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BioC experimental data: CHECK report for XhybCasneuf on petty

This page was generated on 2015-10-07 16:21:36 -0700 (Wed, 07 Oct 2015).

Package 234/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XhybCasneuf 1.6.0
Tineke Casneuf
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/XhybCasneuf
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 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 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: XhybCasneuf
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XhybCasneuf_1.6.0.tar.gz
StartedAt: 2015-10-07 10:02:44 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 10:04:42 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 118.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: XhybCasneuf.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XhybCasneuf_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/XhybCasneuf.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XhybCasneuf/DESCRIPTION’ ... OK
* this is package ‘XhybCasneuf’ version ‘1.6.0’
* 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 ‘XhybCasneuf’ can be installed ... [10s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘affy’ ‘ath1121501cdf’ ‘grid’ ‘methods’ ‘RColorBrewer’ ‘tinesath1cdf’
  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
runSimulation: no visible binding for global variable
  ‘generateExprVal.method.mas’
runSimulation: no visible binding for global variable
  ‘generateExprVal.method.liwong’
plotExample,XhybExamples : .local: no visible global function
  definition for ‘brewer.pal’
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  AffysTissue.noBl.rda      202Kb    154Kb       xz
  AffysTissue.rda           741Kb    491Kb       xz
  AffysTissueMC.rda         886Kb    591Kb       xz
  CustomsTissue.noBl.rda    153Kb    120Kb       xz
  CustomsTissue.rda         552Kb    372Kb       xz
  CustomsTissueMC.rda       688Kb    465Kb       xz
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/6s] 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

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/XhybCasneuf.Rcheck/00check.log’
for details.


XhybCasneuf.Rcheck/00install.out:

* installing *source* package ‘XhybCasneuf’ ...
** R
** data
** 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 (XhybCasneuf)

XhybCasneuf.Rcheck/XhybCasneuf-Ex.timings:

nameusersystemelapsed
AffysTissue0.5670.0140.641
CustomsTissue0.1480.0050.158
XhybExamples-class0.0470.0030.050
ex10.0420.0040.047
runSimulation0.2410.0030.244