BioC 3.2: CHECK report for coMET on perceval

Package: coMET

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.2.0.tar.gz

StartedAt: 2015-11-10 03:36:42 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 03:47:14 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 632.6 seconds

RetCode: 0

Status:  OK

CheckDir: coMET.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 coMET_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/coMET.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 ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ 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 ‘coMET’ can be installed ... [33s/34s] 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [77s/270s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     26.137  0.506 200.140
coMET-package  6.056  0.089  25.805
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/17s]
 [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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/coMET.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
COSMICTrack	0.880	0.007	0.888
ClinVarCnvTrack	0.460	0.002	0.463
ClinVarMainTrack	0.491	0.002	0.493
CoreillCNVTrack	0.437	0.002	0.439
DNAseUCSC	0.541	0.002	0.544
GADTrack	0.462	0.002	0.464
GWASTrack	0.091	0.001	0.092
GeneReviewsTrack	0.424	0.001	0.426
HistoneAll	4.493	0.006	4.498
HistoneOne	0.378	0.002	0.381
ISCATrack	0.520	0.002	0.523
RepeatMaskerTrack	0.725	0.002	0.727
chrUCSC2ENSEMBL	0.001	0.000	0.001
chromatinHMMAll	4.598	0.054	4.660
chromatinHMMOne	0.485	0.002	0.487
coMET-package	6.056	0.089	25.805
comet	3.898	0.014	4.013
comet.list	1.347	0.004	1.351
comet.web	26.137	0.506	200.140
cpgIslandsUCSC	0.417	0.003	0.420
gcContent	0.284	0.003	0.287
genesENSEMBL	1.019	0.004	1.024
genesNameENSEMBL	0.005	0.001	0.006
knownGenesUCSC	1.225	0.007	1.232
regulationBiomart	0.368	0.002	0.370
snpBiomart	0.560	0.002	0.564
snpLocationsUCSC	1.601	0.005	1.632
structureBiomart	0.517	0.002	0.519
transcriptENSEMBL	0.894	0.004	0.897
xenorefGenesUCSC	0.729	0.002	0.731