Package: CONFESS

Version: 1.14.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CONFESS_1.14.0.tar.gz

StartedAt: 2020-04-15 03:44:37 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:49:18 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 280.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CONFESS.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CONFESS_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CONFESS.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.0’
* package encoding: UTF-8
* 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 ‘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-3.10-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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
Fluo_CV_prep    38.016  2.940  40.936
Fluo_adjustment 21.368  1.688  23.149
Fluo_modeling   11.744  0.236  12.017
* 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
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/CONFESS.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CONFESS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘CONFESS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 from temporary location
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
** testing if installed package keeps a record of temporary installation path
* DONE (CONFESS)

name	user	system	elapsed
FluoSelection_byRun	0.016	0.000	0.024
Fluo_CV_modeling	0	0	0
Fluo_CV_prep	38.016	2.940	40.936
Fluo_adjustment	21.368	1.688	23.149
Fluo_inspection	2.812	1.012	3.770
Fluo_modeling	11.744	0.236	12.017
Fluo_ordering	0.988	0.068	1.051
LocationMatrix	0.004	0.000	0.004
cluster2outlier	0.000	0.000	0.001
createFluo	0.008	0.000	0.007
defineLocClusters	0.036	0.008	0.116
files	0.000	0.000	0.002
getFluo	0.024	0.004	0.028
getFluo_byRun	0.048	0.016	0.065
pathEstimator	0.000	0.000	0.001
readFiles	0.016	0.000	0.016
simcells	3.168	0.036	3.213
spotEstimator	0	0	0