Jinmiao Chen
| Snapshot Date: 2018-07-16 16:45:11 -0400 (Mon, 16 Jul 2018) |
| URL: https://git.bioconductor.org/packages/cytofkit |
| Branch: RELEASE_3_7 |
| Last Commit: 7073090 |
| Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-07-17 11:14:26 -0400 (Tue, 17 Jul 2018).
| Package 338/1560 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cytofkit 1.12.0 Jinmiao Chen
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: cytofkit |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cytofkit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cytofkit_1.12.0.tar.gz |
| StartedAt: 2018-07-16 23:00:55 -0400 (Mon, 16 Jul 2018) |
| EndedAt: 2018-07-16 23:06:10 -0400 (Mon, 16 Jul 2018) |
| EllapsedTime: 314.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cytofkit.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cytofkit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cytofkit_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/cytofkit.Rcheck’
* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytofkit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytofkit’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cytofkit’ 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
cytof_clusterPlot: no visible global function definition for
‘geom_text’
cytof_progressionPlot: no visible global function definition for ‘aes’
cytof_progressionPlot: no visible binding for global variable
‘Pseudotime’
cytof_progressionPlot: no visible binding for global variable ‘cluster’
cytofkitShinyAPP : <anonymous> : C_ScatterPlotInput: no visible global
function definition for ‘scatterPlot’
cytofkitShinyAPP : <anonymous>: no visible global function definition
for ‘heatMap’
cytofkitShinyAPP : <anonymous> : M_markerExpressionPlotInput: no
visible global function definition for ‘scatterPlot’
cytofkitShinyAPP : <anonymous> : M_stackDensityPlotInput: no visible
global function definition for ‘stackDenistyPlot’
cytofkitShinyAPP : <anonymous> : P_markerPlotInput: no visible global
function definition for ‘cytof_expressionTrends’
Undefined global functions or variables:
Pseudotime aes cluster cytof_expressionTrends geom_text heatMap
scatterPlot stackDenistyPlot
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cytof_progression 12.166 0.692 12.999
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/cytofkit.Rcheck/00check.log’
for details.
cytofkit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cytofkit ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘cytofkit’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c jaccard_coeff.cpp -o jaccard_coeff.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cytofkit.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/cytofkit/libs ** 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 (cytofkit)
cytofkit.Rcheck/tests/runTests.Rout
R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("cytofkit")
Running t-SNE...with seed 42 DONE
RUNIT TEST PROTOCOL -- Mon Jul 16 23:06:00 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
cytofkit 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
13.856 1.275 15.104
cytofkit.Rcheck/cytofkit-Ex.timings
| name | user | system | elapsed | |
| ClusterX | 0.034 | 0.005 | 0.039 | |
| DensVM | 3.027 | 0.104 | 3.151 | |
| Rphenograph | 2.549 | 0.012 | 2.584 | |
| cytof_cluster | 1.766 | 0.069 | 1.845 | |
| cytof_clusterMtrx | 0.010 | 0.001 | 0.012 | |
| cytof_clusterPlot | 0.975 | 0.115 | 1.084 | |
| cytof_clusterStat | 0.016 | 0.002 | 0.019 | |
| cytof_colorPlot | 0.429 | 0.082 | 0.508 | |
| cytof_dimReduction | 1.552 | 0.007 | 1.575 | |
| cytof_exprsExtract | 0.889 | 0.075 | 0.962 | |
| cytof_exprsMerge | 0.891 | 0.077 | 0.969 | |
| cytof_heatmap | 0.076 | 0.006 | 0.082 | |
| cytof_progression | 12.166 | 0.692 | 12.999 | |
| cytof_progressionPlot | 1.897 | 0.213 | 2.107 | |
| cytof_writeResults | 0.003 | 0.000 | 0.004 | |
| cytofkit-package | 0.003 | 0.001 | 0.005 | |
| cytofkit | 0.003 | 0.000 | 0.003 | |
| cytofkitShinyAPP | 0.002 | 0.000 | 0.004 | |
| cytofkit_GUI | 0.001 | 0.000 | 0.001 | |
| fixedLogicleParameters_GUI | 0.002 | 0.000 | 0.001 | |
| getParameters_GUI | 0.001 | 0.000 | 0.001 | |
| launchShinyAPP_GUI | 0.001 | 0.000 | 0.001 | |
| spectral1 | 0.004 | 0.001 | 0.003 | |
| spectral2 | 0.003 | 0.000 | 0.004 | |