Package: cytofkit

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytofkit_1.10.0.tar.gz

StartedAt: 2018-04-12 02:26:49 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:30:02 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 193.5 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 --no-vignettes --timings cytofkit_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cytofkit.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc       5.0Mb
    extdata   3.6Mb
* 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 loading without being on the library search path ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
cytof_progression 10.206   0.57  10.961
* 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-3.6-bioc/meat/cytofkit.Rcheck/00check.log’
for details.

* installing *source* package ‘cytofkit’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/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 /Users/biocbuild/bbs-3.6-bioc/meat/cytofkit.Rcheck/cytofkit/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cytofkit)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 -- Thu Apr 12 02:29:58 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 
  6.897   0.470   7.415 

name	user	system	elapsed
ClusterX	0.123	0.013	0.135
DensVM	2.146	0.069	2.266
Rphenograph	1.182	0.013	1.207
cytof_cluster	2.518	0.139	2.679
cytof_clusterMtrx	0.008	0.001	0.009
cytof_clusterPlot	2.092	0.145	2.218
cytof_clusterStat	0.012	0.001	0.012
cytof_colorPlot	1.053	0.059	1.115
cytof_dimReduction	1.362	0.004	1.390
cytof_exprsExtract	0.887	0.042	0.935
cytof_exprsMerge	0.849	0.044	0.904
cytof_heatmap	0.326	0.024	0.347
cytof_progression	10.206	0.570	10.961
cytof_progressionPlot	4.156	0.284	4.405
cytof_writeResults	0.002	0.001	0.003
cytofkit-package	0.002	0.000	0.003
cytofkit	0.002	0.000	0.001
cytofkitShinyAPP	0.001	0.001	0.002
cytofkit_GUI	0.001	0.000	0.000
fixedLogicleParameters_GUI	0.000	0.001	0.001
getParameters_GUI	0.000	0.000	0.001
launchShinyAPP_GUI	0	0	0
spectral1	0.002	0.000	0.002
spectral2	0.002	0.001	0.002