BioC 3.2: CHECK report for CGHnormaliter on perceval

Package: CGHnormaliter

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGHnormaliter_1.24.0.tar.gz

StartedAt: 2015-10-27 06:12:28 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:15:01 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 152.3 seconds

RetCode: 0

Status:  OK

CheckDir: CGHnormaliter.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGHnormaliter_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CGHnormaliter.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHnormaliter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHnormaliter’ version ‘1.24.0’
* 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 ‘CGHnormaliter’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘CGHbase’ ‘CGHcall’
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.readCghRaw: no visible global function definition for ‘make_cghRaw’
.runCGHcall: no visible global function definition for ‘ExpandCGHcall’
CGHnormaliter: no visible binding for global variable ‘segment’
CGHnormaliter: no visible global function definition for ‘normalize’
CGHnormaliter: no visible global function definition for
  ‘postsegnormalize’
CGHnormaliter.write.table: no visible global function definition for
  ‘segmented’
CGHnormaliter.write.table: no visible global function definition for
  ‘calls’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [99s/99s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
CGHnormaliter 95.807  0.173  96.009
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CGHnormaliter.Rcheck/00check.log’
for details.

* installing *source* package ‘CGHnormaliter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGHnormaliter)

name	user	system	elapsed
CGHnormaliter	95.807	0.173	96.009
CGHnormaliter.write.table	0.659	0.007	0.666