BioC 3.5: CHECK report for CONFESS on tokay2

Package: CONFESS

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings CONFESS_1.4.0.tar.gz

StartedAt: 2017-08-15 22:54:49 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:59:22 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 272.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CONFESS.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings CONFESS_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CONFESS.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CONFESS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CONFESS' version '1.4.0'
* 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 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 'C:/Users/biocbuild/bbs-3.5-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    28.08   0.28   28.53
Fluo_adjustment 18.28   0.02   18.30
simcells         7.97   0.01    7.99
Fluo_modeling    6.40   0.32    6.73
* 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
  'C:/Users/biocbuild/bbs-3.5-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	0.01	0.02	0.03
Fluo_CV_modeling	0	0	0
Fluo_CV_prep	28.08	0.28	28.53
Fluo_adjustment	18.28	0.02	18.30
Fluo_inspection	2.69	0.01	2.70
Fluo_modeling	6.40	0.32	6.73
Fluo_ordering	3.77	0.00	3.80
LocationMatrix	0	0	0
cluster2outlier	0.04	0.00	0.05
createFluo	0.02	0.00	0.02
defineLocClusters	0.04	0.03	0.15
files	0	0	0
getFluo	0.11	0.00	0.11
getFluo_byRun	0.11	0.00	0.11
pathEstimator	0.11	0.00	0.11
readFiles	0.12	0.00	0.12
simcells	7.97	0.01	7.99
spotEstimator	0	0	0