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Package 603/631HostnameOS / ArchBUILDCHECKBUILD BIN
triform 1.1.0
Tony Håndstad Developer
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/triform
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: triform
Version: 1.1.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings triform_1.1.0.tar.gz
StartedAt: 2013-01-16 06:47:43 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 06:49:04 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 80.6 seconds
RetCode: 0
Status:  OK 
CheckDir: triform.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/triform.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘triform/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘triform’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘triform’ 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
* 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
findForms1Replicate: no visible binding for global variable ‘CVG.NAMES’
findForms1Replicate: no visible binding for global variable ‘CVG’
findForms1Replicate: no visible binding for global variable
  ‘IS.CONTROL’
findForms1Replicate: no visible binding for global variable ‘IS.CENTER’
findForms1Replicate: no visible binding for global variable ‘IS.REP1’
findForms1Replicate: no visible binding for global variable ‘IS.LEFT’
findForms1Replicate: no visible binding for global variable ‘IS.RIGHT’
findForms1Replicate: no visible binding for '<<-' assignment to
  ‘CENTER.CVG’
findForms1Replicate: no visible binding for global variable
  ‘CENTER.CVG’
findForms1Replicate: no visible binding for global variable ‘SIZES’
findForms2Replicates: no visible binding for global variable
  ‘CVG.NAMES’
findForms2Replicates: no visible binding for global variable ‘CVG’
findForms2Replicates: no visible binding for global variable
  ‘IS.CONTROL’
findForms2Replicates: no visible binding for global variable
  ‘IS.CENTER’
findForms2Replicates: no visible binding for global variable ‘IS.LEFT’
findForms2Replicates: no visible binding for global variable ‘IS.REP1’
findForms2Replicates: no visible binding for global variable ‘IS.RIGHT’
findForms2Replicates: no visible binding for global variable ‘IS.REP2’
findForms2Replicates: no visible binding for '<<-' assignment to
  ‘CENTER.CVG’
findForms2Replicates: no visible binding for global variable
  ‘CENTER.CVG’
findForms2Replicates: no visible binding for global variable ‘SIZES’
makeChromosomeCoverFiles: no visible binding for global variable ‘rd’
mergeChromosomeCoverFiles: no visible binding for global variable
  ‘covers’
test.chr: no visible binding for global variable ‘MIN.Z’
test.chr: no visible binding for global variable ‘MIN.SHIFT’
test.chr: no visible binding for global variable ‘MIN.WIDTH’
test.chr: no visible binding for '<<-' assignment to ‘PEAKS’
test.chr: no visible binding for '<<-' assignment to ‘PEAK.INFO’
test.chr: no visible binding for '<<-' assignment to ‘CENTER.CVG’
test.chr: no visible binding for '<<-' assignment to ‘N.PEAKS’
test.chr: no visible binding for global variable ‘TARGET.NAMES’
test.chr: no visible binding for global variable ‘PEAKS’
test.chr: no visible binding for global variable ‘PEAK.INFO’
test.chr: no visible binding for global variable ‘CENTER.CVG’
test.chr: no visible binding for global variable ‘CVG.NAMES’
test.chr: no visible binding for global variable ‘DIRECTIONS’
test.chr: no visible binding for global variable ‘IS.REP2’
test.chr: no visible binding for '<<-' assignment to ‘min.er’
test.chr: no visible binding for global variable ‘MIN.QUANT’
test.chr: no visible binding for global variable ‘min.er’
test.chr: no visible binding for global variable ‘FLANK.DELTA’
test.chr: no visible binding for '<<-' assignment to ‘type.delta’
test.chr: no visible binding for global variable ‘CHR’
test.chr: no visible binding for global variable ‘PEAK.START’
test.chr: no visible binding for global variable ‘PEAK.END’
test.chr: no visible binding for global variable ‘PEAK.FORM’
test.chr: no visible binding for global variable ‘N.PEAKS’
test.genome: no visible binding for global variable ‘MIN.Z’
test.genome: no visible binding for global variable ‘MIN.SHIFT’
test.genome: no visible binding for global variable ‘MIN.WIDTH’
