BioC 3.4: CHECK report for PanVizGenerator on zin1

Package: PanVizGenerator

Version: 1.1.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PanVizGenerator_1.1.3.tar.gz

StartedAt: 2016-09-20 10:17:43 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 10:21:22 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 218.8 seconds

RetCode: 0

Status:  OK

CheckDir: PanVizGenerator.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PanVizGenerator_1.1.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/PanVizGenerator.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PanVizGenerator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PanVizGenerator’ version ‘1.1.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PanVizGenerator’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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
panviz,character: no visible global function definition for ‘read.csv’
panviz,matrix: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL read.csv
Consider adding
  importFrom("utils", "browseURL", "read.csv")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/PanVizGenerator.Rcheck/00check.log’
for details.

* installing *source* package ‘PanVizGenerator’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘FindMyFriends’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘FindMyFriends’
* DONE (PanVizGenerator)

name	user	system	elapsed
PanVizGenerator	0	0	0
getGO	0	0	0
panviz	0.000	0.000	0.001