Package: CONFESS

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CONFESS_1.6.0.tar.gz

StartedAt: 2018-04-11 22:30:23 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:34:15 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 231.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CONFESS.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CONFESS_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CONFESS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CONFESS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CONFESS’ version ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CONFESS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
See ‘/home/biocbuild/bbs-3.6-bioc/meat/CONFESS.Rcheck/00install.out’ for details.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
Fluo_CV_prep    30.056  1.968  31.940
Fluo_adjustment 18.892  0.712  19.564
Fluo_modeling    5.244  0.084   5.340
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/CONFESS.Rcheck/00check.log’
for details.

* installing *source* package ‘CONFESS’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
* DONE (CONFESS)

name	user	system	elapsed
FluoSelection_byRun	0.012	0.000	0.012
Fluo_CV_modeling	0.000	0.000	0.001
Fluo_CV_prep	30.056	1.968	31.940
Fluo_adjustment	18.892	0.712	19.564
Fluo_inspection	2.992	0.776	3.655
Fluo_modeling	5.244	0.084	5.340
Fluo_ordering	3.108	0.164	3.280
LocationMatrix	0.004	0.000	0.005
cluster2outlier	0.044	0.004	0.049
createFluo	0.008	0.000	0.009
defineLocClusters	0.048	0.000	0.200
files	0.000	0.004	0.004
getFluo	0.088	0.004	0.093
getFluo_byRun	0.084	0.008	0.090
pathEstimator	0.104	0.004	0.110
readFiles	0.100	0.008	0.109
simcells	3.832	0.100	3.943
spotEstimator	0.004	0.000	0.000