.lasso: no visible binding for global variable ‘myLoad’
champ.lasso: no visible binding for global variable ‘probe.features’
champ.lasso: no visible binding for global variable ‘probe.450K.VCs.af’
champ.load: no visible global function definition for ‘sampleNames<-’
champ.load: no visible binding for global variable ‘snp.hit’
champ.load: no visible binding for global variable ‘multi.hit’
champ.load: no visible binding for global variable ‘probe.features’
champ.norm: no visible binding for global variable ‘myLoad’
champ.norm: no visible binding for global variable ‘probe.features’
champ.norm: no visible binding for global variable ‘probeInfoALL.lv’
champ.runCombat: no visible binding for global variable ‘myNorm’
champ.runCombat: no visible binding for global variable ‘myLoad’
plotThreshold: no visible binding for global variable ‘probe.features’
* 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’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’
Please remove them from your package.
* checking examples ... [268s/279s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
champ.norm       63.855  4.321  68.282
champ.load       60.288  3.922  73.680
champ.CNA        36.073  0.837  37.454
champ.SVD        25.949  2.499  28.672
champ.runCombat  14.148  0.456  14.612
champ.MVP        13.883  0.450  14.338
champ.TrueMethyl 13.733  0.442  14.181
champ.lasso      13.485  0.326  13.819
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ChAMP.Rcheck/00check.log’
for details.


ChAMP.Rcheck/00install.out:

* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘limma::ebayes’ by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import ‘plyr::desc’ by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import ‘wateRmelon::colnames’ by ‘IRanges::colnames’ when loading ‘ChAMP’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘limma::ebayes’ by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import ‘plyr::desc’ by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import ‘wateRmelon::colnames’ by ‘IRanges::colnames’ when loading ‘ChAMP’
* DONE (ChAMP)

ChAMP.Rcheck/ChAMP-Ex.timings:

nameusersystemelapsed
ChAMP-package0.0010.0000.000
champ.CNA36.073 0.83737.454
champ.MVP13.883 0.45014.338
champ.SVD25.949 2.49928.672
champ.TrueMethyl13.733 0.44214.181
champ.lasso13.485 0.32613.819
champ.load60.288 3.92273.680
champ.norm63.855 4.32168.282
champ.process0.0010.0000.000
champ.runCombat14.148 0.45614.612