BioC 3.3: CHECK report for coMET on morelia

Package: coMET

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.3.0.tar.gz

StartedAt: 2015-10-20 04:42:22 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 04:49:15 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 412.5 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/coMET.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 ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ 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 ‘coMET’ can be installed ... [21s/21s] 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 ... [46s/192s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     13.023  0.266 147.786
coMET-package  4.252  0.092  16.299
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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/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	0.657	0.006	0.662
ClinVarCnvTrack	0.291	0.002	0.299
ClinVarMainTrack	0.405	0.001	0.409
CoreillCNVTrack	0.367	0.002	0.367
DNAseUCSC	0.358	0.002	0.360
GADTrack	0.324	0.002	0.326
GWASTrack	0.054	0.001	0.056
GeneReviewsTrack	0.274	0.002	0.276
HistoneAll	2.854	0.003	2.858
HistoneOne	0.269	0.002	0.271
ISCATrack	0.391	0.001	0.394
RepeatMaskerTrack	0.506	0.002	0.509
chrUCSC2ENSEMBL	0.000	0.000	0.001
chromatinHMMAll	2.678	0.003	2.687
chromatinHMMOne	0.715	0.001	0.744
coMET-package	4.252	0.092	16.299
comet	2.565	0.007	2.573
comet.list	0.864	0.011	0.874
comet.web	13.023	0.266	147.786
cpgIslandsUCSC	0.284	0.001	0.292
gcContent	0.203	0.001	0.204
genesENSEMBL	0.623	0.002	0.625
genesNameENSEMBL	0.003	0.000	0.004
knownGenesUCSC	0.898	0.003	0.900
regulationBiomart	0.376	0.002	0.379
snpBiomart	0.478	0.002	0.495
snpLocationsUCSC	0.995	0.003	1.000
structureBiomart	0.328	0.002	0.329
transcriptENSEMBL	0.522	0.001	0.523
xenorefGenesUCSC	0.417	0.002	0.419