BioC 3.4: CHECK report for RNAprobR on morelia

Package: RNAprobR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAprobR_1.6.0.tar.gz

StartedAt: 2017-04-15 07:29:20 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:32:26 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 186.6 seconds

RetCode: 0

Status:  OK

CheckDir: RNAprobR.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 RNAprobR_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/RNAprobR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.6.0’
* 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 ‘RNAprobR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.all_dc: no visible binding for global variable ‘depth_correction’
.compare_prop: no visible global function definition for ‘pnorm’
.compare_prop_slograt: no visible global function definition for
  ‘pnorm’
.process_oneRNA_euc: no visible global function definition for
  ‘IRanges’
.remove_unannotated: no visible binding for global variable ‘Pos’
.save_bedgraph: no visible global function definition for ‘write.table’
BED2txDb: no visible global function definition for ‘IRanges’
bam2bedgraph: no visible global function definition for ‘aggregate’
comp: no visible global function definition for ‘endoapply’
correct_oversaturation: no visible global function definition for ‘lm’
k2n_calc: no visible global function definition for ‘read.table’
k2n_calc: no visible binding for global variable ‘Barcodes’
k2n_calc: no visible global function definition for ‘quantile’
norm2bedgraph: no visible global function definition for ‘runValue’
norm_df2GR: no visible global function definition for ‘IRanges’
plotRNA: no visible global function definition for ‘plot’
plotRNA: no visible global function definition for ‘points’
plotReads: no visible global function definition for ‘plot’
plotReads: no visible global function definition for ‘segments’
readsamples: no visible binding for global variable ‘read.table’
readsamples: no visible global function definition for ‘IRanges’
swinsor_vector: no visible binding for global variable ‘sd’
winsor: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  Barcodes IRanges Pos aggregate depth_correction endoapply lm plot
  pnorm points quantile read.table runValue sd segments write.table
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "aggregate", "lm", "pnorm", "quantile", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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-3.4-bioc/meat/RNAprobR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
BED2txDb	0.923	0.052	1.076
GR2norm_df	0.201	0.008	0.210
bedgraph2norm	1.017	0.040	1.317
comp	0.099	0.000	0.100
compdata	0.194	0.001	0.208
correct_oversaturation	0.054	0.001	0.117
dtcr	0.248	0.001	0.249
k2n_calc	0.018	0.001	0.158
norm2bedgraph	0.484	0.004	0.708
norm_df2GR	0.021	0.000	0.021
plotRNA	0.171	0.000	0.172
plotReads	0.071	0.001	0.127
readsamples	0.016	0.000	0.077
slograt	0.532	0.002	0.533
swinsor	0.146	0.001	0.147
swinsor_vector	0.030	0.005	0.098
winsor	0.003	0.000	0.057