Package: FlowRepositoryR

Version: 1.18.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:FlowRepositoryR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings FlowRepositoryR_1.18.0.tar.gz

StartedAt: 2020-04-15 03:00:47 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:01:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 36.2 seconds

RetCode: 0

Status:  OK

CheckDir: FlowRepositoryR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:FlowRepositoryR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings FlowRepositoryR_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/FlowRepositoryR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/FlowRepositoryR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL FlowRepositoryR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘FlowRepositoryR’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FlowRepositoryR)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 /home/biocbuild/bbs-3.10-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.


RUNIT TEST PROTOCOL -- Wed Apr 15 03:01:20 2020 
*********************************************** 
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 
  1.900   0.152   4.463 

name	user	system	elapsed
attachmentProxy-class	0.128	0.008	0.354
download-methods	0.328	0.064	1.694
fcsProxy-class	0.092	0.016	0.290
fileProxy-class	0.144	0.016	0.337
flowRep.get	0.080	0.000	0.267
flowRep.ls	0.056	0.012	0.390
flowRep.search	0.076	0.000	0.303
flowRep.submitGeneStatus	0.000	0.000	0.002
flowRep.submitImpcResults	0.000	0.000	0.001
flowRepData-class	0.076	0.000	0.251
flowRepOrganization-class	0.060	0.020	0.278
forgetFlowRepositoryCredentials	0.000	0.000	0.001
getFlowRepositoryURL	0	0	0
id-methods	0.096	0.008	0.335
ilarCodeDescription	0	0	0
impcCodeDescription	0	0	0
impcResultsCopy-methods	0.092	0.020	0.340
is.downloaded-methods	0.108	0.004	0.298
listKnownIlarCodes	0	0	0
setFlowRepositoryCredentials	0	0	0
setFlowRepositoryURL	0	0	0