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BioC experimental data: CHECK report for pumadata on zin2

This page was generated on 2016-10-08 19:29:03 -0700 (Sat, 08 Oct 2016).

Package 217/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pumadata 2.8.0
Richard Pearson
Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/pumadata
Last Changed Rev: 3760 / Revision: 3935
Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 

Summary

Package: pumadata
Version: 2.8.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings pumadata_2.8.0.tar.gz
StartedAt: 2016-10-08 09:59:27 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 10:01:19 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 111.4 seconds
RetCode: 0
Status:  OK 
CheckDir: pumadata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings pumadata_2.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/pumadata.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pumadata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pumadata’ version ‘2.8.0’
* 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 ‘pumadata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 110.0Mb
  sub-directories of 1Mb or more:
    data  109.8Mb
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘oligo’ ‘puma’
  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
File ‘pumadata/R/zzz.R’:
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.onLoad: no visible global function definition for ‘addVigs2WinMenu’
Undefined global functions or variables:
  addVigs2WinMenu
* 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 ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-data-experiment/meat/pumadata.Rcheck/00check.log’
for details.


pumadata.Rcheck/00install.out:

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

pumadata.Rcheck/pumadata-Ex.timings:

nameusersystemelapsed
eset_estrogen_comb0.0990.0040.103
eset_estrogen_mmgmos0.0960.0120.108
eset_estrogen_pmmmgmos0.1080.0080.119
eset_estrogen_rma0.2060.0000.207
pumapca_estrogen0.0040.0040.008