BioC 3.3: CHECK report for cytofkit on oaxaca

Package: cytofkit

Version: 1.4.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytofkit_1.4.10.tar.gz

StartedAt: 2016-10-13 00:42:00 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:45:08 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 188.2 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_1.4.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/cytofkit.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.10’
* 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  7.1Mb
  sub-directories of 1Mb or more:
    doc       2.8Mb
    extdata   4.0Mb
* 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’
Undefined global functions or variables:
  Pseudotime aes cluster geom_text
* 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 8.544  0.363   8.957
* 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-3.3-bioc/meat/cytofkit.Rcheck/00check.log’
for details.

* installing *source* package ‘cytofkit’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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-3.3-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)

name	user	system	elapsed
ClusterX	0.024	0.004	0.048
DensVM	2.543	0.078	2.662
Rphenograph	1.075	0.011	1.108
cytof_cluster	1.698	0.040	1.742
cytof_clusterPlot	0.454	0.035	0.547
cytof_clusterStat	0.012	0.001	0.013
cytof_colorPlot	0.301	0.029	0.328
cytof_dimReduction	1.630	0.004	1.684
cytof_exprsExtract	1.032	0.056	1.086
cytof_exprsMerge	0.816	0.050	0.864
cytof_heatmap	0.036	0.003	0.039
cytof_progression	8.544	0.363	8.957
cytof_progressionPlot	1.006	0.086	1.113
cytof_writeResults	0.002	0.001	0.002
cytofkit-package	0.002	0.000	0.003
cytofkit	0.001	0.000	0.003
cytofkitShinyAPP	0	0	0
cytofkit_GUI	0	0	0
getParameters_GUI	0	0	0
launchShinyAPP_GUI	0.000	0.000	0.001