Package: triform

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings triform_1.20.0.tar.gz

StartedAt: 2018-04-12 10:30:10 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:31:11 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 60.7 seconds

RetCode: 0

Status:  OK

CheckDir: triform.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings triform_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/triform.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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-3.6-bioc/meat/triform.Rcheck/00check.log’
for details.

* 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
* DONE (triform)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("triform") || stop("unable to load triform")
Loading required package: triform
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: yaml
[1] TRUE
> BiocGenerics:::testPackage("triform")
Current directory:/Users/biocbuild/bbs-3.6-bioc/meat/triform.Rcheck/tests


RUNIT TEST PROTOCOL -- Thu Apr 12 10:31:07 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
triform RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.001   0.086   2.099 

name	user	system	elapsed
preprocess	0.001	0.000	0.001
triform-package	0.000	0.000	0.001
triform	0.001	0.000	0.002