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BioC experimental data: CHECK report for RnBeads.hg19 on morelia

This page was generated on 2015-11-25 16:26:43 -0800 (Wed, 25 Nov 2015).

Package 208/258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads.hg19 1.3.0
RnBeadsAnnotationCreator
Snapshot Date: 2015-11-25 07:17:28 -0800 (Wed, 25 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RnBeads.hg19
Last Changed Rev: 3462 / Revision: 3504
Last Changed Date: 2015-10-13 13:20:35 -0700 (Tue, 13 Oct 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 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: RnBeads.hg19
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads.hg19_1.3.0.tar.gz
StartedAt: 2015-11-25 11:10:23 -0800 (Wed, 25 Nov 2015)
EndedAt: 2015-11-25 11:12:43 -0800 (Wed, 25 Nov 2015)
EllapsedTime: 140.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RnBeads.hg19.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 RnBeads.hg19_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/RnBeads.hg19.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads.hg19/DESCRIPTION’ ... OK
* this is package ‘RnBeads.hg19’ version ‘1.3.0’
* 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 ‘RnBeads.hg19’ can be installed ... [7s/10s] OK
* checking installed package size ... NOTE
  installed size is 73.7Mb
  sub-directories of 1Mb or more:
    data  73.7Mb
* 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
Package in Depends field not imported from: ‘GenomicRanges’
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘rnb.set.example’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
  Error : .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details:
    call: initialize(value, ...)
    error: attempt to apply non-function
  Failed with error:  'package 'TxDb.Hsapiens.UCSC.hg19.knownGene' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'RnBeads'
  Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/RnBeads.hg19.Rcheck/00check.log’
for details.


RnBeads.hg19.Rcheck/00install.out:

* installing *source* package ‘RnBeads.hg19’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RnBeads.hg19)