test.genome: no visible binding for global variable ‘CHRS’
test.genome: no visible binding for '<<-' assignment to ‘INFO’
test.genome: no visible binding for global variable ‘INFO’
test.genome: no visible binding for global variable ‘N.PEAKS’
test.init: no visible binding for '<<-' assignment to ‘CHR’
test.init: no visible binding for global variable ‘CHR’
test.init: no visible binding for '<<-' assignment to ‘CVG’
test.init: no visible binding for '<<-' assignment to ‘SIZES’
test.init: no visible binding for global variable ‘N.TYPES’
test.init: no visible binding for global variable ‘SUMCVG.NAMES’
test.init: no visible binding for global variable ‘SIZES’
test.init: no visible binding for global variable ‘chrcovers’
test.init: no visible binding for global variable ‘N.LOCS’
test.init: no visible binding for global variable ‘N.DIRLOCS’
test.init: no visible binding for global variable ‘IS.CONTROL’
test.init: no visible binding for global variable ‘IS.CENTER’
test.init: no visible binding for global variable ‘CVG’
test.init: no visible binding for global variable ‘FLANK.DELTA.PAD’
test.init: no visible binding for global variable ‘FLANK.DELTA’
test.init: no visible binding for global variable ‘CVG.NAMES’
triform: no visible binding for '<<-' assignment to ‘SUMCVG.NAMES’
triform: no visible binding for '<<-' assignment to ‘TARGET.NAMES’
triform: no visible binding for '<<-' assignment to ‘MIN.Z’
triform: no visible binding for global variable ‘MAX.P’
triform: no visible binding for '<<-' assignment to ‘FLANK.DELTA.PAD’
triform: no visible binding for global variable ‘FLANK.DELTA’
triform: no visible binding for '<<-' assignment to ‘N.TYPES’
triform: no visible binding for global variable ‘SUMCVG.NAMES’
triform: no visible binding for '<<-' assignment to ‘TYPES’
triform: no visible binding for global variable ‘N.TYPES’
triform: no visible binding for '<<-' assignment to ‘DIRECTIONS’
triform: no visible binding for '<<-' assignment to ‘N.DIRS’
triform: no visible binding for global variable ‘DIRECTIONS’
triform: no visible binding for '<<-' assignment to ‘LOCATIONS’
triform: no visible binding for '<<-' assignment to ‘N.LOCS’
triform: no visible binding for global variable ‘LOCATIONS’
triform: no visible binding for '<<-' assignment to ‘N.DIRLOCS’
triform: no visible binding for global variable ‘N.DIRS’
triform: no visible binding for global variable ‘N.LOCS’
triform: no visible binding for '<<-' assignment to ‘DIRECTION’
triform: no visible binding for '<<-' assignment to ‘LOCATION’
triform: no visible binding for '<<-' assignment to ‘TYPE’
triform: no visible binding for global variable ‘TYPES’
triform: no visible binding for global variable ‘N.DIRLOCS’
triform: no visible binding for '<<-' assignment to ‘CVG.NAMES’
triform: no visible binding for global variable ‘TYPE’
triform: no visible binding for global variable ‘DIRECTION’
triform: no visible binding for global variable ‘LOCATION’
triform: no visible binding for '<<-' assignment to ‘IS.LEFT’
triform: no visible binding for global variable ‘CVG.NAMES’
triform: no visible binding for '<<-' assignment to ‘IS.RIGHT’
triform: no visible binding for '<<-' assignment to ‘IS.CENTER’
triform: no visible binding for '<<-' assignment to ‘IS.REP1’
triform: no visible binding for '<<-' assignment to ‘IS.REP2’
triform: no visible binding for '<<-' assignment to ‘IS.CONTROL’
triform: no visible binding for global variable ‘TARGET.NAMES’
triform : <anonymous>: no visible binding for global variable
  ‘CVG.NAMES’
triform: no visible binding for global variable ‘MIN.Z’
triform: no visible binding for global variable ‘MIN.SHIFT’
triform: no visible binding for global variable ‘MIN.WIDTH’
triform: no visible binding for global variable ‘CHRS’
triform: no visible binding for global variable ‘COVER.PATH’
triform: no visible binding for global variable ‘OUTPUT.PATH’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/triform.Rcheck/00check.log’
for details.

triform.Rcheck/00install.out:

* installing *source* package ‘triform’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘triform.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (triform)

triform.Rcheck/triform-Ex.timings:

nameusersystemelapsed
preprocess0.0120.0000.010
triform-package0.0120.0000.010
triform0.0120.0000.012