BioC 3.4: CHECK report for CONFESS on tokay1

Package: CONFESS

Version: 1.2.2

Command: C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings CONFESS_1.2.2.tar.gz

StartedAt: 2017-04-14 21:40:39 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:44:52 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 252.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CONFESS.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings CONFESS_1.2.2.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/CONFESS.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.2.2'
* 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-3.4-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    30.11   0.44   30.55
Fluo_adjustment 23.14   0.01   23.16
Fluo_modeling    5.39   0.12    5.52
* 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-3.4-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	0.00	0.01
Fluo_CV_modeling	0	0	0
Fluo_CV_prep	30.11	0.44	30.55
Fluo_adjustment	23.14	0.01	23.16
Fluo_inspection	1.88	0.04	1.90
Fluo_modeling	5.39	0.12	5.52
Fluo_ordering	0.84	0.03	0.94
LocationMatrix	0	0	0
cluster2outlier	0	0	0
createFluo	0	0	0
defineLocClusters	0.05	0.00	0.08
getFluo	0.03	0.00	0.03
getFluo_byRun	0.04	0.00	0.05
pathEstimator	0	0	0
readFiles	0.02	0.00	0.01
simcells	4.87	0.06	4.94
spotEstimator	0	0	0