triform 1.17.0
Thomas Carroll
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/triform | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings triform_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/triform.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.17.0’
* 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 ‘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.
* 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 global function definition for ‘as’
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 global function definition for ‘as’
findForms2Replicates: no visible binding for global variable ‘SIZES’
makeChromosomeCoverFiles: no visible binding for global variable ‘rd’
makeRangedData: no visible global function definition for ‘read.delim’
makeRangedData: no visible global function definition for ‘as’
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 global function definition for ‘pnorm’
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 : <anonymous>: no visible global function definition for ‘ccf’
test.chr : <anonymous>: no visible binding for global variable ‘lag’
test.chr : <anonymous>: no visible binding for global variable ‘acf’
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 global function definition for ‘flush.console’
test.genome: no visible binding for global variable ‘INFO’
test.genome: no visible binding for global variable ‘N.PEAKS’
test.genome: no visible global function definition for ‘write.table’
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’
test.init : <anonymous>: no visible global function definition for
‘Rle’
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 global function definition for ‘qnorm’
triform: no visible binding for global variable ‘MAX.P’
triform: no visible binding for '<<-' assignment to ‘FLANK.DELTA.PAD’
triform: no visible global function definition for ‘Rle’
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’
Undefined global functions or variables:
CENTER.CVG CHR CHRS COVER.PATH CVG CVG.NAMES DIRECTION DIRECTIONS
FLANK.DELTA FLANK.DELTA.PAD INFO IS.CENTER IS.CONTROL IS.LEFT IS.REP1
IS.REP2 IS.RIGHT LOCATION LOCATIONS MAX.P MIN.QUANT MIN.SHIFT
MIN.WIDTH MIN.Z N.DIRLOCS N.DIRS N.LOCS N.PEAKS N.TYPES OUTPUT.PATH
PEAK.END PEAK.FORM PEAK.INFO PEAK.START PEAKS Rle SIZES SUMCVG.NAMES
TARGET.NAMES TYPE TYPES acf as ccf chrcovers covers flush.console lag
min.er pnorm qnorm rd read.delim write.table
Consider adding
importFrom("methods", "as")
importFrom("stats", "acf", "ccf", "lag", "pnorm", "qnorm")
importFrom("utils", "flush.console", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/triform.Rcheck/00check.log’
for details.