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BioC experimental data: CHECK report for Neve2006 on zin2

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

Package 193/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Neve2006 0.10.0
VJ Carey
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/Neve2006
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: Neve2006
Version: 0.10.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Neve2006_0.10.0.tar.gz
StartedAt: 2016-10-08 09:52:19 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 09:53:37 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 77.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Neve2006.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Neve2006_0.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/Neve2006.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 ‘Neve2006/DESCRIPTION’ ... OK
* this is package ‘Neve2006’ version ‘0.10.0’
* 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 ‘Neve2006’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 70.6Mb
  sub-directories of 1Mb or more:
    data     15.1Mb
    extdata  54.6Mb
* 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:
  ‘Biobase’ ‘annotate’ ‘hgu133a.db’ ‘methods’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataDims’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[,cghExSet: no visible global function definition for ‘assayDataNew’
[,cghExSet: no visible global function definition for ‘exprs’
[,cghExSet: no visible global function definition for ‘phenoData’
initialize,cghExSet: no visible global function definition for
  ‘assayDataNew’
logRatios,cghExSet: no visible global function definition for
  ‘assayDataElement’
logRatios,cghSet: no visible global function definition for
  ‘assayDataElement’
show,cghExSet: no visible global function definition for ‘storageMode’
show,cghExSet: no visible global function definition for ‘selectSome’
show,cghExSet: no visible global function definition for ‘featureNames’
show,cghExSet: no visible global function definition for ‘dims’
show,cghExSet: no visible global function definition for ‘phenoData’
show,cghExSet: no visible global function definition for
  ‘experimentData’
show,cghExSet: no visible global function definition for ‘annotation’
Undefined global functions or variables:
  annotation assayDataElement assayDataNew dims experimentData exprs
  featureNames phenoData selectSome storageMode
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-data-experiment/meat/Neve2006.Rcheck/00check.log’
for details.


Neve2006.Rcheck/00install.out:

* installing *source* package ‘Neve2006’ ...
** 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 (Neve2006)

Neve2006.Rcheck/Neve2006-Ex.timings:

nameusersystemelapsed
cghExSet-class1.0200.0081.027
logRatios0.0630.0000.074
neveCGHmatch1.0290.0031.040