Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:28:21 -0400 (Thu, 12 Apr 2018).
Package 325/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CytoML 1.4.1 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: CytoML |
Version: 1.4.1 |
Command: rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_1.4.1.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CytoML.buildbin-libdir --install="check:CytoML-install.out" --force-multiarch --no-vignettes --timings CytoML_1.4.1.tar.gz |
StartedAt: 2018-04-11 23:20:11 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 23:27:50 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 458.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CytoML.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CytoML.buildbin-libdir CytoML.Rcheck && mkdir CytoML.buildbin-libdir CytoML.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CytoML.buildbin-libdir CytoML_1.4.1.tar.gz >CytoML.Rcheck\00install.out 2>&1 && cp CytoML.Rcheck\00install.out CytoML-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CytoML.buildbin-libdir --install="check:CytoML-install.out" --force-multiarch --no-vignettes --timings CytoML_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CytoML.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'CytoML/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CytoML' version '1.4.1' * 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 whether package 'CytoML' 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 * loading checks for arch 'i386' ** 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 loading without being on the library search path ... OK * loading checks for arch 'x64' ** 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'flowUtils:::.fuEnv' 'flowUtils:::smartTreeParse' 'flowWorkspace:::.cpp_getCompensation' 'flowWorkspace:::.fix_channel_slash' 'flowWorkspace:::.groupByTree' 'flowWorkspace:::compute.timestep' 'flowWorkspace:::isHidden' 'flowWorkspace:::isNegated' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .preprocessorDiva: no visible global function definition for 'menu' .preprocessorDiva: no visible binding for global variable 'specimen' .preprocessorDiva: no visible binding for global variable 'sampleSelected' GatingSet2flowJo: no visible global function definition for 'pData<-' addCustomInfo : <anonymous>: no visible global function definition for 'is' addGate: no visible binding for global variable 'id' addGate: no visible binding for global variable 'gate_id' addGate: no visible binding for global variable 'fcs' addGate: no visible binding for global variable 'gate_def' addGate: no visible binding for global variable 'name' compare.counts: no visible binding for global variable 'population' compare.counts: no visible binding for global variable 'parent' compare.counts: no visible binding for global variable 'count' compare.counts: no visible binding for global variable 'parent_count' compare.counts: no visible global function definition for '.' compare.counts: no visible binding for global variable 'fcs_filename' constructPopNode: no visible global function definition for 'is' constructPopNode : <anonymous>: no visible global function definition for 'is' constructTree : <anonymous>: no visible binding for global variable 'slot' constructTree: no visible binding for global variable 'id' constructTree: no visible binding for global variable 'name' export_comp_trans: no visible global function definition for 'logtGml2' extend.ellipsoidGate: no visible global function definition for 'as' extend.polygonGate : <anonymous>: no visible binding for global variable 'y' extend.polygonGate : <anonymous>: no visible binding for global variable 'x' extend.polygonGate: no visible binding for global variable 'id' extend.polygonGate: no visible binding for global variable 'x' extend.polygonGate: no visible binding for global variable 'y' extend.polygonGate: no visible binding for global variable 'is.smaller' extend.polygonGate: no visible global function definition for 'rgb' extend.rectangleGate: no visible global function definition for 'as' gateNode.ellipsoidGate: no visible global function definition for 'as' inverse.ellipsoidGate: no visible global function definition for 'as' inverse.rectangleGate: no visible global function definition for 'as' openDiva: no visible global function definition for 'new' read.gatingML.cytobank: no visible global function definition for 'is' read.gatingML.cytobank: no visible binding for global variable 'id' read.gatingML.cytobank: no visible binding for global variable 'comp_ref' read.gatingML.cytobank : <anonymous>: no visible global function definition for 'is' read.gatingML.cytobank: no visible global function definition for 'as' xmlTag: no visible global function definition for 'is' compensate,GatingSet-graphGML: no visible global function definition for 'is' getSamples,divaWorkspace: no visible global function definition for 'selectMethod' getTransformations,graphGML : <anonymous>: no visible global function definition for 'extends' transform,ellipsoidGate: no visible global function definition for 'as' Undefined global functions or variables: . as comp_ref count extends fcs fcs_filename gate_def gate_id id is is.smaller logtGml2 menu name new pData<- parent parent_count population rgb sampleSelected selectMethod slot specimen x y Consider adding importFrom("grDevices", "rgb") importFrom("methods", "as", "extends", "is", "new", "selectMethod", "slot") importFrom("utils", "menu") 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed compare.counts 5.75 0.23 12.38 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed compare.counts 8.12 0.35 9.05 cytobank2GatingSet 6.72 0.25 7.11 GatingSet2cytobank 3.73 0.13 5.07 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CytoML.Rcheck/00check.log' for details.
CytoML.Rcheck/00install.out
install for i386 * installing *source* package 'CytoML' ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'CytoML' finding HTML links ... done GatingSet2cytobank html GatingSet2flowJo html addCustomInfo html compare.counts html compensate-GatingSet-graphGML-method html constructTree html cytobank2GatingSet html divaWorkspace-class html finding level-2 HTML links ... done extend html gating-methods html getChildren-graphGML-character-method html getCompensationMatrices-graphGML-method html getGate-graphGML-character-method html getNodes-graphGML-method html getParent-graphGML-character-method html getTransformations-graphGML-method html graphGML-class html matchPath html openDiva html parse.gateInfo html plot-graphGML-missing-method html range.GatingHierarchy html read.gatingML.cytobank html show-graphGML-method html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'CytoML' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'CytoML' as CytoML_1.4.1.zip * DONE (CytoML) In R CMD INSTALL In R CMD INSTALL
CytoML.Rcheck/tests_i386/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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. > library(testthat) > library(CytoML) > > > test_check("CytoML") Loading required package: flowCore Attaching package: 'flowCore' The following object is masked from 'package:base': sort Loading required package: ncdfFlow Loading required package: RcppArmadillo Loading required package: BH Loading required package: ggplot2 Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file. windows version of flowJo workspace recognized. version X windows version of flowJo workspace recognized. version X windows version of flowJo workspace recognized. version X == testthat results =========================================================== OK: 12127 SKIPPED: 0 FAILED: 0 > > #devtools::test("˜/rglab/workspace/CytoML") > > > #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R") > #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R") > > proc.time() user system elapsed 87.34 4.09 93.37 |
CytoML.Rcheck/tests_x64/testthat.Rout R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 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. > library(testthat) > library(CytoML) > > > test_check("CytoML") Loading required package: flowCore Attaching package: 'flowCore' The following object is masked from 'package:base': sort Loading required package: ncdfFlow Loading required package: RcppArmadillo Loading required package: BH Loading required package: ggplot2 Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file. Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file. windows version of flowJo workspace recognized. version X windows version of flowJo workspace recognized. version X windows version of flowJo workspace recognized. version X == testthat results =========================================================== OK: 12127 SKIPPED: 0 FAILED: 0 > > #devtools::test("˜/rglab/workspace/CytoML") > > > #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R") > #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R") > > proc.time() user system elapsed 112.09 3.32 116.67 |
CytoML.Rcheck/examples_i386/CytoML-Ex.timings
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CytoML.Rcheck/examples_x64/CytoML-Ex.timings
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