BioC 3.2: CHECK report for RNAprobR on perceval

Package: RNAprobR

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAprobR_1.1.2.tar.gz

StartedAt: 2015-08-24 04:41:15 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:45:25 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 250.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RNAprobR.Rcheck

Warnings: 1

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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_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RNAprobR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.1.2’
* 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 ... [23s/23s] 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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’
norm_df2GR: no visible global function definition for ‘IRanges’
norm2bedgraph: no visible global function definition for ‘runValue’
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 ... [17s/17s] 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.754	0.090	0.844
GR2norm_df	0.343	0.009	0.352
bedgraph2norm	1.463	0.018	1.481
comp	0.189	0.001	0.191
compdata	0.344	0.003	0.348
correct_oversaturation	0.079	0.001	0.080
dtcr	0.424	0.003	0.428
k2n_calc	0.013	0.001	0.014
norm2bedgraph	0.641	0.006	0.647
norm_df2GR	0.045	0.000	0.046
plotRNA	0.314	0.003	0.316
plotReads	0.179	0.005	0.184
readsamples	0.032	0.001	0.032
slograt	0.459	0.003	0.467
swinsor	0.277	0.002	0.279
swinsor_vector	0.048	0.004	0.052
winsor	0.005	0.001	0.006