BioC 3.1: CHECK report for coMET on morelia

Package: coMET

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.0.0.tar.gz

StartedAt: 2015-10-09 00:36:50 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:45:51 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 541.3 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/coMET.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.0’
* 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 ... [30s/33s] 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 ... [80s/206s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
comet.web       18.342  1.866 130.921
coMET-package    6.750  0.878  19.631
comet            5.418  0.692   6.088
HistoneAll       5.468  0.505   6.008
chromatinHMMAll  5.036  0.510   5.559
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/17s]
 [16s/18s] 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-3.1-bioc/meat/coMET.Rcheck/00check.log’
for details.

* installing *source* package ‘coMET’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (coMET)

name	user	system	elapsed
COSMICTrack	1.069	0.102	1.170
ClinVarCnvTrack	0.600	0.046	0.641
ClinVarMainTrack	0.674	0.052	0.719
CoreillCNVTrack	0.585	0.057	0.636
DNAseUCSC	0.680	0.063	0.735
GADTrack	0.586	0.054	0.634
GWASTrack	0.101	0.007	0.138
GeneReviewsTrack	0.517	0.036	0.548
HistoneAll	5.468	0.505	6.008
HistoneOne	0.500	0.044	0.549
ISCATrack	0.657	0.061	0.712
RepeatMaskerTrack	0.954	0.100	1.045
chrUCSC2ENSEMBL	0.001	0.000	0.001
chromatinHMMAll	5.036	0.510	5.559
chromatinHMMOne	0.661	0.068	0.723
coMET-package	6.750	0.878	19.631
comet	5.418	0.692	6.088
comet.list	1.644	0.364	1.980
comet.web	18.342	1.866	130.921
cpgIslandsUCSC	0.513	0.053	1.130
gcContent	0.291	0.026	1.723
genesENSEMBL	1.165	0.128	1.370
genesNameENSEMBL	0.004	0.001	0.005
knownGenesUCSC	1.628	0.147	1.775
regulationBiomart	0.503	0.039	0.538
snpBiomart	0.713	0.063	0.814
snpLocationsUCSC	1.969	0.219	2.286
structureBiomart	0.652	0.060	0.740
transcriptENSEMBL	1.084	0.120	1.226
xenorefGenesUCSC	0.878	0.095	1.021