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CHECK report for FlowRepositoryR on merida2

This page was generated on 2018-10-17 08:54:44 -0400 (Wed, 17 Oct 2018).

Package 516/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowRepositoryR 1.12.0
Josef Spidlen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/FlowRepositoryR
Branch: RELEASE_3_7
Last Commit: 426f804
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running 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
###
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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.



Installation output

FlowRepositoryR.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output

FlowRepositoryR.Rcheck/tests/runTests.Rout


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 

Example timings

FlowRepositoryR.Rcheck/FlowRepositoryR-Ex.timings

nameusersystemelapsed
attachmentProxy-class0.1140.0150.484
download-methods0.1080.0181.444
fcsProxy-class0.0380.0040.280
fileProxy-class0.0350.0040.274
flowRep.get0.0250.0020.259
flowRep.ls0.0200.0050.294
flowRep.search0.0120.0011.770
flowRep.submitGeneStatus0.0060.0000.006
flowRep.submitImpcResults0.0060.0010.006
flowRepData-class0.0320.0020.270
flowRepOrganization-class0.0220.0010.258
forgetFlowRepositoryCredentials0.0020.0000.002
getFlowRepositoryURL0.0000.0000.001
id-methods0.0420.0020.254
ilarCodeDescription0.0010.0000.002
impcCodeDescription0.0020.0000.001
impcResultsCopy-methods0.0390.0020.246
is.downloaded-methods0.0420.0020.298
listKnownIlarCodes0.0020.0000.002
setFlowRepositoryCredentials0.0020.0000.002
setFlowRepositoryURL0.0030.0000.004