BioC 3.3: CHECK report for riboSeqR on morelia

Package: riboSeqR

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings riboSeqR_1.5.1.tar.gz

StartedAt: 2015-10-22 10:32:44 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:34:42 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 118.4 seconds

RetCode: 0

Status:  OK

CheckDir: riboSeqR.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 riboSeqR_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/riboSeqR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘riboSeqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘riboSeqR’ version ‘1.5.1’
* 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 ‘riboSeqR’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
.readAlignments : <anonymous>: no visible global function definition
  for ‘scanBam’
.readAlignments : <anonymous>: no visible global function definition
  for ‘IRanges’
.tableOverlaps: no visible global function definition for ‘seqlevels’
findCDS: no visible global function definition for ‘IRanges’
plotCDS : <anonymous> : <anonymous>: no visible global function
  definition for ‘seqlevels’
Undefined global functions or variables:
  IRanges scanBam seqlevels
* 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 ... [47s/47s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotTranscript 5.902  0.072   6.011
filterHits     5.703  0.089   5.829
plotCDS        5.513  0.064   5.671
rnaCounts      5.368  0.064   5.441
sliceCounts    5.290  0.065   5.397
frameShift     5.197  0.054   5.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/3s] 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/riboSeqR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
filterHits	5.703	0.089	5.829
findCDS	0.170	0.001	0.171
frameCounting	4.828	0.058	4.925
frameShift	5.197	0.054	5.262
lengthDist	2.700	0.039	2.743
plotCDS	5.513	0.064	5.671
plotTranscript	5.902	0.072	6.011
readRibodata	2.668	0.039	2.757
rnaCounts	5.368	0.064	5.441
sliceCounts	5.290	0.065	5.397