BioC 3.3: CHECK report for cytofkit on zin2

Package: cytofkit

Version: 1.4.10

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cytofkit_1.4.10.tar.gz

StartedAt: 2016-10-13 01:03:44 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:06:13 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 148.7 seconds

RetCode: 0

Status:  OK

CheckDir: cytofkit.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cytofkit_1.4.10.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/cytofkit.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.10’
* 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  7.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    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 8.622  0.152   9.251
* 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-3.3-bioc/meat/cytofkit.Rcheck/00check.log’
for details.

* installing *source* package ‘cytofkit’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c jaccard_coeff.cpp -o jaccard_coeff.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o cytofkit.so RcppExports.o jaccard_coeff.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/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	0.014	0.012	0.026
DensVM	2.172	0.115	2.313
Rphenograph	1.022	0.000	1.023
cytof_cluster	1.385	0.008	1.399
cytof_clusterPlot	0.365	0.020	0.384
cytof_clusterStat	0.012	0.000	0.012
cytof_colorPlot	0.273	0.012	0.285
cytof_dimReduction	1.199	0.000	1.228
cytof_exprsExtract	0.991	0.008	1.003
cytof_exprsMerge	0.808	0.016	0.824
cytof_heatmap	0.04	0.00	0.04
cytof_progression	8.622	0.152	9.251
cytof_progressionPlot	1.005	0.044	1.048
cytof_writeResults	0.001	0.000	0.002
cytofkit-package	0.002	0.000	0.002
cytofkit	0.002	0.000	0.001
cytofkitShinyAPP	0.000	0.000	0.001
cytofkit_GUI	0.001	0.000	0.000
getParameters_GUI	0	0	0
launchShinyAPP_GUI	0.001	0.000	0.000