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BioC 3.1: CHECK report for ChAMP on zin2

This page was generated on 2015-10-09 09:25:49 -0700 (Fri, 09 Oct 2015).

Package 151/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 1.6.2
Tiffany Morris
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/ChAMP
Last Changed Rev: 108563 / Revision: 109384
Last Changed Date: 2015-09-16 05:57:48 -0700 (Wed, 16 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChAMP
Version: 1.6.2
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ChAMP_1.6.2.tar.gz
StartedAt: 2015-10-08 23:13:15 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:20:36 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 440.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChAMP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ChAMP_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ChAMP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.2’
* 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 ... [19s/22s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
  Warning: replacing previous import by ‘IRanges::desc’ when loading ‘ChAMP’
  Warning: replacing previous import by ‘IRanges::colnames’ when loading ‘ChAMP’
See ‘/home/biocbuild/bbs-3.1-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 ... [168s/211s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
champ.CNA        31.172  0.341  39.624
champ.load       29.692  0.335  40.367
champ.norm       28.803  0.071  36.182
champ.SVD        21.070  0.161  26.065
champ.runCombat  12.169  0.021  15.037
champ.MVP        11.754  0.079  14.755
champ.TrueMethyl 11.750  0.020  14.457
champ.lasso      11.339  0.031  13.488
* 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/ChAMP.Rcheck/00check.log’
for details.


ChAMP.Rcheck/00install.out:

* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::colnames’ when loading ‘ChAMP’
** 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’
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::desc’ when loading ‘ChAMP’
Warning: replacing previous import by ‘IRanges::colnames’ when loading ‘ChAMP’
* DONE (ChAMP)

ChAMP.Rcheck/ChAMP-Ex.timings:

nameusersystemelapsed
ChAMP-package0.0010.0000.001
champ.CNA31.172 0.34139.624
champ.MVP11.754 0.07914.755
champ.SVD21.070 0.16126.065
champ.TrueMethyl11.750 0.02014.457
champ.lasso11.339 0.03113.488
champ.load29.692 0.33540.367
champ.norm28.803 0.07136.182
champ.process0.0000.0000.001
champ.runCombat12.169 0.02115.037