BioC 3.2: CHECK report for coMET on perceval

Package: coMET

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coMET_1.1.0.tar.gz

StartedAt: 2015-08-23 23:30:03 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:41:27 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 683.9 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_1.1.0.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 (2015-08-14 r69078)
* 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 ‘1.1.0’
* 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 ... [42s/54s] 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 ... [102s/221s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
comet.web       29.804  2.108 140.621
coMET-package    8.320  0.994  20.333
HistoneAll       6.443  0.530   6.889
comet            5.163  0.782   5.820
chromatinHMMAll  4.940  0.470   5.322
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/20s]
 [20s/20s] 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	2.106	0.095	2.179
ClinVarCnvTrack	0.711	0.147	0.850
ClinVarMainTrack	0.719	0.069	0.785
CoreillCNVTrack	0.654	0.059	0.700
DNAseUCSC	0.715	0.065	0.775
GADTrack	0.607	0.053	0.649
GWASTrack	0.121	0.012	0.133
GeneReviewsTrack	0.601	0.051	0.641
HistoneAll	6.443	0.530	6.889
HistoneOne	0.535	0.048	0.574
ISCATrack	0.734	0.068	0.798
RepeatMaskerTrack	1.018	0.095	1.128
chrUCSC2ENSEMBL	0.001	0.001	0.002
chromatinHMMAll	4.940	0.470	5.322
chromatinHMMOne	0.728	0.068	0.778
coMET-package	8.320	0.994	20.333
comet	5.163	0.782	5.820
comet.list	1.776	0.455	2.205
comet.web	29.804	2.108	140.621
cpgIslandsUCSC	0.634	0.055	0.674
gcContent	0.316	0.026	0.335
genesENSEMBL	1.170	0.102	1.244
genesNameENSEMBL	0.006	0.001	0.007
knownGenesUCSC	1.501	0.138	1.603
regulationBiomart	0.515	0.042	0.546
snpBiomart	0.742	0.065	0.792
snpLocationsUCSC	1.829	0.174	1.965
structureBiomart	0.612	0.052	0.649
transcriptENSEMBL	1.041	0.089	1.104
xenorefGenesUCSC	0.868	0.076	0.922