BioC 2.12: CHECK report for FunciSNP on george2

Package: FunciSNP

Version: 1.2.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings FunciSNP_1.2.0.tar.gz

StartedAt: 2013-10-09 01:50:07 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:01:15 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 668.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FunciSNP.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/FunciSNP.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.0’
* 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 ... [62s/63s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated 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
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 ... WARNING
Codoc mismatches from documentation object 'getFSNPs':
getFSNPs
  Code: function(snp.regions.file, bio.features.loc = NULL,
                 built.in.biofeatures = TRUE, par.threads =
                 detectCores()/2, verbose = par.threads < 2, method.p =
                 "BH", search.window = 2e+05, primary.server = "ebi")
  Docs: function(snp.regions.file, bio.features.loc = NULL,
                 built.in.biofeatures = TRUE, par.threads =
                 detectCores()/2, verbose = par.threads < 2, method.p =
                 "BH", search.window = 2e+05)
  Argument names in code not in docs:
    primary.server

* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
FunciSNP-package 7.057  0.108   7.176
FunciSNPtable    5.061  0.372   5.448
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-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	1.060	0.004	1.064
FunciSNP-package	7.057	0.108	7.176
FunciSNPAnnotateSummary	1.388	0.100	1.507
FunciSNPbed	1.512	0.012	1.543
FunciSNPidsFromSummary	0.004	0.000	0.005
FunciSNPplot	4.420	0.068	4.504
FunciSNPsummaryOverlaps	1.468	0.076	1.543
FunciSNPtable	5.061	0.372	5.448
TSList-class	0.028	0.000	0.028
TagSNP-class	0.036	0.000	0.033
getFSNPs	1.500	0.156	1.676