BioC 3.3: CHECK report for cytofkit on linux2.bioconductor.org

Package: cytofkit

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cytofkit_1.3.0.tar.gz

StartedAt: 2015-10-27 03:09:34 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:12:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 168.1 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_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/cytofkit.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.3.0’
* 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 ... [6s/6s] 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 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [99s/96s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
densVM_cluster 91.045  2.462  91.177
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [4s/4s] 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: OK

* installing *source* package ‘cytofkit’ ...
** 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
clust_mean_heatmap	0.203	0.000	0.201
clust_percentage_heatmap	0.036	0.000	0.036
clust_state	0.013	0.000	0.012
cluster_gridPlot	0.405	0.025	0.419
cluster_plot	0.281	0.023	0.294
cytof_dimReduction	0.927	0.000	0.918
cytof_tsne_densvm	0.000	0.000	0.002
cytof_tsne_densvm_GUI	0	0	0
cytof_write_results	0.000	0.000	0.001
cytofkit	0.000	0.000	0.001
densVM_cluster	91.045	2.462	91.177
fcs_lgcl	0.124	0.010	0.133
fcs_lgcl_merge	0.121	0.010	0.131
peaksGamma_plot	0.108	0.010	0.115