BioC 3.1: CHECK report for coMET on zin2

Package: coMET

Version: 1.0.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.0.0.tar.gz

StartedAt: 2015-10-08 23:52:14 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-09 00:01:35 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 561.0 seconds

RetCode: 0

Status:  OK

CheckDir: coMET.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/coMET.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [22s/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 ... [52s/201s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     13.456  0.451 135.117
coMET-package  4.475  0.235  18.880
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/17s]
 [11s/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
  ‘/home/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	0.699	0.028	0.909
ClinVarCnvTrack	0.370	0.024	0.467
ClinVarMainTrack	0.407	0.009	0.567
CoreillCNVTrack	0.391	0.025	0.701
DNAseUCSC	0.440	0.012	0.471
GADTrack	0.367	0.015	0.389
GWASTrack	0.069	0.000	0.070
GeneReviewsTrack	0.341	0.015	0.361
HistoneAll	3.575	0.125	4.765
HistoneOne	0.314	0.024	0.502
ISCATrack	0.450	0.006	0.806
RepeatMaskerTrack	0.618	0.020	1.147
chrUCSC2ENSEMBL	0.001	0.000	0.001
chromatinHMMAll	3.297	0.138	4.848
chromatinHMMOne	0.433	0.017	0.599
coMET-package	4.475	0.235	18.880
comet	3.413	0.206	4.309
comet.list	1.030	0.092	1.765
comet.web	13.456	0.451	135.117
cpgIslandsUCSC	0.336	0.006	0.481
gcContent	0.194	0.008	0.202
genesENSEMBL	0.730	0.047	1.254
genesNameENSEMBL	0.004	0.000	0.004
knownGenesUCSC	0.963	0.041	1.307
regulationBiomart	0.323	0.009	0.631
snpBiomart	0.421	0.025	0.579
snpLocationsUCSC	1.160	0.030	1.512
structureBiomart	0.393	0.020	0.413
transcriptENSEMBL	0.681	0.005	1.132
xenorefGenesUCSC	0.515	0.042	0.670