BioC 3.4: CHECK report for CONFESS on morelia

Package: CONFESS

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CONFESS_1.1.2.tar.gz

StartedAt: 2016-09-20 04:59:06 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:02:58 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 232.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CONFESS.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CONFESS_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CONFESS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.2’
* 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 ... 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
See ‘/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 sizes of PDF files under ‘inst/doc’ ... 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    29.477  3.600  32.739
Fluo_adjustment 22.328  1.806  23.964
* 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
  ‘/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 in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
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 in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘stats::BIC’ by ‘flowMerge::BIC’ when loading ‘CONFESS’
* DONE (CONFESS)

name	user	system	elapsed
FluoSelection_byRun	0.024	0.001	0.026
Fluo_CV_modeling	0	0	0
Fluo_CV_prep	29.477	3.600	32.739
Fluo_adjustment	22.328	1.806	23.964
Fluo_inspection	2.670	1.349	3.821
Fluo_modeling	3.751	0.401	4.146
Fluo_ordering	0.802	0.084	0.891
LocationMatrix	0.005	0.000	0.005
cluster2outlier	0.002	0.000	0.002
createFluo	0.014	0.001	0.015
defineLocClusters	0.033	0.005	0.065
getFluo	0.038	0.003	0.041
getFluo_byRun	0.052	0.013	0.063
pathEstimator	0.001	0.001	0.001
readFiles	0.016	0.001	0.018
simcells	3.548	0.277	3.823
spotEstimator	0	0	0