Package: CONFESS

Version: 1.11.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CONFESS_1.11.2.tar.gz

StartedAt: 2019-04-08 23:40:54 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:45:32 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 277.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CONFESS.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CONFESS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CONFESS_1.11.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CONFESS.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.11.2’
* 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-3.9-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    40.741  3.504  43.717
Fluo_adjustment 20.840  1.939  22.437
Fluo_modeling   12.683  0.239  12.924
* 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-3.9-bioc/meat/CONFESS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CONFESS
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* installing to library ‘/home/biocbuild/bbs-3.9-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	0.019	0.000	0.107
Fluo_CV_modeling	0	0	0
Fluo_CV_prep	40.741	3.504	43.717
Fluo_adjustment	20.840	1.939	22.437
Fluo_inspection	3.009	1.017	3.765
Fluo_modeling	12.683	0.239	12.924
Fluo_ordering	1.023	0.093	1.328
LocationMatrix	0.006	0.000	0.007
cluster2outlier	0.002	0.000	0.002
createFluo	0.012	0.000	0.013
defineLocClusters	0.058	0.009	0.104
files	0.003	0.000	0.003
getFluo	0.035	0.003	0.050
getFluo_byRun	0.059	0.013	0.087
pathEstimator	0.001	0.000	0.001
readFiles	0.016	0.000	0.016
simcells	1.555	0.043	1.651
spotEstimator	0	0	0