Multiple platform build/check report for BioC 3.7 - CHECK report for cytofkit on tokay2

Package: cytofkit

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cytofkit.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cytofkit_1.12.0.tar.gz

StartedAt: 2018-06-25 01:25:06 -0400 (Mon, 25 Jun 2018)

EndedAt: 2018-06-25 01:31:06 -0400 (Mon, 25 Jun 2018)

EllapsedTime: 360.3 seconds

RetCode: 0

Status: OK

CheckDir: cytofkit.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cytofkit.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cytofkit_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cytofkit.Rcheck'
* using R version 3.5.0 Patched (2018-05-03 r74699)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'cytofkit' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.6Mb
    libs      1.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytofkit/libs/i386/cytofkit.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
cytof_progression 13.03   0.52   13.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
cytof_progression 12.88    0.7   13.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/cytofkit.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cytofkit_1.12.0.tar.gz && rm -rf cytofkit.buildbin-libdir && mkdir cytofkit.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cytofkit.buildbin-libdir cytofkit_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cytofkit_1.12.0.zip && rm cytofkit_1.12.0.tar.gz cytofkit_1.12.0.zip
###
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100 3722k  100 3722k    0     0  36.6M      0 --:--:-- --:--:-- --:--:-- 39.0M

install for i386

* installing *source* package 'cytofkit' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cytofkit.dll tmp.def RcppExports.o jaccard_coeff.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/cytofkit.buildbin-libdir/cytofkit/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cytofkit'
    finding HTML links ... done
    ClusterX                                html  
    DensVM                                  html  
    Rphenograph                             html  
    cytof_addToFCS                          html  
    cytof_cluster                           html  
    cytof_clusterMtrx                       html  
    cytof_clusterPlot                       html  
    cytof_clusterStat                       html  
    cytof_colorPlot                         html  
    cytof_dimReduction                      html  
    finding level-2 HTML links ... done

    cytof_exprsExtract                      html  
    cytof_exprsMerge                        html  
    cytof_heatmap                           html  
    cytof_progression                       html  
    cytof_progressionPlot                   html  
    cytof_writeResults                      html  
    cytofkit-package                        html  
    cytofkit                                html  
    cytofkitNews                            html  
    cytofkitShinyAPP                        html  
    cytofkit_GUI                            html  
    fixedLogicleParameters_GUI              html  
    getParameters_GUI                       html  
    launchShinyAPP_GUI                      html  
    spectral1                               html  
    spectral2                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'cytofkit' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cytofkit.dll tmp.def RcppExports.o jaccard_coeff.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/cytofkit.buildbin-libdir/cytofkit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cytofkit' as cytofkit_1.12.0.zip
* DONE (cytofkit)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cytofkit' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.0 Patched (2018-05-03 r74699) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 Jun 25 01:30:50 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 
   8.20    0.60    8.78


R version 3.5.0 Patched (2018-05-03 r74699) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 Jun 25 01:31:01 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 
  10.18    0.50   10.68

name	user	system	elapsed
ClusterX	0.05	0.00	0.05
DensVM	3.22	0.05	4.15
Rphenograph	2.64	0.00	2.72
cytof_cluster	1.61	0.04	1.66
cytof_clusterMtrx	0.00	0.02	0.30
cytof_clusterPlot	0.64	0.03	0.67
cytof_clusterStat	0.03	0.00	0.03
cytof_colorPlot	0.22	0.02	0.23
cytof_dimReduction	0.98	0.00	0.99
cytof_exprsExtract	1.03	0.09	1.12
cytof_exprsMerge	1.41	0.06	1.47
cytof_heatmap	0.05	0.00	0.05
cytof_progression	13.03	0.52	13.69
cytof_progressionPlot	2.33	0.50	2.82
cytof_writeResults	0	0	0
cytofkit-package	0	0	0
cytofkit	0	0	0
cytofkitShinyAPP	0	0	0
cytofkit_GUI	0	0	0
fixedLogicleParameters_GUI	0	0	0
getParameters_GUI	0	0	0
launchShinyAPP_GUI	0	0	0
spectral1	0	0	0
spectral2	0	0	0

name	user	system	elapsed
ClusterX	0.03	0.00	0.04
DensVM	2.36	0.02	2.37
Rphenograph	2.95	0.01	2.98
cytof_cluster	1.52	0.02	1.53
cytof_clusterMtrx	0	0	0
cytof_clusterPlot	0.54	0.05	0.58
cytof_clusterStat	0	0	0
cytof_colorPlot	0.29	0.00	0.29
cytof_dimReduction	0.83	0.01	0.85
cytof_exprsExtract	1.25	0.03	1.28
cytof_exprsMerge	1.49	0.02	1.50
cytof_heatmap	0.04	0.00	0.05
cytof_progression	12.88	0.70	13.59
cytof_progressionPlot	1.11	0.08	1.19
cytof_writeResults	0	0	0
cytofkit-package	0	0	0
cytofkit	0	0	0
cytofkitShinyAPP	0	0	0
cytofkit_GUI	0	0	0
fixedLogicleParameters_GUI	0	0	0
getParameters_GUI	0	0	0
launchShinyAPP_GUI	0	0	0
spectral1	0	0	0
spectral2	0	0	0

CHECK report for cytofkit on tokay2

Summary

Command output

Installation output

Tests output

Example timings