BioC 3.6: CHECK report for FlowRepositoryR on veracruz1

Package: FlowRepositoryR

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FlowRepositoryR_1.9.0.tar.gz

StartedAt: 2017-08-16 03:08:02 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:08:43 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 41.1 seconds

RetCode: 0

Status:  OK

CheckDir: FlowRepositoryR.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 FlowRepositoryR_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/FlowRepositoryR.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 ‘FlowRepositoryR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FlowRepositoryR’ version ‘1.9.0’
* 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 ‘FlowRepositoryR’ 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 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
attachmentProxy: no visible global function definition for ‘new’
fcsProxy: no visible global function definition for ‘new’
flowRep.search: no visible global function definition for ‘is’
flowRepData: no visible global function definition for ‘new’
flowRepOrganization: no visible global function definition for ‘new’
attachments<-,flowRepData: no visible global function definition for
  ‘is’
fcs.files<-,flowRepData: no visible global function definition for ‘is’
impc.experiments<-,flowRepData: no visible global function definition
  for ‘is’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... 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 ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/FlowRepositoryR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
attachmentProxy-class	0.181	0.008	0.505
download-methods	0.387	0.012	1.951
fcsProxy-class	0.031	0.001	0.273
fileProxy-class	0.029	0.002	0.250
flowRep.get	0.025	0.001	0.256
flowRep.ls	0.017	0.003	0.306
flowRep.search	0.011	0.002	0.332
flowRep.submitGeneStatus	0.003	0.000	0.004
flowRep.submitImpcResults	0.003	0.000	0.003
flowRepData-class	0.029	0.002	0.269
flowRepOrganization-class	0.017	0.001	0.248
forgetFlowRepositoryCredentials	0.001	0.000	0.000
getFlowRepositoryURL	0.001	0.000	0.001
id-methods	0.037	0.002	0.272
ilarCodeDescription	0.001	0.000	0.001
impcCodeDescription	0.001	0.000	0.001
impcResultsCopy-methods	0.038	0.002	0.276
is.downloaded-methods	0.041	0.001	0.295
listKnownIlarCodes	0.001	0.000	0.001
setFlowRepositoryCredentials	0.001	0.000	0.001
setFlowRepositoryURL	0.001	0.000	0.001