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

This page was generated on 2015-08-22 17:45:03 -0700 (Sat, 22 Aug 2015).

Package 202/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads.hg19 1.1.4
RnBeadsAnnotationCreator
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RnBeads.hg19
Last Changed Rev: 3384 / Revision: 3391
Last Changed Date: 2015-08-19 13:58:42 -0700 (Wed, 19 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS YES, new version is higher than in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: RnBeads.hg19
Version: 1.1.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads.hg19_1.1.4.tar.gz
StartedAt: 2015-08-22 09:54:21 -0700 (Sat, 22 Aug 2015)
EndedAt: 2015-08-22 09:57:49 -0700 (Sat, 22 Aug 2015)
EllapsedTime: 207.6 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_1.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/RnBeads.hg19.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 ‘RnBeads.hg19/DESCRIPTION’ ... OK
* this is package ‘RnBeads.hg19’ version ‘1.1.4’
* 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 ... [10s/12s] 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-3.2-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)