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BioC 3.0: CHECK report for ChAMP on perceval

This page was generated on 2015-04-10 09:58:58 -0700 (Fri, 10 Apr 2015).

Package 141/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 1.4.1
Tiffany Morris
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ChAMP
Last Changed Rev: 100997 / Revision: 102249
Last Changed Date: 2015-03-22 14:32:15 -0700 (Sun, 22 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: ChAMP
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChAMP_1.4.1.tar.gz
StartedAt: 2015-04-09 23:38:24 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:51:32 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 787.5 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 --no-multiarch ChAMP_1.4.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChAMP.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.1’
* 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 ... [39s/40s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
See ‘/Users/biocbuild/bbs-3.0-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.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.lasso: no visible global function definition for ‘GRanges’
champ.lasso: no visible global function definition for ‘IRanges’
champ.lasso: no visible global function definition for ‘countOverlaps’
champ.lasso: no visible global function definition for ‘findOverlaps’
champ.load: no visible global function definition for ‘sampleNames<-’
champ.load: no visible binding for global variable ‘probe.features’
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.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’
champ.SVD: no visible binding for global variable ‘myNorm’
champ.SVD: 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 ... [381s/382s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
champ.norm      82.161  9.283  91.597
champ.load      78.210  8.658  87.716
champ.CNA       69.926  1.638  71.662
champ.SVD       49.365  5.660  55.148
champ.lasso     17.142  1.134  18.321
champ.MVP       16.517  1.414  17.971
champ.runCombat 16.411  1.378  17.862
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChAMP.Rcheck/00check.log’
for details.

ChAMP.Rcheck/00install.out:

* installing *source* package ‘ChAMP’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘RPMM::ebayes’ when loading ‘ChAMP’
* DONE (ChAMP)

ChAMP.Rcheck/ChAMP-Ex.timings:

nameusersystemelapsed
ChAMP-package0.0000.0000.001
champ.CNA69.926 1.63871.662
champ.MVP16.517 1.41417.971
champ.SVD49.365 5.66055.148
champ.lasso17.142 1.13418.321
champ.load78.210 8.65887.716
champ.norm82.161 9.28391.597
champ.process0.0000.0000.001
champ.runCombat16.411 1.37817.862