triform 1.6.0
Tony Handstad Developer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/triform | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings triform_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/triform.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.6.0’
* 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 ... [4s/4s] 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
* 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 loading without being on the library search path ... 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 ... [2s/2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [2s/2s]
[2s/2s] 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
‘/home/biocbuild/bbs-2.14-bioc/meat/triform.Rcheck/00check.log’
for details.