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BioC experimental data: CHECK report for PREDAsampledata on perceval

This page was generated on 2014-04-04 17:29:16 -0700 (Fri, 04 Apr 2014).

Package 139/181HostnameOS / ArchBUILDCHECKBUILD BIN
PREDAsampledata 0.2.8
Francesco Ferrari
Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/PREDAsampledata
Last Changed Rev: 2533 / Revision: 2768
Last Changed Date: 2013-10-14 15:00:20 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: PREDAsampledata
Version: 0.2.8
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PREDAsampledata_0.2.8.tar.gz
StartedAt: 2014-04-04 11:32:53 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 11:51:26 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 1112.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: PREDAsampledata.Rcheck
Warnings: 1

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/PREDAsampledata.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PREDAsampledata/DESCRIPTION’ ... OK
* this is package ‘PREDAsampledata’ version ‘0.2.8’
* 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 ‘PREDAsampledata’ can be installed ... [14s/24s] OK
* checking installed package size ... NOTE
  installed size is 116.5Mb
  sub-directories of 1Mb or more:
    data        95.8Mb
    sampledata  20.7Mb
* checking package 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘affy’ ‘annotate’ ‘Biobase’ ‘gahgu133plus2.db’ ‘gahgu133plus2cdf’
  ‘methods’ ‘PREDA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
  AffybatchRCC.RData               61.4Mb   37.5Mb       xz
  ExpressionSetRCC.RData            9.1Mb    7.7Mb       xz
  GEanalysisResults.RData           1.1Mb    599Kb       xz
  SODEGIRCNDataForPREDA.RData      10.6Mb    4.7Mb       xz
  SODEGIRCNanalysisResults.RData    3.1Mb    2.3Mb       xz
  SODEGIRGEDataForPREDA.RData       2.1Mb    1.8Mb       xz
  SODEGIRGEanalysisResults.RData    5.1Mb    4.0Mb       xz
  gaExpressionSetRCC.RData          3.3Mb    2.8Mb       xz
* checking examples ... [21s/22s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
AffybatchRCC 11.165  0.449  11.703
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/PREDAsampledata.Rcheck/00check.log’
for details.

PREDAsampledata.Rcheck/00install.out:

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

PREDAsampledata.Rcheck/PREDAsampledata-Ex.timings:

nameusersystemelapsed
AffybatchRCC11.165 0.44911.703
ExpressionSetRCC0.3530.0350.388
GEanalysisResults0.7570.0720.829
SODEGIRCNDataForPREDA0.4990.0400.569
SODEGIRCNanalysisResults0.1610.0190.180
SODEGIRGEDataForPREDA0.1050.0130.218
SODEGIRGEanalysisResults0.2050.0250.254
gaExpressionSetRCC0.1040.0170.122