BioC 3.2: CHECK report for QuartPAC on perceval

Package: QuartPAC

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QuartPAC_1.2.0.tar.gz

StartedAt: 2015-10-27 11:20:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:24:52 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 259.6 seconds

RetCode: 0

Status:  OK

CheckDir: QuartPAC.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 QuartPAC_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/QuartPAC.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuartPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuartPAC’ version ‘1.2.0’
* 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 ‘QuartPAC’ can be installed ... [11s/12s] 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
alignPositions: no visible global function definition for
  ‘PhredQuality’
alignPositions: no visible global function definition for
  ‘pairwiseAlignment’
constructCanonicalNumbering: no visible global function definition for
  ‘pattern’
constructCanonicalNumbering: no visible global function definition for
  ‘subject’
* 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 ... [91s/94s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
QuartPAC-package          60.900  0.355  62.749
makeAlignedSuperStructure 23.375  0.216  25.547
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [55s/57s]
 [56s/57s] 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-3.2-bioc/meat/QuartPAC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
QuartPAC-package	60.900	0.355	62.749
getMutations	0.048	0.009	0.375
makeAlignedSuperStructure	23.375	0.216	25.547
quartCluster	0.001	0.000	0.001