BioC 3.5: CHECK report for ImmuneSpaceR on veracruz2

Package: ImmuneSpaceR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ImmuneSpaceR_1.4.0.tar.gz

StartedAt: 2017-10-02 04:31:31 -0400 (Mon, 02 Oct 2017)

EndedAt: 2017-10-02 04:32:49 -0400 (Mon, 02 Oct 2017)

EllapsedTime: 78.5 seconds

RetCode: 0

Status:  OK

CheckDir: ImmuneSpaceR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ImmuneSpaceR_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ImmuneSpaceR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ImmuneSpaceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ImmuneSpaceR’ 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 ... 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 ‘ImmuneSpaceR’ 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
File ‘ImmuneSpaceR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("A .netrc file is required to connect to ImmuneSpace. For more information on how to create one, refer to the Configuration section of the introduction vignette.")

See section ‘Good practice’ in '?.onAttach'.

CreateConnection: no visible global function definition for
  ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ImmuneSpaceR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CreateConnection	0.213	0.009	0.383
ISpalette	0.004	0.001	0.004
ImmuneSpaceConnection-class	0.001	0.000	0.000
check_netrc	0.001	0.000	0.002
loadConnection	0.076	0.004	0.088
template_IS	0.001	0.000	0.001
theme_IS	1.723	0.006	1.780
write_netrc	0.001	0.001	0.001