BioC 2.13: CHECK report for triform on moscato1

Package: triform

Version: 1.4.0

Command: rm -rf triform.buildbin-libdir && mkdir triform.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=triform.buildbin-libdir triform_1.4.0.tar.gz >triform-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=triform.buildbin-libdir --install="check:triform-install.out" --force-multiarch --no-vignettes --timings triform_1.4.0.tar.gz && mv triform.buildbin-libdir/* triform.Rcheck/ && rmdir triform.buildbin-libdir

StartedAt: 2014-04-05 07:14:29 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 07:16:05 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 96.5 seconds

RetCode: 0

Status:  OK

CheckDir: triform.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/triform.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'triform/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'triform' version '1.4.0'
* 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 whether package 'triform' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'IRanges' 'yaml'
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [3s]
 [4s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [3s]
 [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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/triform.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'triform' ...
** R
** 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 'triform' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'triform' as triform_1.4.0.zip
* DONE (triform)

name	user	system	elapsed
preprocess	0	0	0
triform-package	0	0	0
triform	0	0	0

name	user	system	elapsed
preprocess	0	0	0
triform-package	0	0	0
triform	0	0	0