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CHECK report for cytofkit on malbec2

This page was generated on 2018-06-25 10:05:21 -0400 (Mon, 25 Jun 2018).

Package 338/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytofkit 1.12.0
Jinmiao Chen , Matthew Myint
Snapshot Date: 2018-06-24 16:46:06 -0400 (Sun, 24 Jun 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)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cytofkit
Version: 1.12.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cytofkit.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cytofkit_1.12.0.tar.gz
StartedAt: 2018-06-24 23:25:55 -0400 (Sun, 24 Jun 2018)
EndedAt: 2018-06-24 23:29:14 -0400 (Sun, 24 Jun 2018)
EllapsedTime: 199.0 seconds
RetCode: 0
Status:  OK 
CheckDir: cytofkit.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cytofkit.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cytofkit_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/cytofkit.Rcheck’
* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-pc-linux-gnu (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 12.036  0.128  12.188
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/cytofkit.Rcheck/00check.log’
for details.



Installation output

cytofkit.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL cytofkit
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘cytofkit’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c jaccard_coeff.cpp -o jaccard_coeff.o
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o cytofkit.so RcppExports.o jaccard_coeff.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/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)

Tests output

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-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.

> BiocGenerics:::testPackage("cytofkit")
  Running t-SNE...with seed 42  DONE


RUNIT TEST PROTOCOL -- Sun Jun 24 23:29:12 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 
  8.520   0.416   8.914 

Example timings

cytofkit.Rcheck/cytofkit-Ex.timings

nameusersystemelapsed
ClusterX0.0400.0000.041
DensVM2.2320.0242.277
Rphenograph2.1400.0042.144
cytof_cluster1.4000.0521.456
cytof_clusterMtrx0.0120.0000.010
cytof_clusterPlot0.5880.0200.606
cytof_clusterStat0.0080.0000.008
cytof_colorPlot0.1760.0200.197
cytof_dimReduction0.9400.0000.951
cytof_exprsExtract0.6560.0360.691
cytof_exprsMerge0.7000.0240.723
cytof_heatmap0.0640.0000.073
cytof_progression12.036 0.12812.188
cytof_progressionPlot1.2400.0641.304
cytof_writeResults0.0040.0000.002
cytofkit-package0.0040.0000.002
cytofkit0.0000.0000.001
cytofkitShinyAPP0.0040.0000.001
cytofkit_GUI000
fixedLogicleParameters_GUI0.0000.0000.001
getParameters_GUI0.0040.0000.001
launchShinyAPP_GUI000
spectral10.0040.0000.002
spectral20.0000.0000.001