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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for GateFinder on nebbiolo1

To the developers/maintainers of the GateFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GateFinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 692/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GateFinder 1.12.0  (landing page)
Nima Aghaeepour
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GateFinder
git_branch: RELEASE_3_13
git_last_commit: fd719d2
git_last_commit_date: 2021-05-19 12:34:27 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GateFinder
Version: 1.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GateFinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GateFinder_1.12.0.tar.gz
StartedAt: 2021-10-14 09:54:42 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:55:41 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 59.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GateFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GateFinder.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GateFinder_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GateFinder.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GateFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GateFinder’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘GateFinder’ 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.GateFinder
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ah2sp: no visible global function definition for ‘CRS’
.ah2sp: no visible global function definition for ‘anglesArc’
.ah2sp: no visible global function definition for ‘Line’
.ah2sp: no visible global function definition for ‘Lines’
.ah2sp: no visible global function definition for ‘SpatialLines’
.ah2sp: no visible global function definition for ‘slot’
.ah2sp : <anonymous>: no visible global function definition for ‘slot’
.ah2sp: no visible global function definition for ‘SpatialPolygons’
.ah2sp: no visible global function definition for ‘Polygons’
.ah2sp : <anonymous>: no visible global function definition for
  ‘Polygon’
.ah2sp: no visible binding for global variable
  ‘SpatialPolygonsDataFrame’
.ah2sp: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
.binsearch: no visible global function definition for ‘test’
.flowFPOutliers: no visible global function definition for ‘new’
.getBestPoly: no visible global function definition for ‘quantile’
.getBestPoly: no visible global function definition for ‘chull’
.getBestPoly: no visible global function definition for ‘ahull’
.getBestPoly : <anonymous>: no visible global function definition for
  ‘ahull’
.getBestPoly : <anonymous>: no visible global function definition for
  ‘chull’
.getGates : <anonymous>: no visible global function definition for
  ‘chull’
.spline.poly: no visible global function definition for ‘spline’
GateFinder: no visible global function definition for ‘median’
GateFinder: no visible global function definition for ‘new’
plot.GateFinder: no visible global function definition for ‘par’
plot.GateFinder: no visible global function definition for ‘colors’
plot.GateFinder: no visible global function definition for ‘points’
plot.GateFinder: no visible global function definition for ‘axis’
plot.GateFinder: no visible global function definition for ‘box’
plot.GateFinder: no visible global function definition for ‘lines’
plot,GatingProjection-ANY: no visible global function definition for
  ‘par’
plot,GatingProjection-ANY: no visible global function definition for
  ‘lines’
plot,GatingProjection-ANY: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  CRS Line Lines Polygon Polygons SpatialLines SpatialPolygons
  SpatialPolygonsDataFrame ahull anglesArc axis box chull colors legend
  lines median new par points quantile slot spline test
Consider adding
  importFrom("grDevices", "chull", "colors")
  importFrom("graphics", "axis", "box", "legend", "lines", "par",
             "points")
  importFrom("methods", "new", "slot")
  importFrom("stats", "median", "quantile", "spline")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/GateFinder.Rcheck/00check.log’
for details.



Installation output

GateFinder.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GateFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘GateFinder’ ...
** using staged installation
** R
** data
** 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 (GateFinder)

Tests output

GateFinder.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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('GateFinder')


RUNIT TEST PROTOCOL -- Thu Oct 14 09:55:39 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GateFinder RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.435   0.164   2.584 

Example timings

GateFinder.Rcheck/GateFinder-Ex.timings

nameusersystemelapsed
GateFinder-package0.9560.0250.980
GateFinder0.6620.0070.670
GatingProjection-class0.6060.0030.611
LPSData0.0240.0010.024
plot.GateFinder0.6100.0080.618