Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:29:05 -0400 (Sat, 13 Apr 2019).
Package 574/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GateFinder 1.2.1 Nima Aghaeepour
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | ![]() | ||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: GateFinder |
Version: 1.2.1 |
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:GateFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GateFinder_1.2.1.tar.gz |
StartedAt: 2019-04-13 02:23:22 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 02:26:29 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 186.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GateFinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:GateFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GateFinder_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GateFinder.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GateFinder/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GateFinder' version '1.2.1' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 ... OK * 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 ... NOTE S3 methods shown with full name in documentation object 'plot.GateFinder': 'plot.GateFinder' The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GateFinder.Rcheck/00check.log' for details.
GateFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch GateFinder ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' * installing *source* package 'GateFinder' ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GateFinder' finding HTML links ... done GateFinder-package html GateFinder html GatingProjection-class html LPSData html plot.GateFinder html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GateFinder) Making 'packages.html' ... done In R CMD INSTALL
GateFinder.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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') sROC 0.1-2 loaded RUNIT TEST PROTOCOL -- Sat Apr 13 02:26:25 2019 *********************************************** 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 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 6.29 0.37 6.65
GateFinder.Rcheck/GateFinder-Ex.timings
name | user | system | elapsed | |
GateFinder-package | 0.79 | 0.03 | 0.83 | |
GateFinder | 0.73 | 0.05 | 0.78 | |
GatingProjection-class | 0.75 | 0.00 | 0.75 | |
LPSData | 0.02 | 0.02 | 0.04 | |
plot.GateFinder | 0.92 | 0.01 | 0.93 | |