Package: FunciSNP

Version: 1.24.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:FunciSNP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings FunciSNP_1.24.0.tar.gz

StartedAt: 2018-10-16 00:30:11 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:34:27 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 255.8 seconds

RetCode: 0

Status:  OK

CheckDir: FunciSNP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:FunciSNP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings FunciSNP_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/FunciSNP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-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 ‘1.24.0’
* 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 ‘FunciSNP’ can be installed ... 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 ... 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 global function definition for 'data'
AnnotateSummary: no visible binding for global variable
  'TSS.human.GRCh37'
AnnotateSummary: no visible binding for global variable 'lincRNA'
AnnotateSummary: no visible binding for global variable 'refseqgenes'
ChiSquaredPvalue : <anonymous>: no visible global function definition
  for 'fisher.test'
ChiSquaredPvalue: no visible global function definition for 'p.adjust'
CreateCorrelatedSNPs: no visible global function definition for
  'timestamp'
CreatePopulations: no visible global function definition for
  'read.delim'
FunciSNPbed: no visible global function definition for 'write.table'
FunciSNPplot: no visible binding for global variable 'R.squared'
FunciSNPplot: no visible global function definition for 'pdf'
FunciSNPplot: no visible global function definition for 'plot'
FunciSNPplot: no visible global function definition for 'abline'
FunciSNPplot: no visible global function definition for 'text'
FunciSNPplot: no visible global function definition for 'dev.off'
FunciSNPplot: no visible binding for global variable 'r.2'
FunciSNPplot: no visible binding for global variable
  'distance.from.tag'
FunciSNPplot: no visible global function definition for 'as.dendrogram'
FunciSNPplot: no visible global function definition for 'hclust'
FunciSNPplot: no visible global function definition for 'dist'
FunciSNPplot: no visible global function definition for
  'order.dendrogram'
FunciSNPplot: no visible binding for global variable 'sig'
FunciSNPplot: no visible binding for global variable 'variable'
FunciSNPplot: no visible binding for global variable 'value'
ReadRegionsFile: no visible global function definition for 'read.table'
bedColors: no visible global function definition for 'colorRampPalette'
bedColors: no visible global function definition for 'col2rgb'
bedColors: no visible global function definition for 'png'
bedColors: no visible global function definition for 'box'
bedColors: no visible global function definition for 'par'
bedColors: no visible global function definition for 'axis'
bedColors: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  R.squared TSS.human.GRCh37 abline as.dendrogram axis box col2rgb
  colorRampPalette data dev.off dist distance.from.tag fisher.test
  hclust lincRNA order.dendrogram p.adjust par pdf plot png r.2
  read.delim read.table refseqgenes sig text timestamp value variable
  write.table
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off",
             "pdf", "png")
  importFrom("graphics", "abline", "axis", "box", "par", "plot", "text")
  importFrom("stats", "as.dendrogram", "dist", "fisher.test", "hclust",
             "order.dendrogram", "p.adjust")
  importFrom("utils", "data", "read.delim", "read.table", "timestamp",
             "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/FunciSNP.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL FunciSNP
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘FunciSNP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.000	0.000	0.002
FunciSNP-package	1.000	0.024	1.025
FunciSNPAnnotateSummary	0.948	0.032	0.982
FunciSNPbed	0.216	0.040	0.254
FunciSNPidsFromSummary	0.000	0.000	0.001
FunciSNPplot	1.744	0.012	1.759
FunciSNPsummaryOverlaps	0.152	0.024	0.174
FunciSNPtable	1.760	0.152	1.916
TSList-class	0.000	0.000	0.001
TagSNP-class	0.000	0.000	0.001
getFSNPs	0.160	0.004	0.165