BioC 3.5: CHECK report for RNAprobR on toluca2

Package: RNAprobR

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAprobR_1.7.0.tar.gz

StartedAt: 2017-04-23 09:14:28 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:18:21 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 233.5 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RNAprobR.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 ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.7.0’
* 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’
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 segments write.table
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "aggregate", "lm", "pnorm", "quantile")
  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-3.5-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	2.527	0.154	2.716
GR2norm_df	0.651	0.007	0.665
bedgraph2norm	3.504	0.016	3.596
comp	0.238	0.001	0.241
compdata	0.376	0.002	0.387
correct_oversaturation	0.083	0.001	0.084
dtcr	0.464	0.002	0.495
k2n_calc	0.163	0.000	0.164
norm2bedgraph	0.909	0.004	0.940
norm_df2GR	0.023	0.000	0.024
plotRNA	0.233	0.001	0.235
plotReads	0.244	0.002	0.248
readsamples	0.022	0.001	0.022
slograt	0.340	0.001	0.347
swinsor	0.231	0.002	0.239
swinsor_vector	0.039	0.002	0.042
winsor	0.004	0.000	0.004