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BioC experimental data: CHECK report for RnBeads.mm9 on moscato2

This page was generated on 2015-10-07 16:21:31 -0700 (Wed, 07 Oct 2015).

Package 200/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads.mm9 1.0.0
Fabian Mueller
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/RnBeads.mm9
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 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 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: RnBeads.mm9
Version: 1.0.0
Command: rm -rf RnBeads.mm9.buildbin-libdir RnBeads.mm9.Rcheck && mkdir RnBeads.mm9.buildbin-libdir RnBeads.mm9.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RnBeads.mm9.buildbin-libdir RnBeads.mm9_1.0.0.tar.gz >RnBeads.mm9.Rcheck\00install.out 2>&1 && cp RnBeads.mm9.Rcheck\00install.out RnBeads.mm9-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RnBeads.mm9.buildbin-libdir --install="check:RnBeads.mm9-install.out" --force-multiarch --no-vignettes --timings RnBeads.mm9_1.0.0.tar.gz
StartedAt: 2015-10-07 11:45:18 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 12:10:23 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 1505.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RnBeads.mm9.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   rm -rf RnBeads.mm9.buildbin-libdir RnBeads.mm9.Rcheck && mkdir RnBeads.mm9.buildbin-libdir RnBeads.mm9.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RnBeads.mm9.buildbin-libdir RnBeads.mm9_1.0.0.tar.gz >RnBeads.mm9.Rcheck\00install.out 2>&1 && cp RnBeads.mm9.Rcheck\00install.out RnBeads.mm9-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RnBeads.mm9.buildbin-libdir --install="check:RnBeads.mm9-install.out" --force-multiarch --no-vignettes --timings RnBeads.mm9_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-data-experiment/meat/RnBeads.mm9.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RnBeads.mm9/DESCRIPTION' ... OK
* this is package 'RnBeads.mm9' version '1.0.0'
* 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 whether package 'RnBeads.mm9' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 78.2Mb
  sub-directories of 1Mb or more:
    data  78.1Mb
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Missing link or links in documentation object 'mm9.Rd':
  'rnb.get.assemblies' 'rnb.get.chromosomes' 'rnb.get.annotation'
  'rnb.set.annotation' 'rnb.get.mapping' 'rnb.annotation.size'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'analysis.options' 'rnb.set.example' 'sites' 'regions'
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                    old_size new_size compress
  example.rrbs.mm9.blood.skin.RData    1.9Mb    1.1Mb       xz
  mm9.CpG.RData                       71.2Mb   44.1Mb       xz
  mm9.regions.RData                    5.0Mb    1.9Mb       xz
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  'E:/biocbld/bbs-3.1-data-experiment/meat/RnBeads.mm9.Rcheck/00check.log'
for details.


RnBeads.mm9.Rcheck/00install.out:


install for i386

* installing *source* package 'RnBeads.mm9' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'RnBeads.mm9' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'RnBeads.mm9' as RnBeads.mm9_1.0.0.zip
* DONE (RnBeads.mm9)