Jinmiao Chen
| Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cytofkit |
| Branch: master |
| Last Commit: d13a480 |
| Last Changed Date: 2018-09-24 12:08:52 -0400 (Mon, 24 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2018-10-29 10:46:09 -0400 (Mon, 29 Oct 2018).
| Package 360/1642 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
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 | [ WARNINGS ] | OK | |
| Package: cytofkit |
| Version: 1.13.2 |
| 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_1.13.2.tar.gz |
| StartedAt: 2018-10-29 00:28:55 -0400 (Mon, 29 Oct 2018) |
| EndedAt: 2018-10-29 00:34:09 -0400 (Mon, 29 Oct 2018) |
| EllapsedTime: 314.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cytofkit.Rcheck |
| Warnings: 1 |
##############################################################################
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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_1.13.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/cytofkit.Rcheck’
* using R Under development (unstable) (2018-04-05 r74542)
* 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 ‘1.13.2’
* 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 ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were declared in NAMESPACE but not found
Warning: Package 'cytofkit' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/cytofkit.Rcheck/00install.out’ for details.
* 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 10.544 0.619 11.213
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/library’ * installing *source* package ‘cytofkit’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/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/3.6/Resources/library/cytofkit/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were declared in NAMESPACE but not found ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were declared in NAMESPACE but not found Warning: Package 'cytofkit' is deprecated and will be removed from Bioconductor version 3.9 * DONE (cytofkit)
cytofkit.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-04-05 r74542) -- "Unsuffered Consequences"
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 Oct 29 00:34:04 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
Warning messages:
1: S3 method 'xts::as.xts.data.table' was declared in NAMESPACE but not found
2: S3 methods 'ggplot2::autoplot.zoo', 'ggplot2::fortify.zoo' were declared in NAMESPACE but not found
3: Package 'cytofkit' is deprecated and will be removed from Bioconductor
version 3.9
>
> proc.time()
user system elapsed
13.861 1.285 15.113
cytofkit.Rcheck/cytofkit-Ex.timings
| name | user | system | elapsed | |
| ClusterX | 0.036 | 0.005 | 0.049 | |
| DensVM | 2.846 | 0.093 | 2.960 | |
| Rphenograph | 2.444 | 0.011 | 2.497 | |
| cytof_cluster | 1.733 | 0.070 | 1.809 | |
| cytof_clusterMtrx | 0.014 | 0.001 | 0.015 | |
| cytof_clusterPlot | 0.992 | 0.108 | 1.094 | |
| cytof_clusterStat | 0.027 | 0.003 | 0.030 | |
| cytof_colorPlot | 0.422 | 0.051 | 0.472 | |
| cytof_dimReduction | 1.629 | 0.006 | 1.646 | |
| cytof_exprsExtract | 0.867 | 0.063 | 0.930 | |
| cytof_exprsMerge | 1.375 | 0.053 | 1.432 | |
| cytof_heatmap | 0.087 | 0.006 | 0.096 | |
| cytof_progression | 10.544 | 0.619 | 11.213 | |
| cytof_progressionPlot | 2.078 | 0.173 | 2.237 | |
| cytof_writeResults | 0.007 | 0.000 | 0.008 | |
| cytofkit-package | 0.013 | 0.000 | 0.014 | |
| cytofkit | 0.009 | 0.000 | 0.010 | |
| cytofkitShinyAPP | 0.005 | 0.000 | 0.004 | |
| cytofkit_GUI | 0.005 | 0.001 | 0.006 | |
| fixedLogicleParameters_GUI | 0.004 | 0.000 | 0.004 | |
| getParameters_GUI | 0.006 | 0.000 | 0.005 | |
| launchShinyAPP_GUI | 0.005 | 0.000 | 0.005 | |
| spectral1 | 0.006 | 0.001 | 0.007 | |
| spectral2 | 0.007 | 0.000 | 0.007 | |