Package: FlowRepositoryR

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowRepositoryR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowRepositoryR_1.12.0.tar.gz

StartedAt: 2018-10-16 21:25:19 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:26:02 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 43.5 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 --install=check:FlowRepositoryR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowRepositoryR_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/FlowRepositoryR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.12.0’
* 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 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-3.7-bioc/meat/FlowRepositoryR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FlowRepositoryR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘FlowRepositoryR’ ...
** R
** 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 (FlowRepositoryR)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("FlowRepositoryR")
File about.txt downloaded.
File GvHD2.fcs downloaded.
Downloading to /Users/biocbuild/bbs-3.7-bioc/meat/FlowRepositoryR.Rcheck/tests/FR-FCM-ZZJ7 
File GvHD2.fcs is downloaded already.
File GvHD8.fcs downloaded.
File about.txt is downloaded already.
File ExampleGate.png downloaded.
Download finished.
Loading required package: bitops


RUNIT TEST PROTOCOL -- Tue Oct 16 21:25:55 2018 
*********************************************** 
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FlowRepositoryR RUnit Tests - 16 test functions, 0 errors, 0 failures
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.122   0.130   6.553 

name	user	system	elapsed
attachmentProxy-class	0.114	0.015	0.484
download-methods	0.108	0.018	1.444
fcsProxy-class	0.038	0.004	0.280
fileProxy-class	0.035	0.004	0.274
flowRep.get	0.025	0.002	0.259
flowRep.ls	0.020	0.005	0.294
flowRep.search	0.012	0.001	1.770
flowRep.submitGeneStatus	0.006	0.000	0.006
flowRep.submitImpcResults	0.006	0.001	0.006
flowRepData-class	0.032	0.002	0.270
flowRepOrganization-class	0.022	0.001	0.258
forgetFlowRepositoryCredentials	0.002	0.000	0.002
getFlowRepositoryURL	0.000	0.000	0.001
id-methods	0.042	0.002	0.254
ilarCodeDescription	0.001	0.000	0.002
impcCodeDescription	0.002	0.000	0.001
impcResultsCopy-methods	0.039	0.002	0.246
is.downloaded-methods	0.042	0.002	0.298
listKnownIlarCodes	0.002	0.000	0.002
setFlowRepositoryCredentials	0.002	0.000	0.002
setFlowRepositoryURL	0.003	0.000	0.004