BioC 3.1: CHECK report for RNAprobR on zin2

Package: RNAprobR

Version: 1.0.2

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.0.2.tar.gz

StartedAt: 2015-10-09 05:03:03 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:05:25 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 141.4 seconds

RetCode: 0

Status:  OK

CheckDir: RNAprobR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/RNAprobR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.0.2’
* 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 ‘RNAprobR’ can be installed ... [13s/13s] 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
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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’
.process_oneRNA_euc: no visible global function definition for
  ‘IRanges’
.remove_unannotated: no visible binding for global variable ‘Pos’
BED2txDb: no visible global function definition for ‘IRanges’
comp: no visible global function definition for ‘endoapply’
k2n_calc: no visible binding for global variable ‘Barcodes’
norm2bedgraph: no visible global function definition for ‘runValue’
norm_df2GR: no visible global function definition for ‘IRanges’
readsamples: no visible global function definition for ‘IRanges’
* 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 ... [11s/11s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/RNAprobR.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAprobR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (RNAprobR)

name	user	system	elapsed
BED2txDb	0.578	0.036	0.625
GR2norm_df	0.275	0.000	0.276
bedgraph2norm	1.125	0.000	1.127
comp	0.159	0.000	0.158
compdata	0.273	0.000	0.272
correct_oversaturation	0.069	0.000	0.068
dtcr	0.317	0.000	0.317
k2n_calc	0.011	0.000	0.011
norm2bedgraph	0.508	0.000	0.508
norm_df2GR	0.035	0.000	0.035
plotRNA	0.212	0.000	0.212
plotReads	0.105	0.000	0.106
readsamples	0.023	0.000	0.022
slograt	0.311	0.000	0.310
swinsor	0.199	0.000	0.199
swinsor_vector	0.037	0.000	0.037
winsor	0.004	0.000	0.004