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BioC 2.12: CHECK report for MBCB on moscato2

This page was generated on 2013-10-09 09:38:49 -0700 (Wed, 09 Oct 2013).

Package 393/671HostnameOS / ArchBUILDCHECKBUILD BIN
MBCB 1.14.0
Jeff Allen
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/MBCB
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: MBCB
Version: 1.14.0
Command: rm -rf MBCB.buildbin-libdir && mkdir MBCB.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MBCB.buildbin-libdir MBCB_1.14.0.tar.gz >MBCB-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=MBCB.buildbin-libdir --install="check:MBCB-install.out" --force-multiarch --no-vignettes --timings MBCB_1.14.0.tar.gz && mv MBCB.buildbin-libdir/* MBCB.Rcheck/ && rmdir MBCB.buildbin-libdir
StartedAt: 2013-10-09 02:55:52 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:56:46 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 54.2 seconds
RetCode: 0
Status:  OK  
CheckDir: MBCB.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/MBCB.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MBCB/DESCRIPTION' ... OK
* this is package 'MBCB' version '1.14.0'
* 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 'MBCB' can be installed ... OK
* checking installed package size ... OK
* 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bg.mcmc: no visible binding for global variable 'obsbead'
bg.mcmc: no visible binding for global variable 'obsnc'
esttruesig: no visible binding for global variable 'obsbead'
esttruesig: no visible binding for global variable 'truesignal'
liksig: no visible binding for global variable 'obsbead'
liksig.all: no visible binding for global variable 'obsbead'
liksig.all: no visible binding for global variable 'obsnc'
liksig.gamnoise: no visible binding for global variable 'nbead'
liksig.gamnoise: no visible binding for global variable 'sortedObsbead'
liksigall.gamnoise: no visible binding for global variable 'obsnc'
mbcb.correct: no visible binding for '<<-' assignment to 'trialNames'
mbcb.correct: no visible binding for '<<-' assignment to 'n.array'
mbcb.correct: no visible binding for '<<-' assignment to 'truesignal'
mbcb.correct: no visible binding for '<<-' assignment to 'truenoise'
mbcb.correct: no visible binding for '<<-' assignment to 'obsbead'
mbcb.correct: no visible binding for '<<-' assignment to 'obsnc'
mbcb.correct: no visible binding for '<<-' assignment to 'nbead'
mbcb.correct: no visible binding for global variable 'n.array'
mbcb.correct: no visible binding for global variable 'mbcbPB'
mbcb.correct: no visible binding for global variable 'obsbead'
mbcb.correct: no visible binding for '<<-' assignment to 'nnc'
mbcb.correct: no visible binding for '<<-' assignment to
  'sortedObsbead'
mbcb.correct: no visible binding for global variable 'obsnc'
mbcb.correct: no visible binding for global variable 'nbead'
mbcb.correct: no visible binding for global variable 'nnc'
mbcb.correct: no visible binding for global variable 'sortedObsbead'
mbcb.gui : actions.norm: no visible binding for global variable
  'main.nb'
mbcb.gui : normalizeData: no visible binding for global variable
  'main.nb'
mbcb.gui : exportData: no visible binding for global variable 'main.nb'
mbcb.gui : exportData : <anonymous>: no visible binding for global
  variable 'outFile'
mbcb.gui : exportData : setOut: no visible binding for '<<-' assignment
  to 'outFile'
mbcb.gui : exportData : setOut: no visible binding for global variable
  'outFile'
mbcb.gui : exportData : eval: no visible binding for '<<-' assignment
  to 'mbcbPB'
mbcb.gui : removeItem: no visible binding for global variable
  'importTab.f.dataList'
mbcb.gui: no visible binding for '<<-' assignment to 'main.nb'
mbcb.gui: no visible binding for global variable 'main.nb'
mbcb.main: no visible binding for global variable 'n.array'
mbcb.main: no visible binding for '<<-' assignment to 'bgCorrSig'
mbcb.main: no visible binding for global variable 'bgCorrSig'
mbcb.parseFile: no visible binding for global variable 'mbcbPB'
mbcb.parseFile: no visible binding for '<<-' assignment to 'types'
mbcb.parseFile: no visible binding for global variable 'types'
mbcb.parseFile: no visible binding for '<<-' assignment to 'sig2'
mbcb.parseFile: no visible binding for global variable 'sig2'
printMBCBOutput: no visible binding for '<<-' assignment to 'dete'
printMBCBOutput: no visible binding for global variable 'mbcbPB'
printMBCBOutput: no visible binding for global variable 'trialNames'
truesig: no visible binding for global variable 'obsbead'
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [3s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/MBCB.Rcheck/00check.log'
for details.

MBCB.Rcheck/00install.out:


install for i386

* installing *source* package 'MBCB' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MBCB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MBCB' as MBCB_1.14.0.zip
* DONE (MBCB)