BioC 3.5: CHECK report for scone on toluca2

Package: scone

Version: 0.99.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scone_0.99.7.tar.gz

StartedAt: 2017-04-23 09:38:53 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:49:18 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 625.4 seconds

RetCode: 0

Status:  OK

CheckDir: scone.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings scone_0.99.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/scone.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘0.99.7’
* 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 ‘scone’ can be installed ... OK
* 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 ... NOTE
Namespace in Imports field not imported from: ‘EDASeq’
  All declared Imports should be used.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/scone.Rcheck/00check.log’
for details.

* installing *source* package ‘scone’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scone)

name	user	system	elapsed
CLR_FN	0.003	0.000	0.003
DESEQ_FN	0.002	0.000	0.003
FQ_FN	0.158	0.002	0.164
SCRAN_FN	0.048	0.003	0.052
SUM_FN	0.001	0.001	0.001
SconeExperiment-class	0.536	0.003	0.573
TMM_FN	0.121	0.000	0.142
UQ_FN	0.002	0.000	0.002
biplot_color	0.013	0.001	0.016
biplot_interactive	0.994	0.005	1.062
control_genes	0.023	0.034	0.057
estimate_ziber	0.072	0.002	0.074
factor_sample_filter	0.433	0.004	0.519
get_bio	0.044	0.000	0.049
get_design	0.609	0.002	0.687
get_negconruv	0.078	0.000	0.086
get_normalized	0.273	0.001	0.309
get_params	0.022	0.001	0.026
get_qc	0.054	0.000	0.060
get_scores	0.049	0.001	0.055
impute_expectation	0.002	0.000	0.003
impute_null	0.001	0.000	0.001
lm_adjust	0.006	0.000	0.006
make_design	0.003	0.000	0.003
metric_sample_filter	0.010	0.001	0.014
scone	0.153	0.001	0.163
sconeReport	0.060	0.000	0.064
scone_easybake	0.057	0.001	0.060
score_matrix	0.007	0.000	0.008
select_methods	0.059	0.000	0.060
simple_FNR_params	0.047	0.001	0.050