BioC 3.5: CHECK report for scone on malbec2

Package: scone

Version: 1.0.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scone_1.0.0.tar.gz

StartedAt: 2017-10-18 02:22:00 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:29:58 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 478.0 seconds

RetCode: 0

Status:  OK

CheckDir: scone.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings scone_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/scone.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scone/DESCRIPTION’ ... OK
* this is package ‘scone’ version ‘1.0.0’
* 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
  ‘/home/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	0.004	0.000	0.002
DESEQ_FN	0.000	0.004	0.001
FQ_FN	0.084	0.000	0.084
SCRAN_FN	0.036	0.000	0.039
SUM_FN	0.000	0.000	0.001
SconeExperiment-class	0.496	0.000	0.496
TMM_FN	0.12	0.00	0.12
UQ_FN	0.000	0.000	0.002
biplot_color	0.012	0.000	0.011
biplot_interactive	0.756	0.000	0.782
control_genes	0.016	0.000	0.017
estimate_ziber	0.040	0.000	0.042
factor_sample_filter	0.296	0.000	0.296
get_bio	0.052	0.000	0.055
get_design	0.476	0.000	0.479
get_negconruv	0.036	0.000	0.038
get_normalized	0.16	0.00	0.16
get_params	0.016	0.000	0.016
get_qc	0.040	0.000	0.041
get_scores	0.032	0.000	0.032
impute_expectation	0.000	0.000	0.001
impute_null	0.000	0.000	0.001
lm_adjust	0.004	0.000	0.004
make_design	0.004	0.000	0.002
metric_sample_filter	0.004	0.004	0.020
scone	0.2	0.0	0.2
sconeReport	0.036	0.000	0.036
scone_easybake	0.044	0.000	0.048
score_matrix	0.004	0.000	0.007
select_methods	0.052	0.000	0.054
simple_FNR_params	0.044	0.000	0.045