Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:52:12 -0400 (Tue, 16 Apr 2019).
Package 364/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CytoML 1.8.1 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: CytoML |
Version: 1.8.1 |
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CytoML_1.8.1.tar.gz |
StartedAt: 2019-04-15 23:17:31 -0400 (Mon, 15 Apr 2019) |
EndedAt: 2019-04-15 23:27:24 -0400 (Mon, 15 Apr 2019) |
EllapsedTime: 592.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CytoML.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CytoML_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CytoML.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CytoML/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CytoML’ version ‘1.8.1’ * 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 for sufficient/correct file permissions ... 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 ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 .preprocessorDiva: no visible binding for global variable ‘specimen’ .preprocessorDiva: no visible binding for global variable ‘sampleSelected’ DerivedParameterNode: no visible global function definition for ‘write.csv’ 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’ constructTree: no visible binding for global variable ‘id’ constructTree: no visible binding for global variable ‘name’ extend.polygonGate: no visible binding for global variable ‘..dim’ 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’ read.gatingML.cytobank: no visible binding for global variable ‘id’ read.gatingML.cytobank: no visible binding for global variable ‘comp_ref’ Undefined global functions or variables: . ..dim comp_ref count fcs fcs_filename gate_def gate_id id is.smaller name parent parent_count population sampleSelected specimen write.csv x y Consider adding importFrom("utils", "write.csv") to your NAMESPACE file. * 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 Examples with CPU or elapsed time > 5s user system elapsed compare.counts 196.920 0.888 41.038 cytobank2GatingSet 196.632 0.768 39.085 getNodes-graphGML-method 6.884 0.024 2.087 read.gatingML.cytobank 6.800 0.036 2.065 getChildren-graphGML-character-method 6.728 0.016 1.917 plot-graphGML-missing-method 6.660 0.012 2.010 extend 5.812 0.012 1.041 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 ‘/home/biocbuild/bbs-3.8-bioc/meat/CytoML.Rcheck/00check.log’ for details.
CytoML.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘CytoML’ ... ** 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 (CytoML)
CytoML.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth" Copyright (C) 2019 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. > library(testthat) > library(CytoML) > > > test_check("CytoML") Loading required package: flowCore 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: 26 SKIPPED: 0 FAILED: 0 > > #devtools::test() > > > #test_file("˜/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R") > #test_file("˜/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R") > #test_file("˜/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R") > # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-cytobank.R") > # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R") > # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-extend.R") > # test_file("˜/rglab/workspace/CytoML/tests/testthat/test-flowJo.R") > > proc.time() user system elapsed 1798.776 6.668 382.410
CytoML.Rcheck/CytoML-Ex.timings
name | user | system | elapsed | |
GatingSet2cytobank | 2.256 | 0.196 | 2.481 | |
GatingSet2flowJo | 1.948 | 0.088 | 2.049 | |
compare.counts | 196.920 | 0.888 | 41.038 | |
cytobank2GatingSet | 196.632 | 0.768 | 39.085 | |
extend | 5.812 | 0.012 | 1.041 | |
getChildren-graphGML-character-method | 6.728 | 0.016 | 1.917 | |
getNodes-graphGML-method | 6.884 | 0.024 | 2.087 | |
openDiva | 0 | 0 | 0 | |
plot-graphGML-missing-method | 6.660 | 0.012 | 2.010 | |
range.GatingHierarchy | 0.000 | 0.000 | 0.001 | |
read.gatingML.cytobank | 6.800 | 0.036 | 2.065 | |