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BioC 3.0: CHECK report for DeconRNASeq on oaxaca

This page was generated on 2015-04-10 10:06:23 -0700 (Fri, 10 Apr 2015).

Package 227/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeconRNASeq 1.8.0
Ting Gong
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/DeconRNASeq
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: DeconRNASeq
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DeconRNASeq_1.8.0.tar.gz
StartedAt: 2015-04-09 22:49:59 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:50:47 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 48.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DeconRNASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DeconRNASeq_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DeconRNASeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeconRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeconRNASeq’ version ‘1.8.0’
* 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 ‘DeconRNASeq’ can be installed ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* 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 ... NOTE
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘grid’ ‘pcaMethods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DeconRNASeq: no visible global function definition for ‘prep’
DeconRNASeq: no visible global function definition for ‘pca’
DeconRNASeq: no visible global function definition for ‘R2cum’
DeconRNASeq: no visible global function definition for ‘ggplot’
DeconRNASeq: no visible global function definition for ‘aes’
DeconRNASeq: no visible global function definition for ‘geom_point’
DeconRNASeq: no visible global function definition for ‘labs’
DeconRNASeq: no visible global function definition for ‘geom_abline’
DeconRNASeq: no visible global function definition for ‘xlab’
DeconRNASeq: no visible global function definition for ‘ylab’
multiplot: no visible global function definition for ‘grid.newpage’
multiplot: no visible global function definition for ‘pushViewport’
multiplot: no visible global function definition for ‘viewport’
multiplot: no visible global function definition for ‘grid.layout’
multiplot : vplayout: no visible global function definition for
  ‘viewport’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/DeconRNASeq.Rcheck/00check.log’
for details.

DeconRNASeq.Rcheck/00install.out:

* installing *source* package ‘DeconRNASeq’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DeconRNASeq)

DeconRNASeq.Rcheck/DeconRNASeq-Ex.timings:

nameusersystemelapsed
DeconRNASeq0.0010.0000.001
all.datasets0.1830.0050.188
array.proportions0.1190.0040.123
array.signatures0.1100.0030.113
condplot0.1100.0030.113
datasets0.1050.0070.112
fraction0.3960.0100.405
liver_kidney0.1140.0070.121
multi_tissue0.4020.0080.410
multiplot0.0030.0000.003
proportions0.1110.0060.118
signatures0.1090.0070.116
x.data0.4020.0080.410
x.signature0.400.010.41
x.signature.filtered0.4060.0100.416
x.signature.filtered.optimal0.3700.0080.378