BioC 3.3: CHECK report for RNAprobR on linux2.bioconductor.org

Package: RNAprobR

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.3.0.tar.gz

StartedAt: 2015-10-27 07:36:44 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:39:11 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 147.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAprobR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RNAprobR_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RNAprobR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.3.0’
* 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 ... [14s/14s] 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’
.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’
Undefined global functions or variables:
  Barcodes IRanges Pos depth_correction endoapply runValue
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] 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-3.3-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	0.758	0.084	0.847
GR2norm_df	0.335	0.000	0.338
bedgraph2norm	1.153	0.001	1.160
comp	0.120	0.000	0.119
compdata	0.245	0.000	0.245
correct_oversaturation	0.051	0.000	0.051
dtcr	0.251	0.000	0.251
k2n_calc	0.010	0.000	0.011
norm2bedgraph	0.461	0.000	0.460
norm_df2GR	0.026	0.000	0.025
plotRNA	0.246	0.000	0.246
plotReads	0.112	0.000	0.114
readsamples	0.028	0.000	0.029
slograt	0.404	0.000	0.404
swinsor	0.258	0.003	0.263
swinsor_vector	0.041	0.001	0.041
winsor	0.004	0.000	0.005