BioC 2.13: CHECK report for FunciSNP on perceval

Package: FunciSNP

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch FunciSNP_1.4.0.tar.gz

StartedAt: 2014-04-05 01:21:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:30:57 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 579.0 seconds

RetCode: 0

Status:  OK

CheckDir: FunciSNP.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/FunciSNP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FunciSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FunciSNP’ version ‘1.4.0’
* 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 ‘FunciSNP’ can be installed ... [54s/56s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘AnnotationDbi’ ‘GenomicRanges’ ‘org.Hs.eg.db’
  All declared Imports should be used.
‘:::’ calls which should be ‘::’:
  ‘Rsamtools:::close.TabixFile’ ‘Rsamtools:::isOpen’
  ‘Rsamtools:::open.TabixFile’
  See the note in ?`:::` about the use of this operator.
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
AnnotateSummary: no visible binding for '<<-' assignment to ‘txdb’
AnnotateSummary: no visible binding for global variable ‘txdb’
FunciSNPplot: no visible binding for global variable ‘R.squared’
FunciSNPplot: no visible binding for global variable ‘r.2’
FunciSNPplot: no visible binding for global variable
  ‘distance.from.tag’
FunciSNPplot: no visible binding for global variable ‘variable’
FunciSNPplot: no visible binding for global variable ‘sig’
FunciSNPplot: no visible binding for global variable ‘value’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘FunciSNP_vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [45s/47s] 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/FunciSNP.Rcheck/00check.log’
for details.

* installing *source* package ‘FunciSNP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FunciSNP)

name	user	system	elapsed
CorrelatedSNPs-class	0.917	0.014	0.978
FunciSNP-package	2.792	0.154	3.114
FunciSNPAnnotateSummary	1.033	0.148	1.225
FunciSNPbed	1.899	0.145	2.129
FunciSNPidsFromSummary	0.002	0.004	0.005
FunciSNPplot	3.397	0.291	3.852
FunciSNPsummaryOverlaps	1.930	0.115	2.094
FunciSNPtable	3.531	0.479	4.209
TSList-class	0.016	0.013	0.033
TagSNP-class	0.016	0.009	0.028
getFSNPs	1.072	0.201	1.353