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BioC 3.5: CHECK report for cytofkit on veracruz2

This page was generated on 2017-10-18 14:32:52 -0400 (Wed, 18 Oct 2017).

Package 309/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytofkit 1.8.4
Jinmiao Chen , Hao Chen , Matthew Myint
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/cytofkit
Branch: RELEASE_3_5
Last Commit: 36d305a
Last Changed Date: 2017-10-13 04:07:38 -0400 (Fri, 13 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cytofkit
Version: 1.8.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytofkit_1.8.4.tar.gz
StartedAt: 2017-10-18 02:24:36 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:27:49 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 193.1 seconds
RetCode: 0
Status:  OK 
CheckDir: cytofkit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytofkit_1.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/cytofkit.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.8.4’
* 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  6.3Mb
  sub-directories of 1Mb or more:
    doc       2.2Mb
    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 9.489  0.515   10.24
* 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-3.5-bioc/meat/cytofkit.Rcheck/00check.log’
for details.


cytofkit.Rcheck/00install.out:

* 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-3.5-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)

cytofkit.Rcheck/cytofkit-Ex.timings:

nameusersystemelapsed
ClusterX0.1270.0120.141
DensVM2.2080.0622.327
Rphenograph1.3290.0141.378
cytof_cluster2.0100.1222.192
cytof_clusterPlot1.6980.1261.896
cytof_clusterStat0.0060.0010.007
cytof_colorPlot0.6380.0460.693
cytof_dimReduction1.2280.0061.260
cytof_exprsExtract0.5590.0360.611
cytof_exprsMerge0.8700.0330.935
cytof_heatmap0.3110.0280.345
cytof_progression 9.489 0.51510.240
cytof_progressionPlot3.3750.2333.629
cytof_writeResults0.0010.0000.002
cytofkit-package0.0010.0010.002
cytofkit0.0010.0000.002
cytofkitShinyAPP0.0010.0000.002
cytofkit_GUI000
fixedLogicleParameters_GUI000
getParameters_GUI0.0000.0000.001
launchShinyAPP_GUI0.0010.0000.000
spectral10.0010.0000.001
spectral20.0010.0010.001